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Wang Z, Li H, Zhou X, Mou Y, Zhang Y, Yu L, Chen X, Wu F, Zhou H, Lin Y, Li C, Liu Y. Identification, validation and candidate gene analysis of major QTL for Supernumerary spikelets in wheat. BMC Genomics 2024; 25:675. [PMID: 38977976 PMCID: PMC11229243 DOI: 10.1186/s12864-024-10540-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/19/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND The number of spikelets per spike is a key trait that affects the yield of bread wheat (Triticum aestivum L.). Identification of the QTL for spikelets per spike and its genetic effects that could be used in molecular assistant breeding in the future. RESULTS In this study, four recombinant inbred line (RIL) populations were generated and used, having YuPi branching wheat (YP), with Supernumerary Spikelets (SS) phenotype, as a common parent. QTL (QSS.sicau-2 A and QSS.sicau-2D) related to SS trait were mapped on chromosomes 2 A and 2D through bulked segregant exome sequencing (BSE-Seq). Fourteen molecular markers were further developed within the localization interval, and QSS.sicau-2 A was narrowed to 3.0 cM covering 7.6 Mb physical region of the reference genome, explaining 13.7 - 15.9% the phenotypic variance. Similarly, the QSS.sicau-2D was narrowed to 1.8 cM covering 2.4 Mb physical region of the reference genome, and it explained 27.4 - 32.9% the phenotypic variance. These two QTL were validated in three different genetic backgrounds using the linked markers. QSS.sicau-2 A was identified as WFZP-A, and QSS.sicau-2D was identified a novel locus, different to the previously identified WFZP-D. Based on the gene expression patterns, gene annotation and sequence analysis, TraesCS2D03G0260700 was predicted to be a potential candidate gene for QSS.sicau-2D. CONCLUSION Two significant QTL for SS, namely QSS.sicau-2 A and QSS.sicau-2D were identified in multiple environments were identified and their effect in diverse genetic populations was assessed. QSS.sicau-2D is a novel QTL associated with the SS trait, with TraesCS2D03G0260700 predicted as its candidate gene.
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Affiliation(s)
- Zhiqiang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
- Chengdu Agricultural College, Chengdu, 611130, Sichuan, China
| | - Haojie Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xinjian Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yuzhou Mou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Ying Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Lang Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xudong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Fangkun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Hong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yu Lin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Caixia Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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Li Y, Hu J, Qu Y, Qiu D, Lin H, Du J, Hou L, Ma L, Wu Q, Zhou Y, Zhang H, Yang L, Liu H, Liu Z, Zhou Y, Li H. Alleles on locus chromosome 4B from different parents confer tiller number and the yield-associated traits in wheat. BMC PLANT BIOLOGY 2024; 24:454. [PMID: 38789943 PMCID: PMC11127307 DOI: 10.1186/s12870-024-05079-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/28/2024] [Indexed: 05/26/2024]
Abstract
Pleiotropy is frequently detected in agronomic traits of wheat (Triticum aestivum). A locus on chromosome 4B, QTn/Ptn/Sl/Sns/Al/Tgw/Gl/Gw.caas-4B, proved to show pleiotropic effects on tiller, spike, and grain traits using a recombinant inbred line (RIL) population of Qingxinmai × 041133. The allele from Qingxinmai increased tiller numbers, and the allele from line 041133 produced better performances of spike traits and grain traits. Another 52 QTL for the eight traits investigated were detected on 18 chromosomes, except for chromosomes 5D, 6D, and 7B. Several genes in the genomic interval of the locus on chromosome 4B were differentially expressed in crown and inflorescence samples between Qingxinmai and line 041133. The development of the KASP marker specific for the locus on chromosome 4B is useful for molecular marker-assisted selection in wheat breeding.
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Affiliation(s)
- Yahui Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinghuang Hu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunfeng Qu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Dan Qiu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huailong Lin
- Jiushenghe Seed Industry Co. Ltd, Changji, 831100, China
| | - Jiuyuan Du
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Lu Hou
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Lin Ma
- Datong Hui and Tu Autonomous County Agricultural Technology Extension Center, Xining, 810100, China
| | - Qiuhong Wu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Zhou
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongjun Zhang
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Yang
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwei Liu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yijun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China.
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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3
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Zhang L, Zhou H, Fu X, Zhou N, Liu M, Bai S, Zhao X, Cheng R, Li S, Zhang D. Identification and map-based cloning of an EMS-induced mutation in wheat gene TaSP1 related to spike architecture. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:119. [PMID: 38709271 DOI: 10.1007/s00122-024-04621-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE A candidate gene TaSP1 related to spike shape was cloned, and the gene-specific marker was developed to efficiently track the superior haplotype in common wheat. Spike shape, an important factor that affects wheat grain yield, is mainly defined by spike length (SPL), spikelet number (SPN), and compactness. Zhoumai32 mutant 1160 (ZM1160), a mutant obtained from ethyl methane sulfonate (EMS) treatment of hexaploid wheat variety Zhoumai32, was used to identify and clone the candidate gene that conditioned the spike shape. Genetic analysis of an F2 population derived from a cross of ZM1160 and Bainong207 suggested that the compact spike shape in ZM1160 was controlled by a single recessive gene, and therefore, the mutated gene was designated as Tasp1. With polymorphic markers identified through bulked segregant analysis (BSA), the gene was mapped to a 2.65-cM interval flanked by markers YZU0852 and MIS46239 on chromosome 7D, corresponding to a 0.42-Mb physical interval of Chinese spring (CS) reference sequences (RefSeq v1.0). To fine map TaSP1, 15 and seven recombinants were, respectively, screened from 1599 and 1903 F3 plants derived from the heterozygous F2 plants. Finally, TaSP1 was delimited to a 21.9 Kb (4,870,562 to 4,892,493 bp) Xmis48123-Xmis48104 interval. Only one high-confidence gene TraesCS7D02G010200 was annotated in this region, which encodes an unknown protein with a putative vWA domain. Quantitative reverse transcription PCR (qRT-PCR) analysis showed that TraesCS7D02G010200 was mainly expressed in the spike. Haplotype analysis of 655 wheat cultivars using the candidate gene-specific marker Xg010200p2 identified a superior haplotype TaSP1b with longer spike and more spikelet number. TaSP1 is beneficial to the improvement in wheat spike shape.
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Affiliation(s)
- Lin Zhang
- School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Huidan Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China
| | - Xian Fu
- School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Niuniu Zhou
- School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Mengjie Liu
- School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Shenglong Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China
| | - Xinpeng Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China
| | - Ruiru Cheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China.
| | - Suoping Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China.
| | - Dale Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China.
- The Zhongzhou Laboratory for Integrative Biology, Zhengzhou, 450000, Henan, China.
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4
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Zhou J, Liu Q, Tian R, Chen H, Wang J, Yang Y, Zhao C, Liu Y, Tang H, Deng M, Xu Q, Jiang Q, Chen G, Qi P, Jiang Y, Chen G, Tang L, Ren Y, Zheng Z, Liu C, Zheng Y, He Y, Wei Y, Ma J. A co-located QTL for seven spike architecture-related traits shows promising breeding use potential in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:31. [PMID: 38267732 DOI: 10.1007/s00122-023-04536-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024]
Abstract
KEY MESSAGE A co-located novel QTL for TFS, FPs, FMs, FFS, FFPs, KWS, and KWPs with potential of improving wheat yield was identified and validated. Spike-related traits, including fertile florets per spike (FFS), kernel weight per spike (KWS), total florets per spike (TFS), florets per spikelet (FPs), florets in the middle spikelet (FMs), fertile florets per spikelet (FFPs), and kernel weight per spikelet (KWPs), are key traits in improving wheat yield. In the present study, quantitative trait loci (QTL) for these traits evaluated under various environments were detected in a recombinant inbred line population (msf/Chuannong 16) mainly genotyped using the 16 K SNP array. Ultimately, we identified 60 QTL, but only QFFS.sau-MC-1A for FFS was a major and stably expressed QTL. It was located on chromosome arm 1AS, where loci for TFS, FPs, FMs, FFS, FFPs, KWS, and KWPs were also simultaneously co-mapped. The effect of QFFS.sau-MC-1A was further validated in three independent segregating populations using a Kompetitive Allele-Specific PCR marker. For the co-located QTL, QFFS.sau-MC-1A, the presence of a positive allele from msf was associate with increases for all traits: + 12.29% TFS, + 10.15% FPs, + 13.97% FMs, + 17.12% FFS, + 14.75% FFPs, + 22.17% KWS, and + 19.42% KWPs. Furthermore, pleiotropy analysis showed that the positive allele at QFFS.sau-MC-1A simultaneously increased the spike length, spikelet number per spike, and thousand-kernel weight. QFFS.sau-MC-1A represents a novel QTL for marker-assisted selection with the potential for improving wheat yield. Four genes, TraesCS1A03G0012700, TraesCS1A03G0015700, TraesCS1A03G0016000, and TraesCS1A03G0016300, which may affect spike development, were predicted in the physical interval harboring QFFS.sau-MC-1A. Our results will help in further fine mapping QFFS.sau-MC-1A and be useful for improving wheat yield.
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Affiliation(s)
- Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qian Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Rong Tian
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huangxin Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaoyao Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Conghao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanlin Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Liwei Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Yong Ren
- Mianyang Academy of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China
| | - Zhi Zheng
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China.
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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Si Y, Tian S, Niu J, Yu Z, Ma S, Lu Q, Wu H, Ling HQ, Zheng S. Dissection and validation of a promising QTL controlling spikelet number on 5B in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:240. [PMID: 37930446 DOI: 10.1007/s00122-023-04488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
KEY MESSAGE Five environmentally stable QTLs for spikelet number per spike and days to heading were identified using a high-genetic map containing 95,444 SNPs, among which QSns.ucas-5B was validated using residual heterozygous line at multiple environments. Spikelet number per spike (SNS) and days to heading (DTH) play pivotal roles in the improvement of wheat yield. In this study, a high-density genetic map for a recombinant inbred lines (RILs) population derived from Zhengnong 17 (ZN17) and Yangbaimai (YBM) was constructed using 95,444 single-nucleotide polymorphism (SNP) markers from the Wheat660K SNP array. Our study identified a total of five environmentally stable QTLs for SNS and DTH, one of which was named QSns.ucas-5B, with a physical interval of approximately 545.4-552.1 Mb on the 5BL chromosome arm. Importantly, the elite haplotype within QSns.ucas-5B showed a consistent and positive effect on SNS, grain number and weight per spike, without extending the days to heading. These findings provide a foundation for future efforts to map and clone the gene(s) responsible for QSns.ucas-5B and further indicate the potential application of the developed and validated InDel marker of QSns.ucas-5B for molecular breeding purposes, aimed at improving wheat grain yield.
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Affiliation(s)
- Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianqing Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhongqing Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Shengwei Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiao Lu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Zhao D, Hu W, Fang Z, Cheng X, Liao S, Fu L. Two QTL regions for spike length showing pleiotropic effects on Fusarium head blight resistance and thousand-grain weight in bread wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:82. [PMID: 37974900 PMCID: PMC10645863 DOI: 10.1007/s11032-023-01427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
Spike length (SL) plays an important role in the yield improvement of wheat and is significantly associated with other traits. Here, we used a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) to construct a genetic linkage map and identify quantitative trait loci (QTL) for SL. A total of 5 QTL were identified for SL, among which QSl.yaas-3A and QSl.yaas-5B are two novel QTL for SL. The YZ1 alleles at QSl.yaas-2D and QSl.yaas-5A, and the YM12 alleles at QSl.yaas-2A, QSl.yaas-3A, and QSl.yaas-5B conferred increasing SL effects. Two major QTL QSl.yaas-5A and QSl.yaas-5B explained 9.11-15.85% and 9.01-12.85% of the phenotypic variations, respectively. Moreover, the positive alleles of QSl.yaas-5A and QSl.yaas-5B could significantly increase Fusarium head blight (FHB) resistance (soil surface inoculation and spray inoculation were used) and thousand-grain weight (TGW) in the RIL population. Kompetitive allele-specific PCR (KASP) markers for QSl.yaas-5A and QSl.yaas-5B were developed and validated in an additional panel of 180 wheat cultivars/lines. The cultivars/lines harboring both the positive alleles of QSl.yaas-5A and QSl.yaas-5B accounted for only 28.33% of the validation populations and had the longest SL, best FHB resistance (using spray inoculation), and highest TGW. A total of 358 and 200 high-confidence annotated genes in QSl.yaas-5A and QSl.yaas-5B were identified, respectively. Some of the genes in these two regions were involved in cell development, disease resistance, and so on. The results of this study will provide a basis for directional breeding of longer SL, higher TGW, and better FHB resistance varieties and a solid foundation for fine-mapping QSl.yaas-5A and QSl.yaas-5B in future. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01427-8.
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Affiliation(s)
- Die Zhao
- College of Agriculture, Yangtze University, Jingzhou, 434025 China
| | - Wenjing Hu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Zhengwu Fang
- College of Agriculture, Yangtze University, Jingzhou, 434025 China
| | - Xiaoming Cheng
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007 China
| | - Sen Liao
- Key Laboratory of Wheat Biology and Genetic Improvement for Low Middle Yangtze Valley, Ministry of Agriculture and Rural Affairs, Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007 China
| | - Luping Fu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, 225009 Jiangsu China
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7
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Zhao C, Zhou J, Li C, You J, Liu Y, Tang H, Deng M, Xu Q, Zhang Y, Jiang Q, Chen G, Qi P, Jiang Y, Wang J, Li W, Pu Z, Chen G, Jiang Y, Zheng Z, Liu C, Zheng Y, Wei Y, Ma J. A major QTL simultaneously increases the number of spikelets per spike and thousand-kernel weight in a wheat line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:213. [PMID: 37740730 DOI: 10.1007/s00122-023-04459-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/31/2023] [Indexed: 09/25/2023]
Abstract
KEY MESSAGE A novel and stably expressed QTL QSNS.sicau-SSY-7A for spikelet number per spike in wheat without negative effects on thousand-kernel weight was identified and validated in different genetic backgrounds. Spikelet number per spike (SNS) is an important determinant of yield in wheat. In the present study, we combined bulked segregant analysis (BSA) and the wheat 660 K single-nucleotide polymorphism (SNP) array to rapidly identify genomic regions associated with SNS from a recombinant inbred line (RIL) population derived from a cross between the wheat lines S849-8 and SY95-71. A genetic map was constructed using Kompetitive Allele Specific PCR markers in the SNP-enriched region on the long arm of chromosome 7A. A major and stably expressed QTL, QSNS.sicau-SSY-7A, was detected in multiple environments. It was located in a 1.6 cM interval on chromosome arm 7AL flanked by the markers AX-109983514 and AX-109820548. This QTL explained 6.86-15.72% of the phenotypic variance, with LOD values ranging from 3.66 to 8.66. Several genes associated with plant growth and development were identified in the interval where QSNS.sicau-SSY-7A was located on the 'Chinese Spring' wheat and wild emmer reference genomes. Furthermore, the effects of QSNS.sicau-SSY-7A and WHEAT ORTHOLOG OFAPO1(WAPO1) on SNS were analyzed. Interestingly, QSNS.sicau-SSY-7A significantly increased SNS without negative effects on thousand-kernel weight, anthesis date and plant height, demonstrating its great potential for breeding aimed at improving grain yield. Taken together, these results indicate that QSNS.sicau-SSY-7A is a promising locus for yield improvement, and its linkage markers are helpful for fine mapping and molecular breeding.
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Affiliation(s)
- Conghao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jianing You
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy ofAgricultural Sciences, Chengdu, China
| | - Zhi Zheng
- CSIRO Agriculture and Food, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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8
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Li Z, Luo Q, Deng Y, Du K, Li X, Ren T. Identification and Validation of a Stable Major-Effect Quantitative Trait Locus for Kernel Number per Spike on Chromosome 2D in Wheat ( Triticum aestivum L.). Int J Mol Sci 2023; 24:14289. [PMID: 37762591 PMCID: PMC10531874 DOI: 10.3390/ijms241814289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/12/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
A recombinant inbred line population including 371 lines was developed by a high kernel number per spike (KNPS) genotype T1208 and a low KNPS genotype Chuannong18 (CN18). A genetic linkage map consisting of 11,583 markers was constructed by the Wheat55K SNP Array. The quantitative trait loci (QTLs) related to KNPS were detected in three years. Eight, twenty-seven, and four QTLs were identified using the ICIM-BIP, ICIM-MET, and ICIM-EPI methods, respectively. One QTL, QKnps.sau-2D.1, which was mapped on chromosome 2D, can explain 18.10% of the phenotypic variation (PVE) on average and be considered a major and stable QTL for KNPS. This QTL was located in a 0.89 Mb interval on chromosome 2D and flanked by the markers AX-109283238 and AX-111606890. Moreover, KASP-AX-111462389, a Kompetitive Allele-Specific PCR (KASP) marker which closely linked to QKnps.sau-2D.1, was designed. The genetic effect of QKnps.sau-2D.1 on KNPS was successfully confirmed in two RIL populations. The results also showed that the significant increase of KNPS and 1000-kernel weight (TKW) was caused by QKnps.sau-2D.1 overcoming the disadvantage due to the decrease of spike number (SN) and finally lead to a significant increase of grain yield. In addition, within the interval in which QKnps.sau-2D.1 is located in Chinese Spring reference genomes, only fifteen genes were found, and two genes that might associate with KNPS were identified. QKnps.sau-2D.1 may provide a new resource for the high-yield breeding of wheat in the future.
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Affiliation(s)
- Zhi Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China;
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Qinyi Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Yawen Deng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Ke Du
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Xinli Li
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Tianheng Ren
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China;
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
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9
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Zhang Y, Miao H, Xiao Y, Wang C, Zhang J, Shi X, Xie S, Wang C, Li T, Deng P, Chen C, Zhang H, Ji W. An intron-located single nucleotide variation of TaGS5-3D is related to wheat grain size through accumulating intron retention transcripts. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:193. [PMID: 37606787 DOI: 10.1007/s00122-023-04439-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023]
Abstract
KEY MESSAGE Thirty-three stable QTL for 13 yield-related traits across ten environments were identified in the PD34/MY47 RIL population, and a candidate gene TaGS5-3D in Qmt.nwafu.3D was preliminarily identified to affect grain-related traits through accumulation of specific transcripts. Dissecting the genetic basis of yield-related traits is pivotal for improvement of wheat yield potential. In this study, a recombinant inbred line (RIL) population genotyped by SNP markers was used to detect quantitative trait loci (QTL) related to yield-related traits in ten environments. A total of 102 QTL were detected, including 33 environmentally stable QTL and 69 putative QTL. Among them, Qmt.nwafu.3D was identified as a pleiotropic QTL in the physical interval of 149.77-154.11 Mb containing a potential candidate gene TaGS5-3D. An SNP (T > C) was detected in its ninth intron, and TaGS5-3D-C was validated as a superior allele associated with larger grains using a CAPS marker. Interestingly, we found that TaGS5-3D-C was closely related to significantly up-regulated expression of intron-retained transcript (TaGS5-3D-PD34.1), while TaGS5-3D-T was related to dominant expression of normal splicing transcript (TaGS5-3D-MY47.1). Our results indicated that alternative splicing associated with the SNP T/C could be involved in the regulation of grain-related traits, laying a foundation for the functional analysis of TaGS5-3D and its greater potential application in high-yield wheat breeding.
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Affiliation(s)
- Yaoyuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Hanxiao Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yi Xiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Chao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Junjie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Xiaoxi Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Songfeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China.
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China.
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10
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Zhou J, Li W, Yang Y, Xie X, Liu J, Liu Y, Tang H, Deng M, Xu Q, Jiang Q, Chen G, Qi P, Jiang Y, Chen G, He Y, Ren Y, Tang L, Gou L, Zheng Y, Wei Y, Ma J. A promising QTL QSns.sau-MC-3D.1 likely superior to WAPO1 for the number of spikelets per spike of wheat shows no adverse effects on yield-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:181. [PMID: 37550493 DOI: 10.1007/s00122-023-04429-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023]
Abstract
KEY MESSAGE A likely new locus QSns.sau-MC-3D.1 associated with SNS showing no negative effect on yield-related traits compared to WAPO1 was identified and validated in various genetic populations under multiple environments. The number of spikelets per spike (SNS) is one of the crucial factors determining wheat yield. Thus, improving our understanding of the genes that regulate SNS could help develop wheat varieties with higher yield. In this study, a recombinant inbred line (RIL) population (MC) containing 198 lines derived from a cross between msf and Chuannong 16 (CN16) was used to construct a genetic linkage map using the GenoBaits Wheat 16 K Panel. The genetic map contained 5,991 polymorphic SNP markers spanning 2,813.25 cM. A total of twelve QTL for SNS were detected, and two of them, i.e., QSns.sau-MC-3D.1 and QSns.sau-MC-7A, were stably expressed. QSns.sau-MC-3D.1 had high LOD values ranging from 4.99 to 11.06 and explained 9.71-16.75% of the phenotypic variation. Comparison of QSns.sau-MC-3D.1 with previously reported SNS QTL suggested that it is likely a novel one, and two kompetitive allele-specific PCR (KASP) markers were further developed. The positive effect of QSns.sau-MC-3D.1 was also validated in three biparental populations and a diverse panel containing 388 Chinese wheat accessions. Genetic analysis indicated that WHEAT ORTHOLOG OFAPO1 (WAPO1) was a candidate gene for QSns.sau-MC-7A. Pyramiding of QSns.sau-MC-3D.1 and WAP01 had a great additive effect increasing SNS by 7.10%. Correlation analysis suggested that QSns.sau-MC-3D.1 was likely independent of effective tiller number, plant height, spike length, anthesis date, and thousand kernel weight. However, the H2 haplotype of WAPO1 may affect effective tiller number and plant height. These results indicated that utilization of QSns.sau-MC-3D.1 should be given priority for wheat breeding. Geographical distribution analysis showed that the positive allele of QSns.nsau-MC-3D.1 was dominant in most wheat-producing regions of China, and it has been positively selected among modern cultivars released in China since the 1940s. Gene prediction, qRT-PCR analysis, and sequence alignment suggested that TraesCS3D03G0216800 may be the candidate gene of QSns.nsau-MC-3D.1. Taken together, these results enrich our understanding of the genetic basis of wheat SNS and will be useful for fine mapping and cloning of the gene underlying QSns.sau-MC-3D.1.
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Affiliation(s)
- Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaoyao Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xinlin Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China
| | - Yong Ren
- Mianyang Academy of Agricultural Science, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China
| | - Liwei Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Lulu Gou
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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11
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Yi X, Ye Y, Wang J, Li Z, Li J, Chen Y, Chen G, Ma J, Pu Z, Peng Y, Qi P, Liu Y, Jiang Q, Wang J, Wei Y, Zheng Y, Li W. Identification and validation of two major QTLs for spikelet number per spike in wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1144486. [PMID: 37235013 PMCID: PMC10208070 DOI: 10.3389/fpls.2023.1144486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/23/2023] [Indexed: 05/28/2023]
Abstract
The total number of spikelets (TSPN) and the number of fertile spikelets (FSPN) affect the final number of grains per spikelet in wheat. This study constructed a high-density genetic map using 55K single nucleotide polymorphism (SNP) arrays from a population of 152 recombinant inbred lines (RIL) from crossing the wheat accessions 10-A and B39. Twenty-four quantitative trait loci (QTLs) for TSPN and 18 QTLs for FSPN were localized based on the phenotype in 10 environments in 2019-2021. Two major QTLs, QTSPN/QFSPN.sicau-2D.4 (34.43-47.43 Mb) and QTSPN/QFSPN.sicau-2D.5(32.97-34.43 Mb), explained 13.97%-45.90% of phenotypic variation. Linked kompetitive allele-specific PCR (KASP) markers further validated these two QTLs and revealed that QTSPN.sicau-2D.4 had less effect on TSPN than QTSPN.sicau-2D.5 in 10-A×BE89 (134 RILs) and 10-A×Chuannong 16 (192 RILs) populations, and one population of Sichuan wheat (233 accessions). The alleles combination haplotype 3 with the allele from 10-A of QTSPN/QFSPN.sicau-2D.5 and the allele from B39 of QTSPN.sicau-2D.4 resulted in the highest number of spikelets. In contrast, the allele from B39 for both loci resulted in the lowest number of spikelets. Using bulk-segregant analysis-exon capture sequencing, six SNP hot spots that included 31 candidate genes were identified in the two QTLs. We identified Ppd-D1a from B39 and Ppd-D1d from 10-A and further analyzed Ppd-D1 variation in wheat. These results identified loci and molecular markers with potential utility for wheat breeding and laid a foundation for further fine mapping and cloning of the two loci.
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Affiliation(s)
- Xiaoyu Yi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yingtong Ye
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jinhui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhen Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiamin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuqi Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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12
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Wang S, Wang T, Xuan Q, Qu X, Xu Q, Jiang Q, Pu Z, Li Y, Jiang Y, Chen G, Deng M, Liu Y, Tang H, Chen G, He Y, Gou L, Wei Y, Zheng Y, Ma J. Major and stably expressed QTL for traits related to the mature wheat embryo independent of kernel size. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:90. [PMID: 37000252 DOI: 10.1007/s00122-023-04346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Two major and stably expressed QTL for traits related to mature wheat embryo independent of kernel size were identified and validated in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. As the juvenile of a highly differentiated plant, mature wheat (Triticum aestivum L.) embryos are highly significant to agricultural production. To understand the genetic basis of traits related to wheat embryo size, the embryo of mature kernels in a recombination inbred line that contained 126 lines from four environments was measured. The genetic loci of embryo size, including embryo length (EL), embryo width (EW), embryo area (EA), embryo length/kernel length (EL/KL), embryo width/kernel width (EW/KW), and EL/EW, were identified based on a genetic linkage map constructed based on PCR markers and the Wheat 55 K single nucleotide polymorphism (SNP) array. A total of 50 quantitative trait loci (QTL) for traits related to wheat embryo size were detected. Among them, QEL.sicau-2SY-4A for EL and QEW.sicau-2SY-7B for EW were major and stably expressed and were genetically independent of KL and KW, respectively. Their effects were further verified in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. Further analysis showed that TraesCS4A02G343300 and TraesCS7B02G006800 could be candidate genes for QEL.sicau-2SY-4A and QEW.sicau-2SY-7B, respectively. In addition, significant positive correlations between EL and kernel-related traits and the 1,000-grain weight were detected. Collectively, this study broadens our understanding of the genetic basis of wheat embryo size and will be helpful for the further fine-mapping of interesting loci in the future.
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Affiliation(s)
- Surong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tianyu Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qijing Xuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, 621000, China
| | - Lulu Gou
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Jiang C, Xu Z, Fan X, Zhou Q, Ji G, Chen L, Yu Q, Liao S, Zhao Y, Feng B, Wang T. Identification and validation of quantitative trait loci for fertile spikelet number per spike and grain number per fertile spikelet in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:69. [PMID: 36952062 DOI: 10.1007/s00122-023-04297-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/26/2022] [Indexed: 06/18/2023]
Abstract
A major and stable QTL for fertile spikelet number per spike and grain number per fertile spikelet identified in a 4.96-Mb interval on chromosome 2A was validated in different genetic backgrounds. Fertile spikelet number per spike (FSN) and grain number per fertile spikelet (GNFS) contribute greatly to wheat yield improvement. To detect quantitative trait loci (QTL) associated with FSN and GNFS, we used a recombinant inbred line population crossed by Zhongkemai 13F10 and Chuanmai 42 in eight environments. Two Genomic regions associated with FSN were detected on chromosomes 2A and 6A using bulked segregant exome sequencing analysis. After the genetic linkage maps were constructed, four QTL QFsn.cib-2A, QFsn.cib-6A, QGnfs.cib-2A and QGnfs.cib-6A were identified in three or more environments. Among them, two major QTL QFsn.cib-2A (LOD = 4.67-9.34, PVE = 6.66-13.05%) and QGnfs.cib-2A (LOD = 5.27-11.68, PVE = 7.95-16.71%) were detected in seven and six environments, respectively. They were co-located in the same region, namely QFsn/Gnfs.cib-2A. The developed linked Kompetitive Allele Specific PCR (KASP) markers further validated this QTL in a different genetic background. QFsn/Gnfs.cib-2A showed pleiotropic effects on grain number per spike (GNS) and spike compactness (SC), and had no effect on grain weight. Since QFsn/Gnfs.cib-2A might be a new locus, it and the developed KASP markers can be used in wheat breeding. According to haplotype analysis, QFsn/Gnfs.cib-2A was identified as a target of artificial selection during wheat improvement. Based on haplotype analysis, sequence differences, spatiotemporal expression patterns, and gene annotation, the potential candidate genes for QFsn/Gnfs.cib-2A were predicted. These results provide valuable information for fine mapping and cloning gene(s) underlying QFsn/Gnfs.cib-2A.
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Affiliation(s)
- Cheng Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- College of Life Sciences, Sichuan University, Chengdu, 610064, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangen Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qin Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Zhao
- College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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14
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Liu Z, Zhao P, Lai X, Wang X, Ji W, Xu S. The selection and application of peduncle length QTL QPL_6D.1 in modern wheat (Triticum aestivum L.) breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:32. [PMID: 36897424 DOI: 10.1007/s00122-023-04274-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
QPL_6D.1b displayed an additive effect with Rht-B1b and Rht-D1b in reducing wheat plant height and peduncle length, which confers shorter peduncle length and more kernels per spike, and had been broadly selected by Chinese modern wheat cultivars. Peduncle length (PL), as the key component of wheat plant height (PH), plays critical role in determining wheat lodging resistance and wheat pathogen resistance; then, its breeding selection and genetic basis remain largely unclear. Here the PH and PL were investigated in 406 wheat accessions in eight environments. In this study, a PL preferentially QTL QPL_6D.1 was identified in six environments by GWAS, which explained 13.6-24.2% of wheat PL variations in natural population. The allele QPL_6D.1b displayed a significantly additive effect with Rht-B1b and Rht-D1b in controlling PH and PL and could freely combined with Rht-B1b and Rht-D1b in current wheat cultivars. Haplotypic analysis demonstrates the QPL_6D.1b has been selected by Chinese modern wheat cultivar and confers shorter PL and more kernels per spike, highlighting its potentials in wheat breeding.
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Affiliation(s)
- Zihui Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Peng Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xiangjun Lai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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15
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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Zhang X, Qiao L, Li X, Yang Z, Liu C, Guo H, Zheng J, Zhang S, Chang L, Chen F, Jia J, Yan L, Chang Z. Genetic Incorporation of the Favorable Alleles for Three Genes Associated With Spikelet Development in Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:892642. [PMID: 35592560 PMCID: PMC9111956 DOI: 10.3389/fpls.2022.892642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
The number of spikelets per spike is an important trait that directly affects grain yield in wheat. Three quantitative trait loci (QTLs) associated with spikelet nodes per spike (SNS) were mapped in a population of recombinant inbred lines generated from a cross between two advanced breeding lines of winter wheat based on the phenotypic variation evaluated over six locations/years. Two of the three QTLs are QSns.sxau-2A at the WHEATFRIZZY PANICLE (WFZP) loci and QSns.sxau-7A at the WHEAT ORTHOLOG OF APO1 (WAPO1) loci. The WFZP-A1b allele with a 14-bp deletion at QSns.sxau-2A was associated with increased spikelets per spike. WAPO-A1e, as a novel allele at WAPO1, were regulated at the transcript level that was associated with the SNS trait. The third SNS QTL, QSns.sxau-7D on chromosome 7D, was not associated with homoeologous WAPO-D1 or any other genes known to regulate SNS. The favorable alleles for each of WZFP-A1, WAPO-A1, and QSns.sxau-7D are identified and incorporated to increase up to 3.4 spikelets per spike in the RIL lines. Molecular markers for the alleles were developed. This study has advanced our understanding of the genetic basis of natural variation in spikelet development in wheat.
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Affiliation(s)
- Xiaojun Zhang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Linyi Qiao
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Xin Li
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Zujun Yang
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Huijuan Guo
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Shuwei Zhang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Lifang Chang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Fang Chen
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Juqing Jia
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Zhijian Chang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
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Chen Z, Ke W, He F, Chai L, Cheng X, Xu H, Wang X, Du D, Zhao Y, Chen X, Xing J, Xin M, Guo W, Hu Z, Su Z, Liu J, Peng H, Yao Y, Sun Q, Ni Z. A single nucleotide deletion in the third exon of FT-D1 increases the spikelet number and delays heading date in wheat (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:920-933. [PMID: 34978137 PMCID: PMC9055817 DOI: 10.1111/pbi.13773] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/02/2021] [Accepted: 12/24/2021] [Indexed: 05/31/2023]
Abstract
The spikelet number and heading date are two crucial and correlated traits for yield in wheat. Here, a quantitative trait locus (QTL) analysis was conducted in F8 recombinant inbred lines (RILs) derived from crossing two common wheats with different spikelet numbers. A total of 15 stable QTL influencing total spikelet number (TSN) and heading date (HD) were detected. Notably, FT-D1, a well-known flowering time gene in wheat, was located within the finely mapped interval of a major QTL on 7DS (QTsn/Hd.cau-7D). A causal indel of one G in the third exon of FT-D1 was significantly associated with total spikelet number and heading date. Consistently, CRISPR/Cas9 mutant lines with homozygous mutations in FT-D1 displayed an increase in total spikelet number and heading date when compared with wild type. Moreover, one simple and robust marker developed according to the polymorphic site of FT-D1 revealed that this one G indel had been preferentially selected to adapt to different environments. Collectively, these data provide further insights into the genetic basis of spikelet number and heading date, and the diagnostic marker of FT-D1 will be useful for marker-assisted pyramiding in wheat breeding.
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Affiliation(s)
- Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Fei He
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJCIC‐MCPCIC‐MCPNanjing Agricultural UniversityNanjingChina
| | - Huanwen Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Dejie Du
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Yidi Zhao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Xiyong Chen
- Hebei Crop Genetic Breeding LaboratoryInstitute of Cereal and Oil CropsHebei Academy of Agriculture and Forestry SciencesShijiazhuangChina
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Zhenqi Su
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
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18
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Katz A, Byrne P, Reid S, Bratschun S, Haley S, Pearce S. Identification and validation of a QTL for spikelet number on chromosome arm 6BL of common wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:17. [PMID: 37309457 PMCID: PMC10248590 DOI: 10.1007/s11032-022-01288-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
To provide food security for a growing world population, it will be necessary to increase yields of staple crops such as wheat (Triticum aestivum L.). Yield is a complex, polygenic trait influenced by grain weight and number, which are negatively correlated with one another. Spikelet number is an important determinant of grain number, but allelic variants impacting its expression are often associated with heading date, constraining their use in wheat germplasm that must be adapted for specific environments. Identification and characterization of genetic variants affecting spikelet number will increase selection efficiency through their deployment in breeding programs. In this study, a quantitative trait locus (QTL) on chromosome arm 6BL for spikelet number was identified and validated using an association mapping panel, a recombinant inbred line population, and seven derived heterogeneous inbred families. The superior allele, QSn.csu-6Bb, was associated with an increase of 0.248 to 0.808 spikelets per spike across multiple environments that varied for mean spikelet number. Despite epistatic interactions between QSn.csu-6B and three other loci (WAPO-A1, VRN-D3, and PPD-B1), genotypes with a greater number of superior alleles at these loci consistently exhibit higher spikelet number. The frequency of superior alleles at these loci varies among winter wheat varieties adapted to different latitudes of the US Great Plains, revealing opportunities for breeders to select for increased spikelet number using simple molecular markers. This work lays the foundation for the positional cloning of the genetic variant underlying the QSn.csu-6B QTL to strengthen our understanding of spikelet number determination in wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01288-7.
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Affiliation(s)
- Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Patrick Byrne
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Scott Reid
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Sarah Bratschun
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Scott Haley
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
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19
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Li C, Liu H, Wang J, Pan Q, Wang Y, Wu K, Jia P, Mu Y, Tang H, Xu Q, Jiang Q, Liu Y, Qi P, Zhang X, Huang L, Chen G, Wang J, Wei Y, Zheng Y, Gou L, Yao Q, Lan X, Ma J. Characterization and fine mapping of a lesion mimic mutant (Lm5) with enhanced stripe rust and powdery mildew resistance in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:421-438. [PMID: 34661696 DOI: 10.1007/s00122-021-03973-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
A novel light intensity-dependent lesion mimic mutant with enhanced disease resistance was physiologically, biochemically, and genetically characterized, and the causative gene was fine mapped to a 1.28 Mbp interval containing 17 high-confidence genes. Lesion mimic mutants are ideal for studying disease resistance and programmed cell death photosynthesis in plants to improve crop yield. In this study, a novel light intensity-dependent lesion mimic mutant (MC21) was obtained from the wheat variety Chuannong16 (CN16) by ethyl methane sulfonate treatment. The mutant initially developed tiny lesion spots on the basal part of the leaves, which then gradually proceeded down to leaf sheaths, stems, shells, and awns at the flowering stage. The major agronomic traits were significantly altered in the mutant compared to that in the wild-type CN16. Furthermore, the mutant exhibited a lesion phenotype with degenerated chloroplast structure, decreased chlorophyll content, increased level of reactive oxygen species, and increased resistance to stripe rust and powdery mildew. Genetic analysis indicated that the lesion phenotype was controlled by a novel single semi-dominant nuclear gene. The target gene was mapped on chromosome arm 2AL located between Kompetitive Allele Specific PCR (KASP) markers, KASP-4211 and KASP-5353, and tentatively termed as lesion mimic 5 (Lm5). The fine mapping suggested that Lm5 was located in a 1.28 Mbp interval between markers KASP-5825 and KASP-9366; 17 high-confidence candidate genes were included in this genomic region. This study provides an important foundational step for further cloning of Lm5 using a map-based approach.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qi Pan
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yue Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kunyan Wu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peiying Jia
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaojun Zhang
- College of Agronomy, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lulu Gou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qifu Yao
- College of Agroforestry Engineering and Planning/Guizhou Key Laboratory of Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren, 554300, China.
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Zheng X, Qiao L, Liu Y, Wei N, Zhao J, Wu B, Yang B, Wang J, Zheng J. Genome-Wide Association Study of Grain Number in Common Wheat From Shanxi Under Different Water Regimes. FRONTIERS IN PLANT SCIENCE 2022; 12:806295. [PMID: 35154198 PMCID: PMC8825475 DOI: 10.3389/fpls.2021.806295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Water availability is a crucial environmental factor on grain number in wheat, which is one of the important yield-related traits. In this study, a diverse panel of 282 wheat accessions were phenotyped for grain number per spike (GNS), spikelet number (SN), basal sterile spikelet number (BSSN), and apical sterile spikelet number (ASSN) under different water regimes across two growing seasons. Correlation analysis showed that GNS is significantly correlated with both SN and BSSN under two water regimes. A total of 9,793 single nucleotide polymorphism (SNP) markers from the 15 K wheat array were employed for genome-wide association study (GWAS). A total of 77 significant marker-trait associations (MTAs) for investigated traits as well as 8 MTAs for drought tolerance coefficient (DTC) were identified using the mixed linear model. Favored alleles for breeding were inferred according to their estimated effects on GNS, based on the mean difference of varieties. Frequency changes in favored alleles associated with GNS in modern varieties indicate there is still considerable genetic potential for their use as markers for genome selection of GNS in wheat breeding.
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Affiliation(s)
- Xingwei Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ling Qiao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ye Liu
- College of Life Science, Shanxi University, Taiyuan, China
| | - Naicui Wei
- College of Life Science, Shanxi University, Taiyuan, China
| | - Jiajia Zhao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bangbang Wu
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bin Yang
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Juanling Wang
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jun Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
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21
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You J, Liu H, Wang S, Luo W, Gou L, Tang H, Mu Y, Deng M, Jiang Q, Chen G, Qi P, Peng Y, Tang L, Habib A, Wei Y, Zheng Y, Lan X, Ma J. Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations. FRONTIERS IN PLANT SCIENCE 2021; 12:796397. [PMID: 34975986 PMCID: PMC8716915 DOI: 10.3389/fpls.2021.796397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/26/2021] [Indexed: 05/15/2023]
Abstract
Spike density (SD) is an agronomically important character in wheat. In addition, an optimized spike structure is a key basis for high yields. Identification of quantitative trait loci (QTL) for SD has provided a genetic basis for constructing ideal spike morphologies in wheat. In this study, two recombinant inbred line (RIL) populations (tetraploid RIL AM and hexaploid RIL 20828/SY95-71 (2SY)) previously genotyped using the wheat55K SNP array were used to identify SD QTL. A total of 18 QTL were detected, and three were major and one was stably expressed (QSd.sau-2SY-7A.2, QSd.sau-AM-5A.2, QSd.sau-AM-7B, and QSd.sau-2SY-2D). They can explain up to 23.14, 19.97, 12.00, and 9.44% of phenotypic variation, respectively. QTL × environment and epistatic interactions for SD were further analyzed. In addition, pyramiding analysis further revealed that there were additive effects between QSd.sau-2SY-2D and QSd.sau-2SY-7A.2 in 2SY, and QSd.sau-AM-5A.2 and QSd.sau-AM-7B in AM. Pearson's correlation between SD and other agronomic traits, and effects of major or stable QTL on yield related traits indicated SD significantly impacted spike length (SL), spikelet number per spike (SNS) and kernel length (KL). Several genes related to spike development within the physical intervals of major or stable QTL were predicted and discussed. Collectively, our research identified QTL with potential applications for modern wheat breeding and broadening the genetic basis of SD.
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Affiliation(s)
- Jianing You
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Surong Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Luo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lulu Gou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Liwei Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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22
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Chen L, Li H, Liu Y, Yang J, Hou Y. Genetic identification of a major, novel and stably expressed QTL for effective tiller number from tetraploid wheat. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1996271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Li Chen
- Department of Agriculture and Food Engineering, College of Life Science and Food Engineering, Yibin University, Yibin, Sichuan, PR China
- Office of Agriculture, Department of Food, Yibin Products Quality Supervision and Inspection Institute, Yibin, Sichuan, PR China
| | - Hua Li
- Office of Agriculture, Department of Food, Yibin Products Quality Supervision and Inspection Institute, Yibin, Sichuan, PR China
| | - Yanmei Liu
- Office of Agriculture, Department of Food, Yibin Products Quality Supervision and Inspection Institute, Yibin, Sichuan, PR China
| | - Juan Yang
- Office of Agriculture, Department of Food, Yibin Products Quality Supervision and Inspection Institute, Yibin, Sichuan, PR China
| | - Ying Hou
- Office of Agriculture, Department of Food, Yibin Products Quality Supervision and Inspection Institute, Yibin, Sichuan, PR China
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Yield-Related QTL Clusters and the Potential Candidate Genes in Two Wheat DH Populations. Int J Mol Sci 2021; 22:ijms222111934. [PMID: 34769361 PMCID: PMC8585063 DOI: 10.3390/ijms222111934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9–16.5 Mb), 2B.3, 3B (68.9–214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1–613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3–672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0–56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding.
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24
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Arif MAR, Shokat S, Plieske J, Ganal M, Lohwasser U, Chesnokov YV, Kocherina NV, Kulwal P, Kumar N, McGuire PE, Sorrells ME, Qualset CO, Börner A. A SNP-based genetic dissection of versatile traits in bread wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:960-976. [PMID: 34218494 DOI: 10.1111/tpj.15407] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/14/2021] [Indexed: 05/20/2023]
Abstract
The continuous increase in global population prompts increased wheat production. Future wheat (Triticum aestivum L.) breeding will heavily rely on dissecting molecular and genetic bases of wheat yield and related traits which is possible through the discovery of quantitative trait loci (QTLs) in constructed populations, such as recombinant inbred lines (RILs). Here, we present an evaluation of 92 RILs in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative Mapping Population [ITMI/MP]) using newly generated phenotypic data in 3-year experiments (2015), older phenotypic data (1997-2009), and newly created single nucleotide polymorphism (SNP) marker data based on 92 of the original RILs to search for novel and stable QTLs. Our analyses of more than 15 unique traits observed in multiple experiments included analyses of 46 traits in three environments in the USA, 69 traits in eight environments in Germany, 149 traits in 10 environments in Russia, and 28 traits in four environments in India (292 traits in 25 environments) with 7584 SNPs (292 × 7584 = 2 214 528 data points). A total of 874 QTLs were detected with limit of detection (LOD) scores of 2.01-3.0 and 432 QTLs were detected with LOD > 3.0. Moreover, 769 QTLs could be assigned to 183 clusters based on the common markers and relative proximity of related QTLs, indicating gene-rich regions throughout the A, B, and D genomes of common wheat. This upgraded genotype-phenotype information of ITMI/MP can assist breeders and geneticists who can make crosses with suitable RILs to improve or investigate traits of interest.
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Affiliation(s)
- Mian Abdur Rehman Arif
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Sajid Shokat
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Jörg Plieske
- SGS Institut Fresenius GmbH TraitGenetics Section, Am Schwabeplan 1b, Stadt Seeland, OT Gatersleben, 06466, Germany
| | - Martin Ganal
- SGS Institut Fresenius GmbH TraitGenetics Section, Am Schwabeplan 1b, Stadt Seeland, OT Gatersleben, 06466, Germany
| | - Ulrike Lohwasser
- Resources Genetics and Reproduction Group, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
| | - Yuriy V Chesnokov
- Laboratory of Ecological Genetics and Plant Breeding, Agrophysical Research Institute, Grazhdanskiy pr. 14, St. Petersburg, 195220, Russia
| | - Nataliya V Kocherina
- Laboratory of Ecological Genetics and Plant Breeding, Agrophysical Research Institute, Grazhdanskiy pr. 14, St. Petersburg, 195220, Russia
| | - Pawan Kulwal
- State Level Biotechnology Centre, Mahatma Phule Krishi Vidyapeeth, Rahuri, Ahmednagar, Maharashtra, 413 722, India
| | - Neeraj Kumar
- Department of Plant and Environmental Sciences, Clemson University, 100C Biosystems Research Complex 105 Collings Street, Clemson, SC, 29634-0141, USA
| | - Patrick E McGuire
- Plant Sciences Department, University of California, Mail Stop 3, One Shields Avenue, Davis, CA, 95616, USA
| | - Mark E Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Calvin O Qualset
- Plant Sciences Department, University of California, Mail Stop 3, One Shields Avenue, Davis, CA, 95616, USA
| | - Andreas Börner
- Resources Genetics and Reproduction Group, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
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25
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Zhou J, Li C, You J, Tang H, Mu Y, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Ma J, Gao Y, Habib A, Wei Y, Zheng Y, Lan X, Ma J. Genetic identification and characterization of chromosomal regions for kernel length and width increase from tetraploid wheat. BMC Genomics 2021; 22:706. [PMID: 34592925 PMCID: PMC8482559 DOI: 10.1186/s12864-021-08024-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/13/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Improvement of wheat gercTriticum aestivum L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield for wheat breeders. Wheat related species possesses numerous elite genes that can be introduced into wheat breeding. It is thus vital to explore, identify, and introduce new genetic resources for kernel size from wheat wild relatives to increase wheat yield. RESULTS In the present study, quantitative trait loci (QTL) for kernel length (KL) and width (KW) were detected in a recombinant inbred line (RIL) population derived from a cross between a wild emmer accession 'LM001' and a Sichuan endemic tetraploid wheat 'Ailanmai' using the Wheat 55 K single nucleotide polymorphism (SNP) array-based constructed linkage map and phenotype from six different environments. We identified eleven QTL for KL and KW including two major ones QKL.sicau-AM-3B and QKW.sicau-AM-4B, the positive alleles of which were from LM001 and Ailanmai, respectively. They explained 17.57 to 44.28% and 13.91 to 39.01% of the phenotypic variance, respectively. For these two major QTL, Kompetitive allele-specific PCR (KASP) markers were developed and used to successfully validate their effects in three F3 populations and two natural populations containing a panel of 272 Chinese wheat landraces and that of 300 Chinese wheat cultivars, respectively. QKL.sicau-AM-3B was located at 675.6-695.4 Mb on chromosome arm 3BL. QKW.sicau-AM-4B was located at 444.2-474.0 Mb on chromosome arm 4BL. Comparison with previous studies suggested that these two major QTL were likely new loci. Further analysis indicated that the positive alleles of QKL.sicau-AM-3B and QKW.sicau-AM-4B had a great additive effect increasing TKW by 6.01%. Correlation analysis between KL and other agronomic traits showed that KL was significantly correlated to spike length, length of uppermost internode, TKW, and flag leaf length. KW was also significantly correlated with TKW. Four genes, TRIDC3BG062390, TRIDC3BG062400, TRIDC4BG037810, and TRIDC4BG037830, associated with kernel development were predicted in physical intervals harboring these two major QTL on wild emmer and Chinese Spring reference genomes. CONCLUSIONS Two stable and major QTL for KL and KW across six environments were detected and verified in three biparental populations and two natural populations. Significant relationships between kernel size and yield-related traits were identified. KASP markers tightly linked the two major QTL could contribute greatly to subsequent fine mapping. These results suggested the application potential of wheat related species in wheat genetic improvement.
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Affiliation(s)
- Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jianing You
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yutian Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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26
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Pretini N, Vanzetti LS, Terrile II, Donaire G, González FG. Mapping QTL for spike fertility and related traits in two doubled haploid wheat (Triticum aestivum L.) populations. BMC PLANT BIOLOGY 2021; 21:353. [PMID: 34311707 PMCID: PMC8314532 DOI: 10.1186/s12870-021-03061-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/23/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND In breeding programs, the selection of cultivars with the highest yield potential consisted in the selection of the yield per se, which resulted in cultivars with higher grains per spike (GN) and occasionally increased grain weight (GW) (main numerical components of the yield). In this study, quantitative trait loci (QTL) for GW, GN and spike fertility traits related to GN determination were mapped using two doubled haploid (DH) populations (Baguette Premium 11 × BioINTA 2002 and Baguette 19 × BioINTA 2002). RESULTS In total 305 QTL were identified for 14 traits, out of which 12 QTL were identified in more than three environments and explained more than 10% of the phenotypic variation in at least one environment. Eight hotspot regions were detected on chromosomes 1A, 2B, 3A, 5A, 5B, 7A and 7B in which at least two major and stable QTL sheared confidence intervals. QTL on two of these regions (R5A.1 and R5A.2) have previously been described, but the other six regions are novel. CONCLUSIONS Based on the pleiotropic analysis within a robust physiological model we conclude that two hotspot genomic regions (R5A.1 and R5A.2) together with the QGW.perg-6B are of high relevance to be used in marker assisted selection in order to improve the spike yield potential. All the QTL identified for the spike related traits are the first step to search for their candidate genes, which will allow their better manipulation in the future.
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Affiliation(s)
- Nicole Pretini
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA, CONICET-UNNOBA-UNSADA), Monteagudo 2772 CP 2700, Pergamino, Buenos Aires, Argentina.
| | - Leonardo S Vanzetti
- Instituto Nacional de Tecnología Agropecuaria (INTA), EEA INTA Marcos Juárez. Ruta 12 s/n CP 2850, Marcos Juárez, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 CP C1425FQB, Buenos Aires, Argentina
| | - Ignacio I Terrile
- Instituto Nacional de Tecnología Agropecuaria (INTA), EEA INTA Pergamino. Ruta 32, km 4,5 CP 2700, Pergamino, Buenos Aires, Argentina
| | - Guillermo Donaire
- Instituto Nacional de Tecnología Agropecuaria (INTA), EEA INTA Marcos Juárez. Ruta 12 s/n CP 2850, Marcos Juárez, Córdoba, Argentina
| | - Fernanda G González
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA, CONICET-UNNOBA-UNSADA), Monteagudo 2772 CP 2700, Pergamino, Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), EEA INTA Pergamino. Ruta 32, km 4,5 CP 2700, Pergamino, Buenos Aires, Argentina
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Hu Z, Wang Y, Liu J, Li Y, Wang Y, Huang J, Ai Y, Chen P, He Y, Aftab MN, Wang L, Peng L. Integrated NIRS and QTL assays reveal minor mannose and galactose as contrast lignocellulose factors for biomass enzymatic saccharification in rice. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:144. [PMID: 34174936 PMCID: PMC8235839 DOI: 10.1186/s13068-021-01987-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/05/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Identifying lignocellulose recalcitrant factors and exploring their genetic properties are essential for enhanced biomass enzymatic saccharification in bioenergy crops. Despite genetic modification of major wall polymers has been implemented for reduced recalcitrance in engineered crops, it could most cause a penalty of plant growth and biomass yield. Alternatively, it is increasingly considered to improve minor wall components, but an applicable approach is required for efficient assay of large population of biomass samples. Hence, this study collected total of 100 rice straw samples and characterized all minor wall monosaccharides and biomass enzymatic saccharification by integrating NIRS modeling and QTL profiling. RESULTS By performing classic chemical analyses and establishing optimal NIRS equations, this study examined four minor wall monosaccharides and major wall polymers (acid-soluble lignin/ASL, acid-insoluble lignin/AIL, three lignin monomers, crystalline cellulose), which led to largely varied hexoses yields achieved from enzymatic hydrolyses after two alkali pretreatments were conducted with large population of rice straws. Correlation analyses indicated that mannose and galactose can play a contrast role for biomass enzymatic saccharification at P < 0.0 l level (n = 100). Meanwhile, we found that the QTLs controlling mannose, galactose, lignin-related traits, and biomass saccharification were co-located. By combining NIRS assay with QTLs maps, this study further interpreted that the mannose-rich hemicellulose may assist AIL disassociation for enhanced biomass enzymatic saccharification, whereas the galactose-rich polysaccharides should be effectively extracted with ASL from the alkali pretreatment for condensed AIL association with cellulose microfibrils. CONCLUSIONS By integrating NIRS assay with QTL profiling for large population of rice straw samples, this study has identified that the mannose content of wall polysaccharides could positively affect biomass enzymatic saccharification, while the galactose had a significantly negative impact. It has also sorted out that two minor monosaccharides could distinctively associate with lignin deposition for wall network construction. Hence, this study demonstrates an applicable approach for fast assessments of minor lignocellulose recalcitrant factors and biomass enzymatic saccharification in rice, providing a potential strategy for bioenergy crop breeding and biomass processing.
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Affiliation(s)
- Zhen Hu
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering and, Nanomaterial Application in Automobiles, College of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Youmei Wang
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering and, Nanomaterial Application in Automobiles, College of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China
| | - Jingyuan Liu
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering and, Nanomaterial Application in Automobiles, College of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China
| | - Yuqi Li
- Laboratory of Biomass Engineering and, Nanomaterial Application in Automobiles, College of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering and, Nanomaterial Application in Automobiles, College of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China
| | - Jiangfeng Huang
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Yuanhang Ai
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering and, Nanomaterial Application in Automobiles, College of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering and, Nanomaterial Application in Automobiles, College of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Lingqiang Wang
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Laboratory of Biomass Engineering and, Nanomaterial Application in Automobiles, College of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China.
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Utilization of a Wheat50K SNP Microarray-Derived High-Density Genetic Map for QTL Mapping of Plant Height and Grain Traits in Wheat. PLANTS 2021; 10:plants10061167. [PMID: 34201388 PMCID: PMC8229693 DOI: 10.3390/plants10061167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 11/22/2022]
Abstract
Plant height is significantly correlated with grain traits, which is a component of wheat yield. The purpose of this study is to investigate the main quantitative trait loci (QTLs) that control plant height and grain-related traits in multiple environments. In this study, we constructed a high-density genetic linkage map using the Wheat50K SNP Array to map QTLs for these traits in 198 recombinant inbred lines (RILs). The two ends of the chromosome were identified as recombination-rich areas in all chromosomes except chromosome 1B. Both the genetic map and the physical map showed a significant correlation, with a correlation coefficient between 0.63 and 0.99. However, there was almost no recombination between 1RS and 1BS. In terms of plant height, 1RS contributed to the reduction of plant height by 3.43 cm. In terms of grain length, 1RS contributed to the elongation of grain by 0.11 mm. A total of 43 QTLs were identified, including eight QTLs for plant height (PH), 11 QTLs for thousand grain weight (TGW), 15 QTLs for grain length (GL), and nine QTLs for grain width (GW), which explained 1.36–33.08% of the phenotypic variation. Seven were environment-stable QTLs, including two loci (Qph.nwafu-4B and Qph.nwafu-4D) that determined plant height. The explanation rates of phenotypic variation were 7.39–12.26% and 20.11–27.08%, respectively. One QTL, Qtgw.nwafu-4B, which influenced TGW, showed an explanation rate of 3.43–6.85% for phenotypic variation. Two co-segregating KASP markers were developed, and the physical locations corresponding to KASP_AX-109316968 and KASP_AX-109519968 were 25.888344 MB and 25.847691 MB, respectively. Qph.nwafu-4B, controlling plant height, and Qtgw.nwafu-4B, controlling TGW, had an obvious linkage relationship, with a distance of 7–8 cM. Breeding is based on molecular markers that control plant height and thousand-grain weight by selecting strains with low plant height and large grain weight. Another QTL, Qgw.nwafu-4D, which determined grain width, had an explanation rate of 3.43–6.85%. Three loci that affected grain length were Qgl.nwafu-5A, Qgl.nwafu-5D.2, and Qgl.nwafu-6B, illustrating the explanation rates of phenotypic variation as 6.72–9.59%, 5.62–7.75%, and 6.68–10.73%, respectively. Two QTL clusters were identified on chromosomes 4B and 4D.
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Li Y, Li L, Zhao M, Guo L, Guo X, Zhao D, Batool A, Dong B, Xu H, Cui S, Zhang A, Fu X, Li J, Jing R, Liu X. Wheat FRIZZY PANICLE activates VERNALIZATION1-A and HOMEOBOX4-A to regulate spike development in wheat. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1141-1154. [PMID: 33368973 PMCID: PMC8196646 DOI: 10.1111/pbi.13535] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/27/2020] [Accepted: 12/14/2020] [Indexed: 05/22/2023]
Abstract
Kernel number per spike determined by the spike or inflorescence development is one important agricultural trait for wheat yield that is critical for global food security. While a few important genes for wheat spike development were identified, the genetic regulatory mechanism underlying supernumerary spikelets (SSs) is still unclear. Here, we cloned the wheat FRIZZY PANICLE (WFZP) gene from one local wheat cultivar. WFZP is specifically expressed at the sites where the spikelet meristem and floral meristem are initiated, which differs from the expression patterns of its homologs FZP/BD1 in rice and maize, indicative of its functional divergence during species differentiation. Moreover, WFZP directly activates VERNALIZATION1 (VRN1) and wheat HOMEOBOX4 (TaHOX4) to regulate the initiation and development of spikelet. The haplotypes analysis showed that the favourable alleles of WFZP associated with spikelet number per spike (SNS) were preferentially selected during breeding. Our findings provide insights into the molecular and genetic mechanisms underlying wheat spike development and characterize the WFZP as elite resource for wheat molecular breeding with enhanced crop yield.
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Affiliation(s)
- Yongpeng Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Meicheng Zhao
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Lin Guo
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
- Ministry of Education Key Laboratory of Molecular and Cellular BiologyHebei Collaboration Innovation Center for Cell SignalingHebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityShijiazhuangChina
| | - Xinxin Guo
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Dan Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular BiologyHebei Collaboration Innovation Center for Cell SignalingHebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityShijiazhuangChina
| | - Aamana Batool
- University of Chinese Academy of SciencesBeijingChina
- Key Laboratory of Agricultural Water ResourcesHebei Laboratory of Agricultural Water‐SavingCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesShijiazhuangChina
| | - Baodi Dong
- Key Laboratory of Agricultural Water ResourcesHebei Laboratory of Agricultural Water‐SavingCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesShijiazhuangChina
| | - Hongxing Xu
- Key Laboratory of Agricultural Water ResourcesHebei Laboratory of Agricultural Water‐SavingCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesShijiazhuangChina
- State Key Laboratory of Crop Stress Adaptation and ImprovementState Key laboratory of Cotton BiologySchool of Life SciencesHenan UniversityKaifengChina
| | - Sujuan Cui
- Ministry of Education Key Laboratory of Molecular and Cellular BiologyHebei Collaboration Innovation Center for Cell SignalingHebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityShijiazhuangChina
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Junming Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xigang Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
- Ministry of Education Key Laboratory of Molecular and Cellular BiologyHebei Collaboration Innovation Center for Cell SignalingHebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityShijiazhuangChina
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Pretini N, Alonso MP, Vanzetti LS, Pontaroli AC, González FG. The physiology and genetics behind fruiting efficiency: a promising spike trait to improve wheat yield potential. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3987-4004. [PMID: 33681978 DOI: 10.1093/jxb/erab080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Fruiting efficiency (FE, grains per g of spike dry weight at anthesis) was proposed as a promising spike trait to improve wheat yield potential, based on its functional relationship with grain number determination and the evidence of trait variability in elite germplasm. During the last few years, we have witnessed great advances in the understanding of the physiological and genetic basis of this trait. The present review summarizes the recent heritability estimations and the genetic gains obtained when fruiting efficiency was measured at maturity (FEm, grains per g of chaff) and used as selection criterion. In addition, we propose spike ideotypes for contrasting fruiting efficiencies based on the fertile floret efficiency (FFE, fertile florets per g of spike dry weight at anthesis) and grain set (grains per fertile floret), together with other spike fertility-related traits. We also review novel genes and quantitative trait loci available for using marker-assisted selection for fruiting efficiency and other spike fertility traits. The possible trade-off between FE and grain weight and the genes reported to alter this relation are also considered. Finally, we discuss the benefits and future steps towards the use of fruiting efficiency as a selection criterion in breeding programs.
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Affiliation(s)
- Nicole Pretini
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA, CONICET-UNNOBA-UNSADA), Monteagudo 2772 CP 2700, Pergamino, Buenos Aires, Argentina
| | - María P Alonso
- Unidad Integrada Balcarce [Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata -Instituto Nacional de Tecnología Agropecuaria (INTA), EEA INTA Balcarce], Ruta 226 km 73.5 CP 7620, Balcarce, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 CP C1425FQB, Buenos Aires, Argentina
| | - Leonardo S Vanzetti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 CP C1425FQB, Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA). EEA INTA Marcos Juárez, Ruta 12 s/n CP 2850, Marcos Juárez, Córdoba, Argentina
| | - Ana C Pontaroli
- Unidad Integrada Balcarce [Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata -Instituto Nacional de Tecnología Agropecuaria (INTA), EEA INTA Balcarce], Ruta 226 km 73.5 CP 7620, Balcarce, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 CP C1425FQB, Buenos Aires, Argentina
| | - Fernanda G González
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA, CONICET-UNNOBA-UNSADA), Monteagudo 2772 CP 2700, Pergamino, Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA). EEA INTA Pergamino, Ruta 32, km 4,5 CP 2700, Pergamino, Buenos Aires, Argentina
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31
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Zhou H, Riche AB, Hawkesford MJ, Whalley WR, Atkinson BS, Sturrock CJ, Mooney SJ. Determination of wheat spike and spikelet architecture and grain traits using X-ray Computed Tomography imaging. PLANT METHODS 2021; 17:26. [PMID: 33750418 PMCID: PMC7945051 DOI: 10.1186/s13007-021-00726-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/26/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Wheat spike architecture is a key determinant of multiple grain yield components and detailed examination of spike morphometric traits is beneficial to explain wheat grain yield and the effects of differing agronomy and genetics. However, quantification of spike morphometric traits has been very limited because it relies on time-consuming manual measurements. RESULTS In this study, using X-ray Computed Tomography imaging, we proposed a method to efficiently detect the 3D architecture of wheat spikes and component spikelets by clustering grains based on their Euclidean distance and relative positions. Morphometric characteristics of wheat spikelets and grains, e.g., number, size and spatial distribution along the spike can be determined. Two commercial wheat cultivars, one old, Maris Widgeon, and one modern, Siskin, were studied as examples. The average grain volume of Maris Widgeon and Siskin did not differ, but Siskin had more grains per spike and therefore greater total grain volume per spike. The spike length and spikelet number were not statistically different between the two cultivars. However, Siskin had a higher spikelet density (number of spikelets per unit spike length), with more grains and greater grain volume per spikelet than Maris Widgeon. Spatial distribution analysis revealed the number of grains, the average grain volume and the total grain volume of individual spikelets varied along the spike. Siskin had more grains and greater grain volumes per spikelet from spikelet 6, but not spikelet 1-5, compared with Maris Widgeon. The distribution of average grain volume along the spike was similar for the two wheat cultivars. CONCLUSION The proposed method can efficiently extract spike, spikelet and grain morphometric traits of different wheat cultivars, which can contribute to a more detailed understanding of the sink of wheat grain yield.
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Affiliation(s)
- Hu Zhou
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
| | | | | | | | - Brian S. Atkinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
| | - Craig J. Sturrock
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
| | - Sacha J. Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
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Ren T, Fan T, Chen S, Li C, Chen Y, Ou X, Jiang Q, Ren Z, Tan F, Luo P, Chen C, Li Z. Utilization of a Wheat55K SNP array-derived high-density genetic map for high-resolution mapping of quantitative trait loci for important kernel-related traits in common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:807-821. [PMID: 33388883 DOI: 10.1007/s00122-020-03732-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/18/2020] [Indexed: 05/19/2023]
Abstract
This study mapped QTLs associated with kernel-related traits by high-density genetic map. Five new major and stable QTLs for KL, KDR, SN, and KWPS were mapped in multiple environments. In the present study, a recombinant inbred line population including 371 lines derived from the cross of Chuannong18 and T1208 was genotyped using the Wheat55K single nucleotide polymorphism array. A novel high-density genetic map consisting of 11,583 markers spanning 4192.62 cM and distributed across 21 wheat chromosomes was constructed. QTLs for important kernel-related traits were mapped in multiple environments. A total of 96 and 151 QTLs were mapped by using the ICIM method and the MET method, respectively. And a total of 114 digenic epistatic QTLs were also detected across 21 chromosomes, and the epistatic effects of each trait were analyzed. BLAST analysis showed that 23 QTLs for different kernel-related traits were first time mapped and five of them were major and stable QTLs for kernel diameter ratio (121.34-126.83 cM on 4BS), spike number per square meter (71.32-73.84 cM on 2DS), kernel weight per spike (71.32-75.26 cM on 2DS), and kernel length (16.78-31.64 cM on 6A and 51.63-58.40 cM on 3D), respectively. Fifteen QTL clusters that contained 58 QTLs were also detected, and all most stable QTLs were contained in these QTL clusters. Significant correlations between different traits were detected and discussed. These results lay the foundation for fine mapping and cloning of the gene(s) underlying the stable QTLs detected in this study.
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Affiliation(s)
- Tianheng Ren
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
| | - Tao Fan
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Shulin Chen
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, WenjiangChengdu, 611130, Sichuan, China
| | - Chunsheng Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, WenjiangChengdu, 611130, Sichuan, China
| | - Yongyan Chen
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, WenjiangChengdu, 611130, Sichuan, China
| | - Xia Ou
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, WenjiangChengdu, 611130, Sichuan, China
| | - Qing Jiang
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, WenjiangChengdu, 611130, Sichuan, China
| | - Zhenglong Ren
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, WenjiangChengdu, 611130, Sichuan, China
| | - Feiquan Tan
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, WenjiangChengdu, 611130, Sichuan, China
| | - Peigao Luo
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, WenjiangChengdu, 611130, Sichuan, China
| | | | - Zhi Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- Provincial Key Laboratory for Plant Genetics and Breeding, WenjiangChengdu, 611130, Sichuan, China.
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Li T, Deng G, Tang Y, Su Y, Wang J, Cheng J, Yang Z, Qiu X, Pu X, Zhang H, Liang J, Yu M, Wei Y, Long H. Identification and Validation of a Novel Locus Controlling Spikelet Number in Bread Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:611106. [PMID: 33719283 PMCID: PMC7952655 DOI: 10.3389/fpls.2021.611106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/29/2021] [Indexed: 05/24/2023]
Abstract
Spikelet number is an important target trait for wheat yield improvement. Thus, the identification and verification of novel quantitative trait locus (QTL)/genes controlling spikelet number are essential for dissecting the underlying molecular mechanisms and hence for improving grain yield. In the present study, we constructed a high-density genetic map for the Kechengmai1/Chuanmai42 doubled haploid (DH) population using 13,068 single-nucleotide polymorphism (SNP) markers from the Wheat 55K SNP array. A comparison between the genetic and physical maps indicated high consistence of the marker orders. Based on this genetic map, a total of 27 QTLs associated with total spikelet number per spike (TSN) and fertile spikelet number per spike (FSN) were detected on chromosomes 1B, 1D, 2B, 2D, 3D, 4A, 4D, 5A, 5B, 5D, 6A, 6B, and 7D in five environments. Among them, five QTLs on chromosome 2D, 3D, 5A, and 7D were detected in multiple environments and combined QTL analysis, explaining the phenotypic variance ranging from 3.64% to 23.28%. Particularly, QTsn/Fsn.cib-3D for TSN and FSN [phenotypic variation explained (PVE) = 5.97-23.28%, limit of detection (LOD) = 3.73-18.51] is probably a novel locus and located in a 4.5-cM interval on chromosome arm 3DL flanking by the markers AX-110914105 and AX-109429351. This QTL was further validated in other two populations with different genetic backgrounds using the closely linked Kompetitive Allele-Specific PCR (KASP) marker KASP_AX-110914105. The results indicated that QTsn/Fsn.cib-3D significantly increased the TSN (5.56-7.96%) and FSN (5.13-9.35%), which were significantly correlated with grain number per spike (GNS). We also preliminary analyzed the candidate genes within this locus by sequence similarity, spatial expression patterns, and collinearity analysis. These results provide solid foundation for future fine mapping and cloning of QTsn/Fsn.cib-3D. The developed and validated KASP markers could be utilized in molecular breeding aiming to increase the grain yield in wheat.
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Affiliation(s)
- Tao Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yanyan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yan Su
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jinhui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jie Cheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xuebing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Mo Z, Zhu J, Wei J, Zhou J, Xu Q, Tang H, Mu Y, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Li W, Wei Y, Zheng Y, Lan X, Ma J. The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat ( Triticum turgidum L.) Population: Chinese Landrace "Ailanmai" × Wild Emmer. FRONTIERS IN PLANT SCIENCE 2021; 12:732837. [PMID: 34531890 PMCID: PMC8439258 DOI: 10.3389/fpls.2021.732837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/18/2021] [Indexed: 05/08/2023]
Abstract
Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace "Ailanmai" × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71-29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.
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Affiliation(s)
- Ziqiang Mo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiatai Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Xiujin Lan
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Jian Ma
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Tu Y, Liu H, Liu J, Tang H, Mu Y, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Pu Z, Chen G, Peng Y, Jiang Y, Xu Q, Kang H, Lan X, Wei Y, Zheng Y, Ma J. QTL mapping and validation of bread wheat flag leaf morphology across multiple environments in different genetic backgrounds. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:261-278. [PMID: 33026461 DOI: 10.1007/s00122-020-03695-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/22/2020] [Indexed: 05/24/2023]
Abstract
Eight major and stably expressed QTL for flag leaf morphology across eleven environments were identified and validated using newly developed KASP markers in seven biparental populations with different genetic backgrounds. Flag leaf morphology is a determinant trait influencing plant architecture and yield potential in wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population with a 55 K SNP-based constructed genetic map was used to map quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), area (FLA), angle (FLANG), opening angle (FLOA), and bend angle (FLBA) in eleven environments. Eight major QTL were detected in 11 environments with 5.73-54.38% of explained phenotypic variation. These QTL were successfully verified using the newly developed Kompetitive Allele Specific PCR (KASP) markers in six biparental populations with different genetic backgrounds. Among these 8 major QTL, two co-located intervals were identified. Significant interactions for both FLL- and FLW-related QTL were detected. Comparison analysis showed that QFll.sau-SY-2B and QFla.sau-SY-2B are likely new loci. Significant relationships between flag leaf- and yield-related traits were observed and discussed. Several genes associated with leaf development including the ortholog of maize ZmRAVL1, a B3-domain transcription factor involved in regulation of leaf angle, were predicted in physical intervals harboring these major QTL on reference genomes of bread wheat 'Chinese spring', T. turgidum, and Aegilops tauschii. Taken together, these results broaden our understanding on genetic basis of flag leaf morphology and provide clues for fine mapping and marker-assisted breeding wheat with optimized plant architecture for promising loci.
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Affiliation(s)
- Yang Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanying Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Qu X, Liu J, Xie X, Xu Q, Tang H, Mu Y, Pu Z, Li Y, Ma J, Gao Y, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Habib A, Wei Y, Zheng Y, Lan X, Ma J. Genetic Mapping and Validation of Loci for Kernel-Related Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:667493. [PMID: 34163507 PMCID: PMC8215603 DOI: 10.3389/fpls.2021.667493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/22/2021] [Indexed: 05/11/2023]
Abstract
Kernel size (KS) and kernel weight play a key role in wheat yield. Phenotypic data from six environments and a Wheat55K single-nucleotide polymorphism array-based constructed genetic linkage map from a recombinant inbred line population derived from the cross between the wheat line 20828 and the line SY95-71 were used to identify quantitative trait locus (QTL) for kernel length (KL), kernel width (KW), kernel thickness (KT), thousand-kernel weight (TKW), kernel length-width ratio (LWR), KS, and factor form density (FFD). The results showed that 65 QTLs associated with kernel traits were detected, of which the major QTLs QKL.sicau-2SY-1B, QKW.sicau-2SY-6D, QKT.sicau-2SY-2D, and QTKW.sicau-2SY-2D, QLWR.sicau-2SY-6D, QKS.sicau-2SY-1B/2D/6D, and QFFD.sicau-2SY-2D controlling KL, KW, KT, TKW, LWR, KS, and FFD, and identified in multiple environments, respectively. They were located on chromosomes 1BL, 2DL, and 6DS and formed three QTL clusters. Comparison of genetic and physical interval suggested that only QKL.sicau-2SY-1B located on chromosome 1BL was likely a novel QTL. A Kompetitive Allele Specific Polymerase chain reaction (KASP) marker, KASP-AX-109379070, closely linked to this novel QTL was developed and used to successfully confirm its effect in two different genetic populations and three variety panels consisting of 272 Chinese wheat landraces, 300 Chinese wheat cultivars most from the Yellow and Huai River Valley wheat region, and 165 Sichuan wheat cultivars. The relationships between kernel traits and other agronomic traits were detected and discussed. A few predicted genes involved in regulation of kernel growth and development were identified in the intervals of these identified major QTL. Taken together, these stable and major QTLs provide valuable information for understanding the genetic composition of kernel yield and provide the basis for molecular marker-assisted breeding.
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Affiliation(s)
- Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xinlin Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yang Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yutian Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Xiujin Lan,
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Jian Ma, ;
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37
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Ren T, Fan T, Chen S, Ou X, Chen Y, Jiang Q, Diao Y, Sun Z, Peng W, Ren Z, Tan F, Li Z. QTL Mapping and Validation for Kernel Area and Circumference in Common Wheat via High-Density SNP-Based Genotyping. FRONTIERS IN PLANT SCIENCE 2021; 12:713890. [PMID: 34484276 PMCID: PMC8415916 DOI: 10.3389/fpls.2021.713890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/20/2021] [Indexed: 05/03/2023]
Abstract
As an important component, 1,000 kernel weight (TKW) plays a significant role in the formation of yield traits of wheat. Kernel size is significantly positively correlated to TKW. Although numerous loci for kernel size in wheat have been reported, our knowledge on loci for kernel area (KA) and kernel circumference (KC) remains limited. In the present study, a recombinant inbred lines (RIL) population containing 371 lines genotyped using the Wheat55K SNP array was used to map quantitative trait loci (QTLs) controlling the KA and KC in multiple environments. A total of 54 and 44 QTLs were mapped by using the biparental population or multienvironment trial module of the inclusive composite interval mapping method, respectively. Twenty-two QTLs were considered major QTLs. BLAST analysis showed that major and stable QTLs QKc.sau-6A.1 (23.12-31.64 cM on 6A) for KC and QKa.sau-6A.2 (66.00-66.57 cM on 6A) for KA were likely novel QTLs, which explained 22.25 and 20.34% of the phenotypic variation on average in the 3 year experiments, respectively. Two Kompetitive allele-specific PCR (KASP) markers, KASP-AX-109894590 and KASP-AX-109380327, were developed and tightly linked to QKc.sau-6A.1 and QKa.sau-6A.2, respectively, and the genetic effects of the different genotypes in the RIL population were successfully confirmed. Furthermore, in the interval where QKa.sau-6A.2 was located on Chinese Spring and T. Turgidum ssp. dicoccoides reference genomes, only 11 genes were found. In addition, digenic epistatic QTLs also showed a significant influence on KC and KA. Altogether, the results revealed the genetic basis of KA and KC and will be useful for the marker-assisted selection of lines with different kernel sizes, laying the foundation for the fine mapping and cloning of the gene(s) underlying the stable QTLs detected in this study.
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Affiliation(s)
- Tianheng Ren
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- *Correspondence: Tianheng Ren
| | - Tao Fan
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Shulin Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Xia Ou
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Yongyan Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Qing Jiang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Yixin Diao
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Zixin Sun
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Wanhua Peng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Zhenglong Ren
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Feiquan Tan
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Zhi Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- Zhi Li
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38
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Lin Y, Zhou K, Hu H, Jiang X, Yu S, Wang Q, Li C, Ma J, Chen G, Yang Z, Liu Y. Multi-Locus Genome-Wide Association Study of Four Yield-Related Traits in Chinese Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2021; 12:665122. [PMID: 34484253 PMCID: PMC8415402 DOI: 10.3389/fpls.2021.665122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/20/2021] [Indexed: 05/13/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important crops in the world. Here, four yield-related traits, namely, spike length, spikelets number, tillers number, and thousand-kernel weight, were evaluated in 272 Chinese wheat landraces in multiple environments. Five multi-locus genome-wide association studies (FASTmrEMMA, ISIS EN-BLASSO, mrMLM, pKWmEB, and pLARmEB) were performed using 172,711 single-nucleotide polymorphisms (SNPs) to identify yield-related quantitative trait loci (QTL). A total of 27 robust QTL were identified by more than three models. Nine of these QTL were consistent with those in previous studies. The remaining 18 QTL may be novel. We identified a major QTL, QTkw.sicau-4B, with up to 18.78% of phenotypic variation explained. The developed kompetitive allele-specific polymerase chain reaction marker for QTkw.sicau-4B was validated in two recombinant inbred line populations with an average phenotypic difference of 16.07%. After combined homologous function annotation and expression analysis, TraesCS4B01G272300 was the most likely candidate gene for QTkw.sicau-4B. Our findings provide new insights into the genetic basis of yield-related traits and offer valuable QTL to breed wheat cultivars via marker-assisted selection.
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Affiliation(s)
- Yu Lin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kunyu Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haiyan Hu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaojun Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shifan Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Zisong Yang
- College of Resources and Environment, Aba Teachers University, Wenchuan, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Yaxi Liu, , orcid.org/0000-0001-6814-7218
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Yang F, Liu Q, Wang Q, Yang N, Li J, Wan H, Liu Z, Yang S, Wang Y, Zhang J, Liu H, Fan X, Ma W, Yang W, Zhou Y. Characterization of the Durum Wheat- Aegilops tauschii 4D(4B) Disomic Substitution Line YL-443 With Superior Characteristics of High Yielding and Stripe Rust Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:745290. [PMID: 34659315 PMCID: PMC8514839 DOI: 10.3389/fpls.2021.745290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/01/2021] [Indexed: 05/10/2023]
Abstract
Durum wheat is one of the important food and cash crops. The main goals in current breeding programs are improving its low yield potential, kernel characteristics, and lack of resistance or tolerance to some biotic and abiotic stresses. In this study, a nascent synthesized hexaploid wheat Lanmai/AT23 is used as the female parent in crosses with its AB genome donor Lanmai. A tetraploid line YL-443 with supernumerary spikelets and high resistance to stripe rust was selected out from the pentaploid F7 progeny. Somatic analysis using multicolor fluorescence in situ hybridization (mc-FISH) revealed that this line is a disomic substitution line with the 4B chromosome pair of Lanmai replaced by the 4D chromosome pair of Aegilops tauschii AT23. Comparing with Lanmai, YL-443 shows an increase in the number of spikelets and florets per spike by 36.3 and 75.9%, respectively. The stripe rust resistance gene Yr28 carried on the 4D chromosome was fully expressed in the tetraploid background. The present 4D(4B) disomic substitution line YL-443 was distinguished from the previously reported 4D(4B) lines with the 4D chromosomes from Chinese Spring (CS). Our study demonstrated that YL-443 can be used as elite germplasm for durum wheat breeding targeting high yield potential and stripe rust resistance. The Yr28-specific PCR marker and the 4D chromosome-specific KASP markers together with its unique features of pubescent leaf sheath and auricles can be utilized for assisting selection in breeding.
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Affiliation(s)
- Fan Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Research Institute, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
- Australia-China Joint Centre for Wheat Improvement, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Qier Liu
- Australia-China Joint Centre for Wheat Improvement, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing, China
| | - Qin Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture, Chengdu, China
| | - Ning Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture, Chengdu, China
| | - Honshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture, Chengdu, China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture, Chengdu, China
| | - Sujie Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
| | - Ying Wang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
| | - Jie Zhang
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture, Chengdu, China
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
| | - Hang Liu
- Australia-China Joint Centre for Wheat Improvement, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wujun Ma
- Australia-China Joint Centre for Wheat Improvement, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- *Correspondence: Wujun Ma
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture, Chengdu, China
- Wuyun Yang
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Yonghong Zhou
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40
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Li C, Tang H, Luo W, Zhang X, Mu Y, Deng M, Liu Y, Jiang Q, Chen G, Wang J, Qi P, Pu Z, Jiang Y, Wei Y, Zheng Y, Lan X, Ma J. A novel, validated, and plant height-independent QTL for spike extension length is associated with yield-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3381-3393. [PMID: 32870326 DOI: 10.1007/s00122-020-03675-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/21/2020] [Indexed: 05/24/2023]
Abstract
A novel, stably expressed, and plant height-independent QTL for spike extension length on 5AS was identified and validated in different populations using a newly developed and tightly linked KASP marker. As an important component of plant height (PH), spike extension length (SEL) plays a significant role in formation of an ideotype in wheat. Despite the fact that numerous loci for SEL in wheat have been reported, our knowledge on PH-independent loci remains to be limited. In this study, two recombinant inbred line (RIL) populations genotyped using the Wheat55K SNP were used to detect quantitative trait loci (QTL) controlling SEL across six environments. A total of 30 QTL for SEL were detected in these two RIL populations, and four of them, i.e., QSEL.sicau-2CN-4D, QSEL.sicau-2SY-4B.2, QSEL.sicau-2SY-4D.1, and QSEL.sicau-2CN-5A, were stably expressed. Genetic and conditional QTL analysis showed that the first three were significantly associated with PH, while the last one, QSEL.sicau-2CN-5A, is independent of PH. Comparison of genetic and physical maps suggested that only QSEL.sicau-2CN-5A located on chromosome arm 5AS is likely a novel QTL. A Kompetitive Allele-Specific PCR (KASP) marker, KASP-AX-110413733, tightly linked to this novel QTL was developed to successfully confirm its effect in three different genetic populations. Further, in the interval where QSEL.sicau-2CN-5A was located on 'Chinese Spring' wheat reference genome, three promising genes mainly expressed in wheat stem were predicated and they all encode the cytochrome P450 that was demonstrated to be closely associated with SEL elongation in rice. In addition, significant correlations between SEL and PH, spikelet number per spike, and thousand-grain weight were also detected. Altogether, our results broaden our understanding on genetic basis of SEL and will be useful for marker-based selection of lines with different SELs and fine mapping the novel and PH-independent QTL QSEL.sicau-2CN-5A.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xuemei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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Jin J, Liu D, Qi Y, Ma J, Zhen W. Major QTL for Seven Yield-Related Traits in Common Wheat (Triticum aestivum L.). Front Genet 2020; 11:1012. [PMID: 33005181 PMCID: PMC7485215 DOI: 10.3389/fgene.2020.01012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 08/10/2020] [Indexed: 11/13/2022] Open
Abstract
Flag leaves, plant height (PH), and spike-related traits are key determinants contributing to yield potential in wheat. In this study, we developed a recombinant inbred line (RIL) population with 94 lines derived from the cross between 'AS985472' and 'Sumai 3.' A genetic map spanned 3553.69 cM in length were constructed using 1978 DArT markers. Severn traits including flag leaf width (FLW), flag leaf length (FLL), PH, anthesis date (AD), spike length (SL), spikelet number spike (SNS), and spike density (SD) were evaluated against this RIL population under three different environments. Combined phenotypic data and genetic map, we identified quantitative trait loci (QTL) for each trait. A total of four major and stably expressed QTLs for FLW, PH, and SD were detected on chromosomes 2D and 4B. Of them, the major QTLs individually explained 10.10 - 30.68% of the phenotypic variation. QTLs with pleiotropic effects were identified on chromosomes 4A and 6D as well. Furthermore, the genetic relationships between seven yield-related traits were detected and discussed. A few genes related to leaf growth and development at the interval of a major locus for FLW on chromosome 2D were predicated. Overall, the present study provided useful information for understanding the genetic basis of yield-related traits and will be useful for marker-assisted selection in wheat breeding.
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Affiliation(s)
- Jingjing Jin
- College of Plant Protection, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Dan Liu
- Neijiang Academy of Agricultural Sciences, Neijiang, China.,School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Yongzhi Qi
- College of Plant Protection, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Wenchao Zhen
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,College of Agronomy, Hebei Agricultural University, Baoding, China
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42
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Pang Y, Liu C, Wang D, St Amand P, Bernardo A, Li W, He F, Li L, Wang L, Yuan X, Dong L, Su Y, Zhang H, Zhao M, Liang Y, Jia H, Shen X, Lu Y, Jiang H, Wu Y, Li A, Wang H, Kong L, Bai G, Liu S. High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat. MOLECULAR PLANT 2020; 13:1311-1327. [PMID: 32702458 DOI: 10.1016/j.molp.2020.07.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/08/2020] [Accepted: 07/17/2020] [Indexed: 05/18/2023]
Abstract
Wheat (Triticum aestivum) is a major staple food crop worldwide. Genetic dissection of important agronomic traits is essential for continuous improvement of wheat yield to meet the demand of the world's growing population. We conducted a large-scale genome-wide association study (GWAS) using a panel of 768 wheat cultivars that were genotyped with 327 609 single-nucleotide polymorphisms generated by genotyping-by-sequencing and detected 395 quantitative trait loci (QTLs) for 12 traits under 7 environments. Among them, 273 QTLs were delimited to ≤1.0-Mb intervals and 7 of them are either known genes (Rht-D, Vrn-B1, and Vrn-D1) that have been cloned or known QTLs (TaGA2ox8, APO1, TaSus1-7B, and Rht12) that were previously mapped. Eight putative candidate genes were identified for three QTLs that enhance spike seed setting and grain size using gene expression data and were validated in three bi-parental populations. Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes in QTLs affecting similar traits. Large r2 values for additive effects observed among the QTLs for most traits indicated that the phenotypes of these identified QTLs were highly predictable. Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL, solidifying the foundation for large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.
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Affiliation(s)
- Yunlong Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Chunxia Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Danfeng Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Paul St Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Wenhui Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Fang He
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China; College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Linzhi Li
- Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Liming Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Xiufang Yuan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Lei Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yu Su
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Huirui Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Meng Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yunlong Liang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Hongze Jia
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Xitong Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yue Lu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Hongming Jiang
- Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Yuye Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Anfei Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA.
| | - Shubing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
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43
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Liu J, Tang H, Qu X, Liu H, Li C, Tu Y, Li S, Habib A, Mu Y, Dai S, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Chen G, Li W, Jiang Y, Wei Y, Lan X, Zheng Y, Ma J. A novel, major, and validated QTL for the effective tiller number located on chromosome arm 1BL in bread wheat. PLANT MOLECULAR BIOLOGY 2020; 104:173-185. [PMID: 32734417 DOI: 10.1007/s11103-020-01035-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/09/2020] [Indexed: 05/24/2023]
Abstract
A novel and major QTL for the effective tiller number was identified on chromosomal arm 1BL and validated in two genetic backgrounds The effective tiller number (ETN) substantially influences plant architecture and the wheat yield improvement. In this study, we constructed a genetic map of the 2SY (20828/SY95-71) recombinant inbred line population based on the Wheat 55K array as well as the simple sequence repeat (SSR) and Kompetitive Allele Specific PCR (KASP) markers. A comparison between the genetic and physical maps indicated the marker positions were consistent in the two maps. Additionally, we identified seven tillering-related quantitative trait locus (QTLs), including Qetn-sau-1B.1, which is a major QTL localized to a 6.17-cM interval flanked by markers AX-89635557 and AX-111544678 on chromosome 1BL. The Qetn-sau-1B.1 QTL was detected in eight environments and explained 12.12-55.71% of the phenotypic variance. Three genes associated with the ETN were detected in the physical interval of Qetn-sau-1B.1. We used a tightly linked KASP marker, KASP-AX-110129912, to further validate this QTL in two other populations with different genetic backgrounds. The results indicated that Qetn-sau-1B.1 significantly increased the ETN by up to 23.5%. The results of this study will be useful for the precise mapping and cloning of Qetn-sau-1B.1.
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Affiliation(s)
- Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuiqing Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shoufeng Dai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Chen Z, Cheng X, Chai L, Wang Z, Du D, Wang Z, Bian R, Zhao A, Xin M, Guo W, Hu Z, Peng H, Yao Y, Sun Q, Ni Z. Pleiotropic QTL influencing spikelet number and heading date in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1825-1838. [PMID: 32016554 DOI: 10.1007/s00122-020-03556-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/24/2020] [Indexed: 05/23/2023]
Abstract
Three pleiotropic QTL regions associated with spikelet number and heading date were identified, with FT-A1 considered the candidate gene for QTspn/Hd.cau-7A. Spikelet number traits and heading date (HD) play key roles in yield improvement of wheat and its wide adaptation to different environments. Here, we used a Recombinant Inbred Lines population derived from a cross between Yi5029 (5029) and Nongda4332 (4332) to construct a high-density genetic linkage map and identify quantitative trait loci (QTL) associated with total spikelet number per spike (TSPN), fertile spikelet number per spike (FSPN), sterile spikelet number per spike (SSPN) and HD. A total of 22 environmentally stable QTL for TSPN, FSPN, SSPN and HD were identified. Notably, three pleiotropic QTL regions for TSPN and HD were detected on chromosomes 2A, 7A and 7D. The QTL associated with TSPN and HD on chromosome 7AS was designated QTspn/Hd.cau-7A. Furthermore, the candidate gene FT-A1 located in the region of QTspn/Hd.cau-7A had a single-nucleotide polymorphism (T-G) within the third exon, which might be the cause of diversity in spikelet number and HD between the two parents. Additionally, we developed a semi-thermal asymmetric reverse PCR (STARP) marker to analyze the geographical distribution and evolution of FT-A1 (T or G) alleles. This study contributes to our understanding of the molecular mechanisms of the four traits (TSPN, FSPN, SSPN and HD) and provides further insights into the genetic relationship between spikelet number traits and HD in wheat.
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Affiliation(s)
- Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Xuejiao Cheng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zihao Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Dejie Du
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhihui Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Ruolin Bian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
- National Plant Gene Research Centre, Beijing, 100193, China.
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45
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Ma J, Tu Y, Zhu J, Luo W, Liu H, Li C, Li S, Liu J, Ding P, Habib A, Mu Y, Tang H, Liu Y, Jiang Q, Chen G, Wang J, Li W, Pu Z, Zheng Y, Wei Y, Kang H, Chen G, Lan X. Flag leaf size and posture of bread wheat: genetic dissection, QTL validation and their relationships with yield-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:297-315. [PMID: 31628527 DOI: 10.1007/s00122-019-03458-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/10/2019] [Indexed: 05/24/2023]
Abstract
Major and environmentally stable QTL for flag leaf-related traits in wheat were identified and validated across ten environments using six populations with different genetic backgrounds. Flag leaf size and posture are two important factors of "ideotype" in wheat. Despite numerous studies on genetic analysis of flag leaf size including flag leaf length (FLL), width (FLW), area (FLA) and the ratio of length/width (FLR), few have focused on flag leaf posture including flag leaf angle (FLANG), opening angle (FLOA) and bend angle (FLBA). Further, the numbers of major, environmentally stable and verified genetic loci for flag leaf-related traits are limited. In this study, QTL for FLL, FLW, FLA, FLR, FLANG, FLOA and FLBA were identified based on a recombinant inbred line population together with values from up to ten different environments. Totally, eight major and stably expressed QTL were identified. Three co-located chromosomal intervals for seven major QTL were identified. The five major QTL QFll.sicau-5B.3 and QFll.sicau-2D.3 for FLL, QFlr.sicau-5B for FLR, QFlw.sicau-2D for FLW and QFla.sicau-2D for FLA were successfully validated by the tightly linked Kompetitive Allele Specific PCR (KASP) markers in the other five populations with different genetic backgrounds. A few genes related to leaf growth and development in intervals for these major QTL were predicated. Significant relationships between flag leaf- and yield-related traits were evidenced by analyses of Pearson correlations, conditional QTL and genetic mapping. Taken together, these results provide valuable information for understanding flag leaf size and posture of "ideotype" as well as fine mapping and breeding utilization of promising loci in bread wheat.
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Affiliation(s)
- Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yang Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuiqin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Puyang Ding
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
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46
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Ma J, Zhang H, Li S, Zou Y, Li T, Liu J, Ding P, Mu Y, Tang H, Deng M, Liu Y, Jiang Q, Chen G, Kang H, Li W, Pu Z, Wei Y, Zheng Y, Lan X. Identification of quantitative trait loci for kernel traits in a wheat cultivar Chuannong16. BMC Genet 2019; 20:77. [PMID: 31619163 PMCID: PMC6796374 DOI: 10.1186/s12863-019-0782-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/26/2019] [Indexed: 12/01/2022] Open
Abstract
Background Kernel length (KL), kernel width (KW) and thousand-kernel weight (TKW) are key agronomic traits in wheat breeding. Chuannong16 (‘CN16’) is a commercial cultivar with significantly longer kernels than the line ‘20828’. To identify and characterize potential alleles from CN16 controlling KL, the previously developed recombinant inbred line (RIL) population derived from the cross ‘20828’ × ‘CN16’ and the genetic map constructed by the Wheat55K SNP array and SSR markers were used to perform quantitative trait locus/loci (QTL) analyses for kernel traits. Results A total of 11 putative QTL associated with kernel traits were identified and they were located on chromosomes 1A (2 QTL), 2B (2 QTL), 2D (3 QTL), 3D, 4A, 6A, and 7A, respectively. Among them, three major QTL, QKL.sicau-2D, QKW.sicau-2D and QTKW.sicau-2D, controlling KL, KW and TKW, respectively, were detected in three different environments. Respectively, they explained 10.88–18.85%, 17.21–21.49% and 10.01–23.20% of the phenotypic variance. Further, they were genetically mapped in the same interval on chromosome 2DS. A previously developed kompetitive allele-specific PCR (KASP) marker KASP-AX-94721936 was integrated in the genetic map and QTL re-mapping finally located the three major QTL in a 1- cM region flanked by AX-111096297 and KASP-AX-94721936. Another two co-located QTL intervals for KL and TKW were also identified. A few predicted genes involved in regulation of kernel growth and development were identified in the intervals of these identified QTL. Significant relationships between kernel traits and spikelet number per spike and anthesis date were detected and discussed. Conclusions Three major and stably expressed QTL associated with KL, KW, and TKW were identified. A KASP marker tightly linked to these three major QTL was integrated. These findings provide information for subsequent fine mapping and cloning the three co-localized major QTL for kernel traits.
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Affiliation(s)
- Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Han Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuiqin Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaya Zou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiajun Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Puyang Ding
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Mu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
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47
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Li T, Ma J, Zou Y, Chen G, Ding P, Zhang H, Yang C, Mu Y, Tang H, Liu Y, Jiang Q, Chen G, Qi P, Wei Y, Zheng Y, Lan X. Quantitative trait loci for seeding root traits and the relationships between root and agronomic traits in common wheat. Genome 2019; 63:27-36. [PMID: 31580743 DOI: 10.1139/gen-2019-0116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A completely developed and vigorous root system can provide a stable platform for aboveground plant organs. To identify loci controlling root traits that could be used in wheat (Triticum aestivum L.) breeding, 199 recombinant inbred lines were used to measure and analyze eight root traits. A total of 18 quantitative trait loci (QTL) located on chromosomes 1A, 2A, 2B, 2D, 4B, 4D, 6A, 7A, and 7B were identified. The phenotypic variation explained by these 18 QTL ranged from 3.27% to 11.75%, and the logarithm of odds scores ranged from 2.50 to 6.58. A comparison of physical intervals indicated several new QTL for root traits were identified. In addition, significant correlations between root and agronomic traits were detected and discussed. The results presented in this study, along with those of previous reports, suggest that chromosomes 2 and 7 likely play important roles in the growth and development of wheat roots.
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Affiliation(s)
- Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yaya Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Puyang Ding
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Han Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Congcong Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R. China
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