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Geethanjali S, Kadirvel P, Periyannan S. Wheat improvement through advances in single nucleotide polymorphism (SNP) detection and genotyping with a special emphasis on rust resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:224. [PMID: 39283360 PMCID: PMC11405505 DOI: 10.1007/s00122-024-04730-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 08/24/2024] [Indexed: 09/22/2024]
Abstract
KEY MESSAGE Single nucleotide polymorphism (SNP) markers in wheat and their prospects in breeding with special reference to rust resistance. Single nucleotide polymorphism (SNP)-based markers are increasingly gaining momentum for screening and utilizing vital agronomic traits in wheat. To date, more than 260 million SNPs have been detected in modern cultivars and landraces of wheat. This rapid SNP discovery was made possible through the release of near-complete reference and pan-genome assemblies of wheat and its wild relatives, coupled with whole genome sequencing (WGS) of thousands of wheat accessions. Further, genotyping customized SNP sites were facilitated by a series of arrays (9 to 820Ks), a cost effective substitute WGS. Lately, germplasm-specific SNP arrays have been introduced to characterize novel traits and detect closely linked SNPs for marker-assisted breeding. Subsequently, the kompetitive allele-specific PCR (KASP) assay was introduced for rapid and large-scale screening of specific SNP markers. Moreover, with the advances and reduction in sequencing costs, ample opportunities arise for generating SNPs artificially through mutations and in combination with next-generation sequencing and comparative genomic analyses. In this review, we provide historical developments and prospects of SNP markers in wheat breeding with special reference to rust resistance where over 50 genetic loci have been characterized through SNP markers. Rust resistance is one of the most essential traits for wheat breeding as new strains of the Puccinia fungus, responsible for rust diseases, evolve frequently and globally.
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Affiliation(s)
- Subramaniam Geethanjali
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia
| | - Palchamy Kadirvel
- Crop Improvement Section, Indian Council of Agricultural Research-Indian Institute of Oilseeds Research, Hyderabad, Telangana, 500030, India
| | - Sambasivam Periyannan
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia.
- School of Agriculture and Environmental Science, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia.
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Awan MJA, Farooq MA, Naqvi RZ, Karamat U, Bukhari SAR, Waqas MAB, Mahmood MA, Buzdar MI, Rasheed A, Amin I, Saeed NA, Mansoor S. Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages. Mol Biol Rep 2024; 51:537. [PMID: 38642174 DOI: 10.1007/s11033-024-09454-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. The genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored. METHODS In this study, hybrid of elite cultivars of wheat were developed via reciprocal crosses (cytoplasm swapping) and phenotypically evaluated. We assessed differential expression profiles of yield-related negative regulators in these cultivars and their F1 hybrids and identified various cis-regulatory signatures by employing bioinformatics tools. Furthermore, the preferential expression patterns of the syntenic triads encoded from A, B, and D subgenomes were assessed to decipher their functional redundancy at six different growth stages. RESULTS Hybrid progenies showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents. Based on the expression profiling, our results indicated significant dynamic transcriptional expression patterns, portraying the different homeolog-dominance at the same stage in the different cultivars and their hybrids. Albeit belonging to same syntenic triads, a dynamic trend was observed in the regulatory signatures of these genes that might be influencing their expression profiles. CONCLUSION These findings can substantially contribute and provide insights for the selective introduction of better cultivars into traditional and hybrid breeding programs which can be harnessed for the improvement of future wheat.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Awais Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Umer Karamat
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sayyad Ali Raza Bukhari
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Abu Bakar Waqas
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Ismail Buzdar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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Qin R, Cao M, Dong J, Chen L, Guo H, Guo Q, Cai Y, Han L, Huang Z, Xu N, Yang A, Xu H, Wu Y, Sun H, Liu X, Ling H, Zhao C, Li J, Cui F. Fine mapping of a major QTL, qKl-1BL controlling kernel length in common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:67. [PMID: 38441674 DOI: 10.1007/s00122-024-04574-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 02/03/2024] [Indexed: 03/07/2024]
Abstract
KEY MESSAGE A major stable QTL, qKl-1BL, for kernel length of wheat was narrowed down to a 2.04-Mb interval on chromosome 1BL; the candidate genes were predicated and the genetic effects on yield-related traits were characterized. As a key factor influencing kernel weight, wheat kernel shape is closely related to yield formation, and in turn affects both wheat processing quality and market value. Fine mapping of the major quantitative trait loci (QTL) for kernel shape could provide genetic resources and a theoretical basis for the genetic improvement of wheat yield-related traits. In this study, a major QTL for kernel length (KL) on 1BL, named qKl-1BL, was identified from the recombinant inbred lines (RIL) in multiple environments based on the genetic map and physical map, with 4.76-21.15% of the phenotypic variation explained. To fine map qKl-1BL, the map-based cloning strategy was used. By using developed InDel markers, the near-isogenic line (NIL) pairs and eight key recombinants were identified from a segregating population containing 3621 individuals derived from residual heterozygous lines (RHLs) self-crossing. In combination with phenotype identification, qKl-1BL was finely positioned into a 2.04-Mb interval, KN1B:698.15-700.19 Mb, with eight differentially expressed genes enriched at the key period of kernel elongation. Based on transcriptome analysis and functional annotation information, two candidate genes for qKl-1BL controlling kernel elongation were identified. Additionally, genetic effect analysis showed that the superior allele of qKl-1BL from Jing411 could increase KL, thousand kernel weight (TKW), and yield per plant (YPP) significantly, as well as kernel bulk density and stability time. Taken together, this study identified a QTL interval for controlling kernel length with two possible candidate genes, which provides an important basis for qKl-1BL cloning, functional analysis, and application in molecular breeding programs.
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Affiliation(s)
- Ran Qin
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Mingsu Cao
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Jizi Dong
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Linqu Chen
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Haoru Guo
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Qingjie Guo
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Yibiao Cai
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Lei Han
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Zhenjie Huang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Ninghao Xu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Aoyu Yang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Huiyuan Xu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Yongzhen Wu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Han Sun
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050000, China
| | - Hongqing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunhua Zhao
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
| | - Junming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050000, China.
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
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Jiang C, Xu Z, Fan X, Zhou Q, Ji G, Liao S, Wang Y, Ma F, Zhao Y, Wang T, Feng B. Genetic dissection of major QTL for grain number per spike on chromosomes 5A and 6A in bread wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2024; 14:1305547. [PMID: 38259947 PMCID: PMC10800429 DOI: 10.3389/fpls.2023.1305547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/08/2023] [Indexed: 01/24/2024]
Abstract
Grain number per spike (GNS) is a crucial component of grain yield and plays a significant role in improving wheat yield. To identify quantitative trait loci (QTL) associated with GNS, a recombinant inbred line (RIL) population derived from the cross of Zhongkemai 13F10 and Chuanmai 42 was employed to conduct QTL mapping across eight environments. Based on the bulked segregant exome sequencing (BSE-Seq), genomic regions associated with GNS were detected on chromosomes 5A and 6A. According to the constructed genetic maps, two major QTL QGns.cib-5A (LOD = 4.35-8.16, PVE = 8.46-14.43%) and QGns.cib-6A (LOD = 3.82-30.80, PVE = 5.44-12.38%) were detected in five and four environments, respectively. QGns.cib-6A is a QTL cluster for other seven yield-related traits. QGns.cib-5A and QGns.cib-6A were further validated using linked Kompetitive Allele Specific PCR (KASP) markers in different genetic backgrounds. QGns.cib-5A exhibited pleiotropic effects on productive tiller number (PTN), spike length (SL), fertile spikelet number per spike (FSN), and ratio of grain length to grain width (GL/GW) but did not significantly affect thousand grain weight (TGW). Haplotype analysis revealed that QGns.cib-5A and QGns.cib-6A were the targets of artificial selection during wheat improvement. Candidate genes for QGns.cib-5A and QGns.cib-6A were predicted by analyzing gene annotation, spatiotemporal expression patterns, and orthologous and sequence differences. These findings will be valuable for fine mapping and map-based cloning of genes underlying QGns.cib-5A and QGns.cib-6A.
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Affiliation(s)
- Cheng Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanlin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fang Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Zhao
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- The Innovative of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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5
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Ye M, Wan H, Yang W, Liu Z, Wang Q, Yang N, Long H, Deng G, Yang Y, Feng H, Zhou Y, Yang C, Li J, Zhang H. Precisely mapping a major QTL for grain weight on chromosome 5B of the founder parent Chuanmai42 in the wheat-growing region of southwestern China. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:146. [PMID: 37258797 DOI: 10.1007/s00122-023-04383-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
KEY MESSAGE QTgw.saas-5B was validated as a major thousand-grain weight-related QTL in a founder parent used for wheat breeding and then precisely mapped to a 0.6 cM interval. Increasing the thousand-grain weight (TGW) is considered to be one of the most important ways to improve yield, which is a core objective among wheat breeders. Chuanmai42, which is a wheat cultivar with high TGW and a high and stable yield, is a parent of more than 30 new varieties grown in southwestern China. In this study, a Chuanmai42-derived recombinant inbred line (RIL) population was used to dissect the genetic basis of TGW. A major QTL (QTgw.saas-5B) mapped to the Xgwm213-Xgwm540 interval on chromosome 5B of Chuanmai42 explained up to 20% of the phenotypic variation. Using 71 recombinants with a recombination in the QTgw.saas-5B interval identified from a secondary RIL population comprising 1818 lines constructed by crossing the QTgw.saas-5B near-isogenic line with the recurrent parent Chuannong16, QTgw.saas-5B was delimited to a 0.6 cM interval, corresponding to a 21.83 Mb physical interval in the Chinese Spring genome. These findings provide the foundation for QTgw.saas-5B cloning and its use in molecular marker-assisted breeding.
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Affiliation(s)
- Meijin Ye
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
| | - Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Qin Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Ning Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yumin Yang
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Hong Feng
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cairong Yang
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China.
| | - Haiqin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
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6
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Yu L, Zhang H, Guan R, Li Y, Guo Y, Qiu L. Genome-Wide Tissue-Specific Genes Identification for Novel Tissue-Specific Promoters Discovery in Soybean. Genes (Basel) 2023; 14:1150. [PMID: 37372330 DOI: 10.3390/genes14061150] [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: 04/18/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Promoters play a crucial role in controlling the spatial and temporal expression of genes at transcriptional levels in the process of higher plant growth and development. The spatial, efficient, and correct regulation of exogenous genes expression, as desired, is the key point in plant genetic engineering research. Constitutive promoters widely used in plant genetic transformation are limited because, sometimes, they may cause potential negative effects. This issue can be solved, to a certain extent, by using tissue-specific promoters. Compared with constitutive promoters, a few tissue-specific promoters have been isolated and applied. In this study, based on the transcriptome data, a total of 288 tissue-specific genes were collected, expressed in seven tissues, including the leaves, stems, flowers, pods, seeds, roots, and nodules of soybean (Glycine max). KEGG pathway enrichment analysis was carried out, and 52 metabolites were annotated. A total of 12 tissue-specific genes were selected via the transcription expression level and validated through real-time quantitative PCR, of which 10 genes showed tissue-specific expression. The 3-kb 5' upstream regions of ten genes were obtained as putative promoters. Further analysis showed that all the 10 promoters contained many tissue-specific cis-elements. These results demonstrate that high-throughput transcriptional data can be used as effective tools, providing a guide for high-throughput novel tissue-specific promoter discovery.
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Affiliation(s)
- Lili Yu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongxia Guan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinghui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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7
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Hong Y, Zhang M, Xu R. Genetic Localization and Homologous Genes Mining for Barley Grain Size. Int J Mol Sci 2023; 24:ijms24054932. [PMID: 36902360 PMCID: PMC10003025 DOI: 10.3390/ijms24054932] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Grain size is an important agronomic trait determining barley yield and quality. An increasing number of QTLs (quantitative trait loci) for grain size have been reported due to the improvement in genome sequencing and mapping. Elucidating the molecular mechanisms underpinning barley grain size is vital for producing elite cultivars and accelerating breeding processes. In this review, we summarize the achievements in the molecular mapping of barley grain size over the past two decades, highlighting the results of QTL linkage analysis and genome-wide association studies. We discuss the QTL hotspots and predict candidate genes in detail. Moreover, reported homologs that determine the seed size clustered into several signaling pathways in model plants are also listed, providing the theoretical basis for mining genetic resources and regulatory networks of barley grain size.
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Affiliation(s)
- Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Halder J, Gill HS, Zhang J, Altameemi R, Olson E, Turnipseed B, Sehgal SK. Genome-wide association analysis of spike and kernel traits in the U.S. hard winter wheat. THE PLANT GENOME 2023; 16:e20300. [PMID: 36636831 DOI: 10.1002/tpg2.20300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/20/2022] [Indexed: 05/10/2023]
Abstract
A better understanding of the genetic control of spike and kernel traits that have higher heritability can help in the development of high-yielding wheat varieties. Here, we identified the marker-trait associations (MTAs) for various spike- and kernel-related traits in winter wheat (Triticum aestivum L.) through genome-wide association studies (GWAS). An association mapping panel comprising 297 hard winter wheat accessions from the U.S. Great Plains was evaluated for eight spike- and kernel-related traits in three different environments. A GWAS using 15,590 single-nucleotide polymorphisms (SNPs) identified a total of 53 MTAs for seven spike- and kernel-related traits, where the highest number of MTAs were identified for spike length (16) followed by the number of spikelets per spike (15) and spikelet density (11). Out of 53 MTAs, 14 were considered to represent stable quantitative trait loci (QTL) as they were identified in multiple environments. Five multi-trait MTAs were identified for various traits including the number of spikelets per spike (NSPS), spikelet density (SD), kernel width (KW), and kernel area (KA) that could facilitate the pyramiding of yield-contributing traits. Further, a significant additive effect of accumulated favorable alleles on the phenotype of four spike-related traits suggested that breeding lines and cultivars with a higher number of favorable alleles could be a valuable resource for breeders to improve yield-related traits. This study improves the understanding of the genetic basis of yield-related traits in hard winter wheat and provides reliable molecular markers that will facilitate marker-assisted selection (MAS) in wheat breeding programs.
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Affiliation(s)
- Jyotirmoy Halder
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Harsimardeep S Gill
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Jinfeng Zhang
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Rami Altameemi
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Eric Olson
- Dep. of Plant, Soil and Microbial Sciences, Michigan State Univ., East Lansing, MI, 48824, USA
| | - Brent Turnipseed
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Sunish K Sehgal
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
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9
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Song J, Xu D, Dong Y, Li F, Bian Y, Li L, Luo X, Fei S, Li L, Zhao C, Zhang Y, Xia X, Ni Z, He Z, Cao S. Fine mapping and characterization of a major QTL for grain weight on wheat chromosome arm 5DL. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3237-3246. [PMID: 35904627 DOI: 10.1007/s00122-022-04182-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
We fine mapped QTL QTKW.caas-5DL for thousand kernel weight in wheat, predicted candidate genes and developed a breeding-applicable marker. Thousand kernel weight (TKW) is an important yield component trait in wheat, and identification of the underlying genetic loci is helpful for yield improvement. We previously identified a stable quantitative trait locus (QTL) QTKW.caas-5DL for TKW in a Doumai/Shi4185 recombinant inbred line (RIL) population. Here we performed fine mapping of QTKW.caas-5DL using secondary populations derived from 15 heterozygous recombinants and delimited the QTL to an approximate 3.9 Mb physical interval from 409.9 to 413.8 Mb according to the Chinese Spring (CS) reference genome. Analysis of genomic synteny showed that annotated genes in the physical interval had high collinearity among CS and eight other wheat genomes. Seven genes with sequence variation and/or differential expression between parents were predicted as candidates for QTKW.caas-5DL based on whole-genome resequencing and transcriptome assays. A kompetitive allele-specific PCR (KASP) marker for QTKW.caas-5DL was developed, and genotyping confirmed a significant association with TKW but not with other yield component traits in a panel of elite wheat cultivars. The superior allele of QTKW.caas-5DL was frequent in a panel of cultivars, suggesting that it had undergone positive selection. These findings not only lay a foundation for map-based cloning of QTKW.caas-5DL but also provide an efficient tool for marker-assisted selection.
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Affiliation(s)
- Jie Song
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100094, China
| | - Dengan Xu
- Shandong Province Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yan Dong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Faji Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Yingjie Bian
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lingli Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xumei Luo
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Shuaipeng Fei
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lei Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Cong Zhao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhongfu Ni
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100094, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
| | - Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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10
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Liu X, Xu Z, Feng B, Zhou Q, Ji G, Guo S, Liao S, Lin D, Fan X, Wang T. Quantitative trait loci identification and breeding value estimation of grain weight-related traits based on a new wheat 50K single nucleotide polymorphism array-derived genetic map. FRONTIERS IN PLANT SCIENCE 2022; 13:967432. [PMID: 36110352 PMCID: PMC9468616 DOI: 10.3389/fpls.2022.967432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
Mining novel and less utilized thousand grain weight (TGW) related genes are useful for improving wheat yield. In this study, a recombinant inbred line population from a cross between Zhongkemai 138 (ZKM138, high TGW) and Chuanmai 44 (CM44, low TGW) was used to construct a new Wheat 50K SNP array-derived genetic map that spanned 1,936.59 cM and contained 4, 139 markers. Based on this map, ninety-one quantitative trait loci (QTL) were detected for eight grain-related traits in six environments. Among 58 QTLs, whose superior alleles were contributed by ZKM138, QTgw.cib-6A was a noticeable major stable QTL and was also highlighted by bulked segregant analysis with RNA sequencing (BSR-Seq). It had a pyramiding effect on TGW enhancement but no significant trade-off effect on grain number per spike or tiller number, with two other QTLs (QTgw.cib-2A.2 and QTgw.cib-6D), possibly explaining the excellent grain performance of ZKM138. After comparison with known loci, QTgw.cib-6A was deduced to be a novel locus that differed from nearby TaGW2 and TaBT1. Seven simple sequence repeat (SSR) and thirty-nine kompetitive allele-specific PCR (KASP) markers were finally developed to narrow the candidate interval of QTgw.cib-6A to 4.1 Mb. Only six genes in this interval were regarded as the most likely candidate genes. QTgw.cib-6A was further validated in different genetic backgrounds and presented 88.6% transmissibility of the ZKM138-genotype and a 16.4% increase of TGW in ZKM138 derivatives. And the geographic pattern of this locus revealed that its superior allele is present in only 6.47% of 433 Chinese modern wheat varieties, indicating its potential contribution to further high-yield breeding.
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Affiliation(s)
- Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaodan Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dian Lin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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11
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Tillett BJ, Hale CO, Martin JM, Giroux MJ. Genes Impacting Grain Weight and Number in Wheat ( Triticum aestivum L. ssp. aestivum). PLANTS (BASEL, SWITZERLAND) 2022; 11:1772. [PMID: 35807724 PMCID: PMC9269389 DOI: 10.3390/plants11131772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/17/2022] [Accepted: 06/27/2022] [Indexed: 05/05/2023]
Abstract
The primary goal of common wheat (T. aestivum) breeding is increasing yield without negatively impacting the agronomic traits or product quality. Genetic approaches to improve the yield increasingly target genes that impact the grain weight and number. An energetic trade-off exists between the grain weight and grain number, the result of which is that most genes that increase the grain weight also decrease the grain number. QTL associated with grain weight and number have been identified throughout the hexaploid wheat genome, leading to the discovery of numerous genes that impact these traits. Genes that have been shown to impact these traits will be discussed in this review, including TaGNI, TaGW2, TaCKX6, TaGS5, TaDA1, WAPO1, and TaRht1. As more genes impacting the grain weight and number are characterized, the opportunity is increasingly available to improve common wheat agronomic yield by stacking the beneficial alleles. This review provides a synopsis of the genes that impact grain weight and number, and the most beneficial alleles of those genes with respect to increasing the yield in dryland and irrigated conditions. It also provides insight into some of the genetic mechanisms underpinning the trade-off between grain weight and number and their relationship to the source-to-sink pathway. These mechanisms include the plant size, the water soluble carbohydrate levels in plant tissue, the size and number of pericarp cells, the cytokinin and expansin levels in developing reproductive tissue, floral architecture and floral fertility.
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Affiliation(s)
| | | | | | - Michael J. Giroux
- Department of Plant Sciences and Plant Pathology, Montana State University, 119 Plant Biosciences Building, Bozeman, MT 59717-3150, USA; (B.J.T.); (C.O.H.); (J.M.M.)
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12
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Lv Q, Li L, Meng Y, Sun H, Chen L, Wang B, Li X. Wheat E3 ubiquitin ligase TaGW2-6A degrades TaAGPS to affect seed size. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 320:111274. [PMID: 35643616 DOI: 10.1016/j.plantsci.2022.111274] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 03/13/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
TaGW2 has been identified as a key determinant of the grain weight in wheat (Triticum aestivum L.). In our previous study, we found that the grain size differs in Chinese Spring (CS) and its TaGW2-6A allelic variant (NIL31). In addition, the expression of the key starch biosynthesis enzyme gene TaAGPS differs significantly in the two materials. However, the underlying molecular mechanism associated with the action of TaGW2-6A has not been reported. In the present study, we found that TaGW2-6A-CS interacted with TaAGPS, whereas TaGW2-6A-NIL31 did not interact with it in vitro and in vivo. Furthermore, we found that the C-terminal LXLX domain (376-424 aa) of TaGW2-6A recognized TaAGPS. However, the TaGW2-6A allelic variant lacked this key interaction region due to premature translation termination. We also found that TaGW2-6A-CS can ubiquitinate TaAGPS and degrade it via the 26 S proteasome pathway. In addition, our analysis of the activity of ADP-glucose pyrophosphorylase (AGPase) indicated that the AGPase level in the endosperm cells was lower in CS than NIL31. Cytological observations demonstrated that the average number of starch granules and the average area of starch granules in endosperm cells were lower in CS than NIL31. The overexpression of TaAGPS positively regulated the seed size in transgenic Arabidopsis. Our findings provide novel insights into the molecular mechanism that allows TaGW2-6A-TaAGPS to regulate seed size via the starch synthesis pathway.
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Affiliation(s)
- Qian Lv
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Liqun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Meng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huimin Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Liuping Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bingxin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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13
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Li W, Yu Y, Chen X, Fang Q, Yang A, Chen X, Wu L, Wang C, Wu D, Ye S, Wu D, Sun G. N6-Methyladenosine dynamic changes and differential methylation in wheat grain development. PLANTA 2022; 255:125. [PMID: 35567638 DOI: 10.1007/s00425-022-03893-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/02/2022] [Indexed: 06/15/2023]
Abstract
More methylation changes occur in late interval than in early interval of wheat seed development with protein and the starch synthesis-related pathway enriched in the later stages. Wheat seed development is a critical process to determining wheat yield and quality, which is controlled by genetics, epigenetics and environments. The N6-methyladenosine (m6A) modification is a reversible and dynamic process and plays regulatory role in plant development and stress responses. To better understand the role of m6A in wheat grain development, we characterized the m6A modification at 10 day post-anthesis (DPA), 20 DPA and 30 DPA in wheat grain development. m6A-seq identified 30,615, 30,326, 27,676 high confidence m6A peaks from the 10DPA, 20DPA, and 30DPA, respectively, and enriched at 3'UTR. There were 29,964, 29,542 and 26,834 unique peaks identified in AN0942_10d, AN0942_20d and AN0942_30d. One hundred and forty-two genes were methylated by m6A throughout seed development, 940 genes methylated in early grain development (AN0942_20d vs AN0942_10d), 1542 genes in late grain development (AN0942_30d vs AN0942_20d), and 1190 genes between early and late development stage (AN0942_30d vs AN0942_10d). KEGG enrichment analysis found that protein-related pathways and the starch synthesis-related pathway were significantly enriched in the later stages of seed development. Our results provide novel knowledge on m6A dynamic changes and its roles in wheat grain development.
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Affiliation(s)
- Wenxiang Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yi Yu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xuanrong Chen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Qian Fang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Anqi Yang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xinyu Chen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Lei Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Chengyu Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, China
| | - Dechuan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Sihong Ye
- Cotton Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001, Anhui, China.
| | - Dexiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, NS, B3H 3C3, Canada.
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14
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Klees S, Heinrich F, Schmitt AO, Gültas M. agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species. BIOLOGY 2022; 11:biology11050684. [PMID: 35625412 PMCID: PMC9138521 DOI: 10.3390/biology11050684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022]
Abstract
Simple Summary In breeding research, the investigation of regulatory SNPs (rSNPs) is becoming increasingly important due to their potential causal role for specific functional traits. Especially for crop species, there is still a lack of systematic analyses to detect rSNPs and their predicted effects on the binding of transcription factors. In this study, we present agReg-SNPdb-Plants, a database storing genome-wide collections of regulatory SNPs for agricultural plant species which can be queried via a web interface. Abstract Single nucleotide polymorphisms (SNPs) that are located in the promoter regions of genes and affect the binding of transcription factors (TFs) are called regulatory SNPs (rSNPs). Their identification can be highly valuable for the interpretation of genome-wide association studies (GWAS), since rSNPs can reveal the biologically causative variant and decipher the regulatory mechanisms behind a phenotype. In our previous work, we presented agReg-SNPdb, a database of regulatory SNPs for agriculturally important animal species. To complement this previous work, in this study we present the extension agReg-SNPdb-Plants storing rSNPs and their predicted effects on TF-binding for 13 agriculturally important plant species and subspecies (Brassica napus, Helianthus annuus, Hordeum vulgare, Oryza glaberrima, Oryza glumipatula, Oryza sativa Indica, Oryza sativa Japonica, Solanum lycopersicum, Sorghum bicolor, Triticum aestivum, Triticum turgidum, Vitis vinifera, and Zea mays). agReg-SNPdb-Plants can be queried via a web interface that allows users to search for SNP IDs, chromosomal regions, or genes. For a comprehensive interpretation of GWAS results or larger SNP-sets, it is possible to download the whole list of SNPs and their impact on transcription factor binding sites (TFBSs) from the website chromosome-wise.
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Affiliation(s)
- Selina Klees
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.H.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Carl-Sprengel-Weg 1, Georg-August University, 37075 Göttingen, Germany
- Correspondence: (S.K.); (M.G.)
| | - Felix Heinrich
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.H.); (A.O.S.)
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.H.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Carl-Sprengel-Weg 1, Georg-August University, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Center for Integrated Breeding Research (CiBreed), Carl-Sprengel-Weg 1, Georg-August University, 37075 Göttingen, Germany
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany
- Correspondence: (S.K.); (M.G.)
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15
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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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16
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Xiong H, Li Y, Guo H, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Liu L. Genetic Mapping by Integration of 55K SNP Array and KASP Markers Reveals Candidate Genes for Important Agronomic Traits in Hexaploid Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:628478. [PMID: 33708233 PMCID: PMC7942297 DOI: 10.3389/fpls.2021.628478] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Agronomic traits such as heading date (HD), plant height (PH), thousand grain weight (TGW), and spike length (SL) are important factors affecting wheat yield. In this study, we constructed a high-density genetic linkage map using the Wheat55K SNP Array to map quantitative trait loci (QTLs) for these traits in 207 recombinant inbred lines (RILs). A total of 37 QTLs were identified, including 9 QTLs for HD, 7 QTLs for PH, 12 QTLs for TGW, and 9 QTLs for SL, which explained 3.0-48.8% of the phenotypic variation. Kompetitive Allele Specific PCR (KASP) markers were developed based on sequencing data and used for validation of the stably detected QTLs on chromosomes 3A, 4B and 6A using 400 RILs. A QTL cluster on chromosome 4B for PH and TGW was delimited to a 0.8 Mb physical interval explaining 12.2-22.8% of the phenotypic variation. Gene annotations and analyses of SNP effects suggested that a gene encoding protein Photosynthesis Affected Mutant 68, which is essential for photosystem II assembly, is a candidate gene affecting PH and TGW. In addition, the QTL for HD on chromosome 3A was narrowed down to a 2.5 Mb interval, and a gene encoding an R3H domain-containing protein was speculated to be the causal gene influencing HD. The linked KASP markers developed in this study will be useful for marker-assisted selection in wheat breeding, and the candidate genes provide new insight into genetic study for those traits in wheat.
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Klees S, Lange TM, Bertram H, Rajavel A, Schlüter JS, Lu K, Schmitt AO, Gültas M. In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data. Int J Mol Sci 2021; 22:E789. [PMID: 33466789 PMCID: PMC7830561 DOI: 10.3390/ijms22020789] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 01/07/2023] Open
Abstract
Regulatory SNPs (rSNPs) are a special class of SNPs which have a high potential to affect the phenotype due to their impact on DNA-binding of transcription factors (TFs). Thus, the knowledge about such rSNPs and TFs could provide essential information regarding different genetic programs, such as tissue development or environmental stress responses. In this study, we use a multi-omics approach by combining genomics, transcriptomics, and proteomics data of two different Brassica napus L. cultivars, namely Zhongshuang11 (ZS11) and Zhongyou821 (ZY821), with high and low oil content, respectively, to monitor the regulatory interplay between rSNPs, TFs and their corresponding genes in the tissues flower, leaf, stem, and root. By predicting the effect of rSNPs on TF-binding and by measuring their association with the cultivars, we identified a total of 41,117 rSNPs, of which 1141 are significantly associated with oil content. We revealed several enriched members of the TF families DOF, MYB, NAC, or TCP, which are important for directing transcriptional programs regulating differential expression of genes within the tissues. In this work, we provide the first genome-wide collection of rSNPs for B. napus and their impact on the regulation of gene expression in vegetative and floral tissues, which will be highly valuable for future studies on rSNPs and gene regulation.
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Affiliation(s)
- Selina Klees
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
| | - Thomas Martin Lange
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
| | - Hendrik Bertram
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
| | - Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
| | - Johanna-Sophie Schlüter
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China;
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
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Luo Q, Zheng Q, Hu P, Liu L, Yang G, Li H, Li B, Li Z. Mapping QTL for agronomic traits under two levels of salt stress in a new constructed RIL wheat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:171-189. [PMID: 32995899 DOI: 10.1007/s00122-020-03689-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
QTL for 15 agronomic traits under two levels of salt stress in dry salinity field were mapped in a new constructed RIL population utilizing a Wheat55K SNP array. Furthermore, eight QTL were validated in a collected natural population. Soil salinity is one of the major abiotic stresses causing serious impact on crop growth, development and yield. As one of the three most important crops in the world, bread wheat (Triticum aestivum L.) is severely affected by salinity, too. In this study, an F7 recombinant inbred line (RIL) population derived from a cross between high-yield wheat cultivar Zhongmai 175 and salt-tolerant cultivar Xiaoyan 60 was constructed. The adult stage performances of the RIL population and their parent lines under low and high levels of salt stress were evaluated for three consecutive growing seasons. Utilizing a Wheat55K SNP array, a high-density genetic linkage map spinning 3250.71 cM was constructed. QTL mapping showed that 90 stable QTL for 15 traits were detected, and they were distributed on all wheat chromosomes except 4D, 6B and 7D. These QTL individually explained 2.34-32.43% of the phenotypic variation with LOD values ranging from 2.68 to 47.15. It was found that four QTL clusters were located on chromosomes 2D, 3D, 4B and 6A, respectively. Notably, eight QTL from the QTL clusters were validated in a collected natural population. Among them, QPh-4B was deduced to be an allele of Rht-B1. In addition, three kompetitive allele-specific PCR (KASP) markers derived from SNPs were successfully designed for three QTL clusters. This study provides an important base for salt-tolerant QTL (gene) cloning in wheat, and the markers, especially the KASP markers, will be useful for marker-assisted selection in salt-tolerant wheat breeding.
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Affiliation(s)
- Qiaoling Luo
- 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
| | - Qi 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.
| | - Pan Hu
- 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
| | - Liqin Liu
- 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
| | - Guotang Yang
- 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
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongwei Li
- 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
| | - Bin Li
- 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
| | - Zhensheng Li
- 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
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Cao J, Shang Y, Xu D, Xu K, Cheng X, Pan X, Liu X, Liu M, Gao C, Yan S, Yao H, Gao W, Lu J, Zhang H, Chang C, Xia X, Xiao S, Ma C. Identification and Validation of New Stable QTLs for Grain Weight and Size by Multiple Mapping Models in Common Wheat. Front Genet 2020; 11:584859. [PMID: 33262789 PMCID: PMC7686802 DOI: 10.3389/fgene.2020.584859] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022] Open
Abstract
Improvement of grain weight and size is an important objective for high-yield wheat breeding. In this study, 174 recombinant inbred lines (RILs) derived from the cross between Jing 411 and Hongmangchun 21 were used to construct a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq). Three mapping methods, including inclusive composite interval mapping (ICIM), genome-wide composite interval mapping (GCIM), and a mixed linear model performed with forward-backward stepwise (NWIM), were used to identify QTLs for thousand grain weight (TGW), grain width (GW), and grain length (GL). In total, we identified 30, 15, and 18 putative QTLs for TGW, GW, and GL that explain 1.1-33.9%, 3.1%-34.2%, and 1.7%-22.8% of the phenotypic variances, respectively. Among these, 19 (63.3%) QTLs for TGW, 10 (66.7%) for GW, and 7 (38.9%) for GL were consistent with those identified by genome-wide association analysis in 192 wheat varieties. Five new stable QTLs, including 3 for TGW (Qtgw.ahau-1B.1, Qtgw.ahau-4B.1, and Qtgw.ahau-4B.2) and 2 for GL (Qgl.ahau-2A.1 and Qgl.ahau-7A.2), were detected by the three aforementioned mapping methods across environments. Subsequently, five cleaved amplified polymorphic sequence (CAPS) markers corresponding to these QTLs were developed and validated in 180 Chinese mini-core wheat accessions. In addition, 19 potential candidate genes for Qtgw.ahau-4B.2 in a 0.31-Mb physical interval were further annotated, of which TraesCS4B02G376400 and TraesCS4B02G376800 encode a plasma membrane H+-ATPase and a serine/threonine-protein kinase, respectively. These new QTLs and CAPS markers will be useful for further marker-assisted selection and map-based cloning of target genes.
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Affiliation(s)
- Jiajia Cao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Yaoyao Shang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Dongmei Xu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Kangle Xu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xinran Cheng
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xu Pan
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xue Liu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Mingli Liu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Chang Gao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Shengnan Yan
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Hui Yao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Wei Gao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Jie Lu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Haiping Zhang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Cheng Chang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shihe Xiao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chuanxi Ma
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
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Wang J, Wang R, Mao X, Zhang J, Liu Y, Xie Q, Yang X, Chang X, Li C, Zhang X, Jing R. RING finger ubiquitin E3 ligase gene TaSDIR1-4A contributes to determination of grain size in common wheat. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5377-5388. [PMID: 32479613 PMCID: PMC7501821 DOI: 10.1093/jxb/eraa271] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/26/2020] [Indexed: 05/16/2023]
Abstract
Salt and drought-induced RING finger1 (SDIR1) is a RING-type E3 ubiquitin ligase that plays a key role in ABA-mediated responses to salinity and drought stress via the ubiquitination pathway in some plant species. However, its function in wheat (Triticum aestivum) is unknown. Here, we isolated a SDIR1 member in wheat, TaSDIR1-4A, and characterized its E3 ubiquitin ligase activity. DNA polymorphism assays showed the presence of two nucleotide variation sites in the promoter region of TaSDIR1-4A, leading to the detection of the haplotypes Hap-4A-1 and Hap-4A-2 in wheat populations. Association analysis showed that TaSDIR1-4A haplotypes were associated with 1000-grain weight (TGW) across a variety of different environments, including well-watered and heat-stress conditions. Genotypes with Hap-4A-2 had higher TGW than those with Hap-4A-1. Phenotypes in both gene-silenced wheat and transgenic Arabidopsis showed that TaSDIR1-4A was a negative regulator of grain size. Gene expression assays indicated that TaSDIR1-4A was most highly expressed in flag leaves, and expression was higher in Hap-4A-1 accessions than in Hap-4A-2 accessions. The difference might be attributable to the fact that TaERF3 (ethylene response factor) can act as a transcriptional repressor of TaSDIR1-4A in Hap-4A-2 but not in Hap-4A-1. Examination of modern wheat varieties shows that the favorable haplotype has been positively selected in breeding programs in China. The functional marker for TaSDIR1-4A developed in this study should be helpful for future wheat breeding.
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Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruitong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jialing Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanna Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Xie
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyuan Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Muhammad A, Hu W, Li Z, Li J, Xie G, Wang J, Wang L. Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS. Int J Mol Sci 2020; 21:ijms21165649. [PMID: 32781752 PMCID: PMC7460857 DOI: 10.3390/ijms21165649] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
Kernel morphology is one of the major yield traits of wheat, the genetic architecture of which is always important in crop breeding. In this study, we performed a genome-wide association study (GWAS) to appraise the genetic architecture of the kernel traits of 319 wheat accessions using 22,905 single nucleotide polymorphism (SNP) markers from a wheat 90K SNP array. As a result, 111 and 104 significant SNPs for Kernel traits were detected using four multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, and pLARmEB) and three single-locus models (FarmCPU, MLM, and MLMM), respectively. Among the 111 SNPs detected by the multi-locus models, 24 SNPs were simultaneously detected across multiple models, including seven for kernel length, six for kernel width, six for kernels per spike, and five for thousand kernel weight. Interestingly, the five most stable SNPs (RAC875_29540_391, Kukri_07961_503, tplb0034e07_1581, BS00074341_51, and BobWhite_049_3064) were simultaneously detected by at least three multi-locus models. Integrating these newly developed multi-locus GWAS models to unravel the genetic architecture of kernel traits, the mrMLM approach detected the maximum number of SNPs. Furthermore, a total of 41 putative candidate genes were predicted to likely be involved in the genetic architecture underlining kernel traits. These findings can facilitate a better understanding of the complex genetic mechanisms of kernel traits and may lead to the genetic improvement of grain yield in wheat.
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Affiliation(s)
- Ali Muhammad
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Weicheng Hu
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Zhaoyang Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Jianguo Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
| | - Guosheng Xie
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Jibin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
- Correspondence: (J.W.); (L.W.)
| | - Lingqiang Wang
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
- Correspondence: (J.W.); (L.W.)
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Gupta PK, Balyan HS, Sharma S, Kumar R. Genetics of yield, abiotic stress tolerance and biofortification in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1569-1602. [PMID: 32253477 DOI: 10.1007/s00122-020-03583-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/13/2020] [Indexed: 05/18/2023]
Abstract
A review of the available literature on genetics of yield and its component traits, tolerance to abiotic stresses and biofortification should prove useful for future research in wheat in the genomics era. The work reviewed in this article mainly covers the available information on genetics of some important quantitative traits including yield and its components, tolerance to abiotic stresses (heat, drought, salinity and pre-harvest sprouting = PHS) and biofortification (Fe/Zn and phytate contents with HarvestPlus Program) in wheat. Major emphasis is laid on the recent literature on QTL interval mapping and genome-wide association studies, giving lists of known QTL and marker-trait associations. Candidate genes for different traits and the cloned and characterized genes for yield traits along with the molecular mechanism are also described. For each trait, an account of the present status of marker-assisted selection has also been included. The details of available results have largely been presented in the form of tables; some of these tables are included as supplementary files.
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Affiliation(s)
- Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India.
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Rahul Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
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23
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Cao P, Liang X, Zhao H, Feng B, Xu E, Wang L, Hu Y. Identification of the quantitative trait loci controlling spike-related traits in hexaploid wheat (Triticum aestivum L.). PLANTA 2019; 250:1967-1981. [PMID: 31529397 DOI: 10.1007/s00425-019-03278-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/08/2019] [Indexed: 05/25/2023]
Abstract
Totally, 48 loci responsible for six spike-related traits were identified in wheat, and a major locus QGl-4A for grain length was mapped and validated for marker-assisted selection in breeding. Wheat yield is determined by the number of spikes, number of grains per spike (GN), and one-thousand kernel weight (TKW), among which GN and TKW are greatly related to the spike development and thus the spike-related traits, including spike length (SL), number of spikelet per spike (SN), grain length (GL) and grain width (GW). To identify the key loci governing the spike-related traits (SL, SN, GN, TKW, GL and GW), we conducted the quantitative trait loci (QTL) analysis combined with wheat 660K SNP chip and Kompetitive allele-specific PCR (KASP) assay, using the F2 and F2:3 populations derived from Luohan6 (LH6) with big spike and grain and Zhengmai366 with small spike and grain, and identified a total of 48 QTLs on 18 chromosomes. Moreover, a major stable QTL for GL on chromosome 4A, designated as QGl-4A, was mapped into a 0.37 cM interval between KASP markers Xib4A-10 and Xib4A-12, corresponding to 20 Mb physical region in the Chinese Spring genome. This QTL explained 17.30% and 5.12% of the phenotypic variation for GL in the F2 and F2:3 populations. Further association analysis of flanking markers Xib4A-10 and Xib4A-12 in 192 wheat varieties showed that these two markers could be used for marker-assisted selection in breeding. These results provide valuable information for map-based cloning of the target genes involved in the regulation of spike-related traits in common wheat.
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Affiliation(s)
- Pei Cao
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaona Liang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Zhao
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Enjun Xu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liming Wang
- Henan Science and Technology University, Luoyang, 471023, Henan, China
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- National Center for Plant Gene Research, Beijing, 100093, China.
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Wang Q, Sun G, Ren X, Du B, Cheng Y, Wang Y, Li C, Sun D. Dissecting the Genetic Basis of Grain Size and Weight in Barley ( Hordeum vulgare L.) by QTL and Comparative Genetic Analyses. FRONTIERS IN PLANT SCIENCE 2019; 10:469. [PMID: 31105718 PMCID: PMC6491919 DOI: 10.3389/fpls.2019.00469] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/28/2019] [Indexed: 05/23/2023]
Abstract
Grain size and weight are crucial components of barley yield and quality and are the target characteristics of domestication and modern breeding. Despite this, little is known about the genetic and molecular mechanisms of grain size and weight in barley. Here, we evaluated nine traits determining grain size and weight, including thousand grain weight (Tgw), grain length (Gl), grain width (Gw), grain length-width ratio (Lwr), grain area (Ga), grain perimeter (Gp), grain diameter (Gd), grain roundness (Gr), and factor form density (Ffd), in a double haploid (DH) population for three consecutive years. Using five mapping methods, we successfully identified 60 reliable QTLs and 27 hotspot regions that distributed on all chromosomes except 6H which controls the nine traits of grain size and weight. Moreover, we also identified 164 barley orthologs of 112 grain size/weight genes from rice, maize, wheat and 38 barley genes that affect grain yield. A total of 45 barley genes or orthologs were identified as potential candidate genes for barley grain size and weight, including 12, 20, 9, and 4 genes or orthologs for barley, rice, maize, and wheat, respectively. Importantly, 20 of them were located in the 14 QTL hotspot regions on chromosome 1H, 2H, 3H, 5H, and 7H, which controls barley grain size and weight. These results indicated that grain size/weight genes of other cereal species might have the same or similar functions in barley. Our findings provide new insights into the understanding of the genetic basis of grain size and weight in barley, and new information to facilitate high-yield breeding in barley. The function of these potential candidate genes identified in this study are worth exploring and studying in detail.
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Affiliation(s)
- Qifei Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Department of Biology, Saint Mary’s University, Halifax, NS, Canada
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Binbin Du
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yun Cheng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yixiang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengdao Li
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, China
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25
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Desiderio F, Zarei L, Licciardello S, Cheghamirza K, Farshadfar E, Virzi N, Sciacca F, Bagnaresi P, Battaglia R, Guerra D, Palumbo M, Cattivelli L, Mazzucotelli E. Genomic Regions From an Iranian Landrace Increase Kernel Size in Durum Wheat. FRONTIERS IN PLANT SCIENCE 2019; 10:448. [PMID: 31057571 PMCID: PMC6482228 DOI: 10.3389/fpls.2019.00448] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/25/2019] [Indexed: 05/27/2023]
Abstract
Kernel size and shape are important parameters determining the wheat profitability, being main determinants of yield and its technological quality. In this study, a segregating population of 118 recombinant inbred lines, derived from a cross between the Iranian durum landrace accession "Iran_249" and the Iranian durum cultivar "Zardak", was used to investigate durum wheat kernel morphology factors and their relationships with kernel weight, and to map the corresponding QTLs. A high density genetic map, based on wheat 90k iSelect Infinium SNP assay, comprising 6,195 markers, was developed and used to perform the QTL analysis for kernel length and width, traits related to kernel shape and weight, and heading date, using phenotypic data from three environments. Overall, a total of 31 different QTLs and 9 QTL interactions for kernel size, and 21 different QTLs and 5 QTL interactions for kernel shape were identified. The landrace Iran_249 contributed the allele with positive effect for most of the QTLs related to kernel length and kernel weight suggesting that the landrace might have considerable potential toward enhancing the existing gene pool for grain shape and size traits and for further yield improvement in wheat. The correlation among traits and co-localization of corresponding QTLs permitted to define 11 clusters suggesting causal relationships between simplest kernel size trait, like kernel length and width, and more complex secondary trait, like kernel shape and weight related traits. Lastly, the recent release of the T. durum reference genome sequence allowed to define the physical interval of our QTL/clusters and to hypothesize novel candidate genes inspecting the gene content of the genomic regions associated to target traits.
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Affiliation(s)
- Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Leila Zarei
- Department of Agronomy and Plant Breeding, Razi University, Kermanshah, Iran
| | - Stefania Licciardello
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | | | | | - Nino Virzi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Fabiola Sciacca
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Raffaella Battaglia
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Massimo Palumbo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
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26
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Sestili F, Pagliarello R, Zega A, Saletti R, Pucci A, Botticella E, Masci S, Tundo S, Moscetti I, Foti S, Lafiandra D. Enhancing grain size in durum wheat using RNAi to knockdown GW2 genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:419-429. [PMID: 30426174 DOI: 10.1007/s00122-018-3229-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/02/2018] [Indexed: 05/21/2023]
Abstract
Knocking down GW2 enhances grain size by regulating genes encoding the synthesis of cytokinin, gibberellin, starch and cell wall. Raising crop yield is a priority task in the light of the continuing growth of the world's population and the inexorable loss of arable land to urbanization. Here, the RNAi approach was taken to reduce the abundance of Grain Weight 2 (GW2) transcript in the durum wheat cultivar Svevo. The effect of the knockdown was to increase the grains' starch content by 10-40%, their width by 4-13% and their surface area by 3-5%. Transcriptomic profiling, based on a quantitative real-time PCR platform, revealed that the transcript abundance of genes encoding both cytokinin dehydrogenase 1 and the large subunit of ADP-glucose pyrophosphorylase was markedly increased in the transgenic lines, whereas that of the genes encoding cytokinin dehydrogenase 2 and gibberellin 3-oxidase was reduced. A proteomic analysis of the non-storage fraction extracted from mature grains detected that eleven proteins were differentially represented in the transgenic compared to wild-type grain: some of these were involved, or at least potentially involved, in cell wall development, suggesting a role of GW2 in the regulation of cell division in the wheat grain.
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Affiliation(s)
- Francesco Sestili
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Riccardo Pagliarello
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Alessandra Zega
- Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Rosaria Saletti
- Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Anna Pucci
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Ermelinda Botticella
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Stefania Masci
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Silvio Tundo
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Ilaria Moscetti
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy
| | - Salvatore Foti
- Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S. Camillo de Lellis, 01100, Viterbo, Italy.
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27
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Wang W, Simmonds J, Pan Q, Davidson D, He F, Battal A, Akhunova A, Trick HN, Uauy C, Akhunov E. Gene editing and mutagenesis reveal inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2463-2475. [PMID: 30136108 PMCID: PMC6208945 DOI: 10.1007/s00122-018-3166-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/14/2018] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE CRISPR-Cas9-based genome editing and EMS mutagenesis revealed inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat. The TaGW2 gene homoeologues have been reported to be negative regulators of grain size (GS) and thousand grain weight (TGW) in wheat. However, the contribution of each homoeologue to trait variation among different wheat cultivars is not well documented. We used the CRISPR-Cas9 system and TILLING to mutagenize each homoeologous gene copy in cultivars Bobwhite and Paragon, respectively. Plants carrying single-copy nonsense mutations in different genomes showed different levels of GS/TGW increase, with TGW increasing by an average of 5.5% (edited lines) and 5.3% (TILLING mutants). In any combination, the double homoeologue mutants showed higher phenotypic effects than the respective single-genome mutants. The double mutants had on average 12.1% (edited) and 10.5% (TILLING) higher TGW with respect to wild-type lines. The highest increase in GS and TGW was shown for triple mutants of both cultivars, with increases in 16.3% (edited) and 20.7% (TILLING) in TGW. The additive effects of the TaGW2 homoeologues were also demonstrated by the negative correlation between the functional gene copy number and GS/TGW in Bobwhite mutants and an F2 population. The highest single-genome increases in GS and TGW in Paragon and Bobwhite were obtained by mutations in the B and D genomes, respectively. These inter-cultivar differences in the phenotypic effects between the TaGW2 gene homoeologues coincide with inter-cultivar differences in the homoeologue expression levels. These results indicate that GS/TGW variation in wheat can be modulated by the dosage of homoeologous genes with inter-cultivar differences in the magnitude of the individual homoeologue effects.
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Affiliation(s)
- Wei Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Qianli Pan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Dwight Davidson
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Abdulhamit Battal
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Yuzuncu Yil University, Van, Turkey
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
- Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
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28
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Henry RJ, Furtado A, Rangan P. Wheat seed transcriptome reveals genes controlling key traits for human preference and crop adaptation. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:231-236. [PMID: 29779965 DOI: 10.1016/j.pbi.2018.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/02/2018] [Accepted: 05/08/2018] [Indexed: 05/23/2023]
Abstract
Analysis of the transcriptome of the developing wheat grain has associated expression of genes with traits involving production (e.g. yield) and quality (e.g. bread quality). Photosynthesis in the grain may be important in retaining carbon that would be lost in respiration during grain filling and may contribute to yield in the late stages of seed formation under warm and dry environments. A small number of genes have been identified as having been selected by humans to optimize the performance of wheat for foods such as bread. Genes determining flour yield in milling have been discovered. Hardness is explained by variations in expression of pin genes. Knowledge of these genes should dramatically improve the efficiency of breeding better climate adapted wheat genotypes.
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Affiliation(s)
- Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Parimalan Rangan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia; Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi 110012, India
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29
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Daba SD, Tyagi P, Brown-Guedira G, Mohammadi M. Genome-Wide Association Studies to Identify Loci and Candidate Genes Controlling Kernel Weight and Length in a Historical United States Wheat Population. FRONTIERS IN PLANT SCIENCE 2018; 9:1045. [PMID: 30123226 PMCID: PMC6086202 DOI: 10.3389/fpls.2018.01045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/27/2018] [Indexed: 05/26/2023]
Abstract
Although kernel weight (KW) is a major component of grain yield, its contribution to yield genetic gain during breeding history has been minimal. This highlights an untapped potential for further increases in yield via improving KW. We investigated variation and genetics of KW and kernel length (KL) via genome-wide association studies (GWAS) using a historical and contemporary soft red winter wheat population representing 200 years of selection and breeding history in the United States. The observed changes of KW and KL over time did not show any conclusive trend. The population showed a structure, which was mainly explained by the time and location of germplasm development. Cluster sharing by germplasm from more than one breeding population was suggestive of episodes of germplasm exchange. Using 2 years of field-based phenotyping, we detected 26 quantitative trait loci (QTL) for KW and 27 QTL for KL with -log10(p) > 3.5. The search for candidate genes near the QTL on the wheat genome version IWGSCv1.0 has resulted in over 500 genes. The predicted functions of several of these genes are related to kernel development, photosynthesis, sucrose and starch synthesis, and assimilate remobilization and transport. We also evaluated the effect of allelic polymorphism of genes previously reported for KW and KL by using Kompetitive Allele Specific PCR (KASP) markers. Only TaGW2 showed significant association with KW. Two genes, i.e., TaSus2-2B and TaGS-D1 showed significant association with KL. Further physiological studies are needed to decipher the involvement of these genes in KW and KL development.
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Affiliation(s)
- Sintayehu D. Daba
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Priyanka Tyagi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Gina Brown-Guedira
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
- Small Grains Genotyping Laboratory, United States Department of Agriculture, Agricultural Research Services, Raleigh, NC, United States
| | - Mohsen Mohammadi
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
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30
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Zhang Y, Li D, Zhang D, Zhao X, Cao X, Dong L, Liu J, Chen K, Zhang H, Gao C, Wang D. Analysis of the functions of TaGW2 homoeologs in wheat grain weight and protein content traits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:857-866. [PMID: 29570880 DOI: 10.1111/tpj.13903] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 05/18/2023]
Abstract
GW2 is emerging as a key genetic determinant of grain weight in cereal crops; it has three homoeologs (TaGW2-A1, -B1 and -D1) in hexaploid common wheat (Triticum aestivum L.). Here, by analyzing the gene editing mutants that lack one (B1 or D1), two (B1 and D1) or all three (A1, B1 and D1) homoeologs of TaGW2, several insights are gained into the functions of TaGW2-B1 and -D1 in common wheat grain traits. First, both TaGW2-B1 and -D1 affect thousand-grain weight (TGW) by influencing grain width and length, but the effect conferred by TaGW2-B1 is stronger than that of TaGW2-D1. Second, there exists functional interaction between TaGW2 homoeologs because the TGW increase shown by a double mutant (lacking B1 and D1) was substantially larger than that of their single mutants. Third, both TaGW2-B1 and -D1 modulate cell number and length in the outer pericarp of developing grains, with TaGW2-B1 being more potent. Finally, TaGW2 homoeologs also affect grain protein content as this parameter was generally increased in the mutants, especially in the lines lacking two or three homoeologs. Consistent with this finding, two wheat end-use quality-related parameters, flour protein content and gluten strength, were considerably elevated in the mutants. Collectively, our data shed light on functional difference between and additive interaction of TaGW2 homoeologs in the genetic control of grain weight and protein content traits in common wheat, which may accelerate further research on this important gene and its application in wheat improvement.
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Affiliation(s)
- Yi Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Da Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dingbo Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoge Zhao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuemin Cao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingli Dong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinxing Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kunling Chen
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huawei Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Caixia Gao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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31
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Sukumaran S, Lopes M, Dreisigacker S, Reynolds M. Genetic analysis of multi-environmental spring wheat trials identifies genomic regions for locus-specific trade-offs for grain weight and grain number. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:985-998. [PMID: 29218375 DOI: 10.1007/s00122-017-3037-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/01/2017] [Indexed: 05/21/2023]
Abstract
GWAS on multi-environment data identified genomic regions associated with trade-offs for grain weight and grain number. Grain yield (GY) can be dissected into its components thousand grain weight (TGW) and grain number (GN), but little has been achieved in assessing the trade-off between them in spring wheat. In the present study, the Wheat Association Mapping Initiative (WAMI) panel of 287 elite spring bread wheat lines was phenotyped for GY, GN, and TGW in ten environments across different wheat growing regions in Mexico, South Asia, and North Africa. The panel genotyped with the 90 K Illumina Infinitum SNP array resulted in 26,814 SNPs for genome-wide association study (GWAS). Statistical analysis of the multi-environmental data for GY, GN, and TGW observed repeatability estimates of 0.76, 0.62, and 0.95, respectively. GWAS on BLUPs of combined environment analysis identified 38 loci associated with the traits. Among them four loci-6A (85 cM), 5A (98 cM), 3B (99 cM), and 2B (96 cM)-were associated with multiple traits. The study identified two loci that showed positive association between GY and TGW, with allelic substitution effects of 4% (GY) and 1.7% (TGW) for 6A locus and 0.2% (GY) and 7.2% (TGW) for 2B locus. The locus in chromosome 6A (79-85 cM) harbored a gene TaGW2-6A. We also identified that a combination of markers associated with GY, TGW, and GN together explained higher variation for GY (32%), than the markers associated with GY alone (27%). The marker-trait associations from the present study can be used for marker-assisted selection (MAS) and to discover the underlying genes for these traits in spring wheat.
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Affiliation(s)
- Sivakumar Sukumaran
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico City, 06600, Mexico.
| | - Marta Lopes
- CIMMYT, P.O. Box 39, Emek, Ankara, 06511, Turkey
| | - Susanne Dreisigacker
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico City, 06600, Mexico
| | - Matthew Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico City, 06600, Mexico
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32
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Zhai H, Feng Z, Du X, Song Y, Liu X, Qi Z, Song L, Li J, Li L, Peng H, Hu Z, Yao Y, Xin M, Xiao S, Sun Q, Ni Z. A novel allele of TaGW2-A1 is located in a finely mapped QTL that increases grain weight but decreases grain number in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:539-553. [PMID: 29150697 PMCID: PMC5814529 DOI: 10.1007/s00122-017-3017-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/04/2017] [Indexed: 05/19/2023]
Abstract
A novel TaGW2-A1 allele was identified from a stable, robust QTL region, which is pleiotropic for thousand grain weight, grain number per spike, and grain morphometric parameters in wheat. Thousand grain weight (TGW) and grain number per spike (GNS) are two crucial determinants of wheat spike yield, and genetic dissection of their relationships can help to fine-tune these two components and maximize grain yield. By evaluating 191 recombinant inbred lines in 11 field trials, we identified five genomic regions on chromosomes 1B, 3A, 3B, 5B, or 7A that solely influenced either TGW or GNS, and a further region on chromosome 6A that concurrently affected TGW and GNS. The QTL of interest on chromosome 6A, which was flanked by wsnp_BE490604A_Ta_2_1 and wsnp_RFL_Contig1340_448996 and designated as QTgw/Gns.cau-6A, was finely mapped to a genetic interval shorter than 0.538 cM using near isogenic lines (NILs). The elite NILs of QTgw/Gns.cau-6A increased TGW by 8.33%, but decreased GNS by 3.05% in six field trials. Grain Weight 2 (TaGW2-A1), a well-characterized gene that negatively regulates TGW and grain width in wheat, was located within the finely mapped interval of QTgw/Gns.cau-6A. A novel and rare TaGW2-A1 allele with a 114-bp deletion in the 5' flanking region was identified in the parent with higher TGW, and it reduced TaGW2-A1 promoter activity and expression. In conclusion, these results expand our knowledge of the genetic and molecular basis of TGW-GNS trade-offs in wheat. The QTLs and the novel TaGW2-A1 allele are likely useful for the development of cultivars with higher TGW and/or higher GNS.
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Affiliation(s)
- Huijie Zhai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhiyu Feng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Xiaofen Du
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, Shanxi, China
| | - Yane Song
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhongqi Qi
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Long Song
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Jiang Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Linghong Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing 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, Beijing 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, Beijing 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, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Shihe Xiao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing 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, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
- National Plant Gene Research Centre, Beijing, 100193, China.
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Wang W, Pan Q, He F, Akhunova A, Chao S, Trick H, Akhunov E. Transgenerational CRISPR-Cas9 Activity Facilitates Multiplex Gene Editing in Allopolyploid Wheat. CRISPR J 2018; 1:65-74. [PMID: 30627700 PMCID: PMC6319321 DOI: 10.1089/crispr.2017.0010] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The CRISPR-Cas9-based multiplexed gene editing (MGE) provides a powerful method to modify multiple genomic regions simultaneously controlling different agronomic traits in crops. We applied the MGE construct built by combining the tandemly arrayed tRNA–gRNA units to generate heritable mutations in the TaGW2, TaLpx-1, and TaMLO genes of hexaploid wheat. The knockout mutations generated by this construct in all three homoeologous copies of one of the target genes, TaGW2, resulted in a substantial increase in seed size and thousand grain weight. We showed that the non-modified gRNA targets in the early generation plants can be edited by CRISPR-Cas9 in the following generations. Our results demonstrate that transgenerational gene editing activity can serve as the source of novel variation in the progeny of CRISPR-Cas9-expressing plants and suggest that the Cas9-inducible trait transfer for crop improvement can be achieved by crossing the plants expressing the gene editing constructs with the lines of interest.
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Affiliation(s)
- Wei Wang
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Qianli Pan
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas.,Integrated Genomics Facility, Kansas State University, Manhattan, Kansas
| | - Shiaoman Chao
- USDA-ARS Cereal Crops Research Unit, Fargo, North Dakota
| | - Harold Trick
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
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Haque E, Taniguchi H, Hassan MM, Bhowmik P, Karim MR, Śmiech M, Zhao K, Rahman M, Islam T. Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges. FRONTIERS IN PLANT SCIENCE 2018; 9:617. [PMID: 29868073 PMCID: PMC5952327 DOI: 10.3389/fpls.2018.00617] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/18/2018] [Indexed: 05/19/2023]
Abstract
The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein9) genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses.
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Affiliation(s)
- Effi Haque
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Md. Mahmudul Hassan
- Division of Genetics, Genomics and Development School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Pankaj Bhowmik
- National Research Council of Canada, Saskatoon, SK, Canada
| | - M. Rezaul Karim
- Department of Biotechnology and Genetic Engineering Jahangirnagar University Savar, Dhaka, Bangladesh
| | - Magdalena Śmiech
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mahfuzur Rahman
- Extension Service, West Virginia University, Morgantown, WV, United States
| | - Tofazzal Islam
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
- Extension Service, West Virginia University, Morgantown, WV, United States
- *Correspondence: Tofazzal Islam
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Geng J, Li L, Lv Q, Zhao Y, Liu Y, Zhang L, Li X. TaGW2-6A allelic variation contributes to grain size possibly by regulating the expression of cytokinins and starch-related genes in wheat. PLANTA 2017; 246:1153-1163. [PMID: 28825220 DOI: 10.1007/s00425-017-2759-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/11/2017] [Indexed: 05/21/2023]
Abstract
Functional allelic variants of TaGW2 - 6A produce large grains, possibly via changes in endosperm cells and dry matter by regulating the expression of cytokinins and starch-related genes via the ubiquitin-proteasome system. In wheat, TaGW2-6A coding region allelic variants are closely related to the grain width and weight, but how this region affects grain development has not been fully elucidated; thus, we explored its influence on grain development based mainly on histological and grain filling analyses. We found that the insertion type (NIL31) TaGW2-6A allelic variants exhibited increases in cell numbers and cell size, thereby resulting in a larger (wider) grain size with an accelerated grain milk filling rate, and increases in grain width and weight. We also found that cytokinin (CK) synthesis genes and key starch biosynthesis enzyme AGPase genes were significantly upregulated in the TaGW2-6A allelic variants, while CK degradation genes and starch biosynthesis-negative regulators were downregulated in the TaGW2-6A allelic variants, which was consistent with the changes in cells and grain filling. Thus, we speculate that TaGW2-6A allelic variants are linked with CK signaling, but they also influence the accumulation of starch by regulating the expression of related genes via the ubiquitin-proteasome system to control the grain size and grain weight.
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Affiliation(s)
- Juan Geng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Liqun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qian Lv
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yi Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Li Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, 712100, Shaanxi, People's Republic of China.
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Liu J, Huang J, Guo H, Lan L, Wang H, Xu Y, Yang X, Li W, Tong H, Xiao Y, Pan Q, Qiao F, Raihan MS, Liu H, Zhang X, Yang N, Wang X, Deng M, Jin M, Zhao L, Luo X, Zhou Y, Li X, Zhan W, Liu N, Wang H, Chen G, Li Q, Yan J. The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice. PLANT PHYSIOLOGY 2017; 175:774-785. [PMID: 28811335 PMCID: PMC5619898 DOI: 10.1104/pp.17.00708] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/12/2017] [Indexed: 05/18/2023]
Abstract
Maize (Zea mays) is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight, and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation. To provide candidate genes for these QTLs, we identified 30 maize genes that are orthologs of 18 rice (Oryza sativa) genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are located in the identified QTLs or within 1 Mb of the significant single-nucleotide polymorphisms. We further confirmed the effects of five genes on maize kernel size/weight in an independent association mapping panel with 540 lines by candidate gene association analysis. Lastly, the function of ZmINCW1, a homolog of rice GRAIN INCOMPLETE FILLING1 that affects seed size and weight, was characterized in detail. ZmINCW1 is close to QTL peaks for kernel size/weight (less than 1 Mb) and contains significant single-nucleotide polymorphisms affecting kernel size/weight in the association panel. Overexpression of this gene can rescue the reduced weight of the Arabidopsis (Arabidopsis thaliana) homozygous mutant line in the AtcwINV2 gene (Arabidopsis ortholog of ZmINCW1). These results indicate that the molecular mechanisms affecting seed development are conserved in maize, rice, and possibly Arabidopsis.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Juan Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Huan Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Liu Lan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongze Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuancheng Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Tong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Qiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mohammad Sharif Raihan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuehai Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaqing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Nannan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Gengshen Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Li W, Yang B. Translational genomics of grain size regulation in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1765-1771. [PMID: 28765985 DOI: 10.1007/s00122-017-2953-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/26/2017] [Indexed: 05/29/2023]
Abstract
Identifying and mapping grain size candidate genes in the wheat genome greatly empowers reverse genetics approaches to improve grain yield potential of wheat. Grain size (GS) or grain weight is believed to be a major driving force for further improvement of wheat yield. Although the large, polyploid genome of wheat poses an obstacle to identifying GS determinants using map-based cloning, a translational genomics approach using GS regulators identified in the model plants rice and Arabidopsis as candidate genes appears to be effective and supports a hypothesis that a conserved genetic network regulates GS in rice and wheat. In this review, we summarize the progress in the studies on GS in the model plants and wheat and identify 45 GS candidate loci in the wheat genome. In silico mapping of these GS loci in the diploid wheat and barley genomes showed (1) several gene families amplified in the wheat lineage, (2) a significant number of the GS genes located in the proximal regions surrounding the centromeres, and (3) more than half of candidate genes to be negative regulators, or their expression negatively related by microRNAs. Identifying and mapping the wheat GS gene homologs will not only facilitate candidate gene analysis, but also open the door to improving wheat yield using reverse genetics approaches by mining desired alleles in landraces and wild ancestors and to developing novel germplasm by TILLING and genome editing technologies.
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Affiliation(s)
- Wanlong Li
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.
| | - Bing Yang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
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Qin L, Zhao J, Li T, Hou J, Zhang X, Hao C. TaGW2, a Good Reflection of Wheat Polyploidization and Evolution. FRONTIERS IN PLANT SCIENCE 2017; 8:318. [PMID: 28326096 PMCID: PMC5339256 DOI: 10.3389/fpls.2017.00318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/22/2017] [Indexed: 05/04/2023]
Abstract
Hexaploid wheat consists of three subgenomes, namely, A, B, and D. These well-characterized ancestral genomes also exist at the diploid and tetraploid levels, thereby rendering wheat as a good model species for studying polyploidization. Here, we performed intra- and inter-species comparative analyses of wheat and its relatives to dissect polymorphism and differentiation of the TaGW2 genes. Our results showed that genetic diversity of TaGW2 decreased with progression from the diploids to tetraploids and hexaploids. The strongest selection occurred in the promoter regions of TaGW2-6A and TaGW2-6B. Phylogenetic trees clearly indicated that Triticum urartu and Ae. speltoides were the donors of the A and B genomes in tetraploid and hexaploid wheats. Haplotypes detected among hexaploid genotypes traced back to the tetraploid level. Fst and π values revealed that the strongest selection on TaGW2 occurred at the tetraploid level rather than in hexaploid wheat. This infers that grain size enlargement, especially increased kernel width, mainly occurred in tetraploid genotypes. In addition, relative expression levels of TaGW2s significantly declined from the diploid level to tetraploids and hexaploids, further indicating that these genes negatively regulate kernel size. Our results also revealed that the polyploidization events possibly caused much stronger differentiation than domestication and breeding.
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Affiliation(s)
- Lin Qin
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Junjie Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xueyong Zhang
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- *Correspondence: Xueyong Zhang
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- Chenyang Hao
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Wang X, Lu X, Wang J, Wang D, Yin Z, Fan W, Wang S, Ye W. Mining and Analysis of SNP in Response to Salinity Stress in Upland Cotton (Gossypium hirsutum L.). PLoS One 2016; 11:e0158142. [PMID: 27355327 PMCID: PMC4927152 DOI: 10.1371/journal.pone.0158142] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/11/2016] [Indexed: 01/14/2023] Open
Abstract
Salinity stress is a major abiotic factor that affects crop output, and as a pioneer crop in saline and alkaline land, salt tolerance study of cotton is particularly important. In our experiment, four salt-tolerance varieties with different salt tolerance indexes including CRI35 (65.04%), Kanghuanwei164 (56.19%), Zhong9807 (55.20%) and CRI44 (50.50%), as well as four salt-sensitive cotton varieties including Hengmian3 (48.21%), GK50 (40.20%), Xinyan96-48 (34.90%), ZhongS9612 (24.80%) were used as the materials. These materials were divided into salt-tolerant group (ST) and salt-sensitive group (SS). Illumina Cotton SNP 70K Chip was used to detect SNP in different cotton varieties. SNPv (SNP variation of the same seedling pre- and after- salt stress) in different varieties were screened; polymorphic SNP and SNPr (SNP related to salt tolerance) were obtained. Annotation and analysis of these SNPs showed that (1) the induction efficiency of salinity stress on SNPv of cotton materials with different salt tolerance index was different, in which the induction efficiency on salt-sensitive materials was significantly higher than that on salt-tolerant materials. The induction of salt stress on SNPv was obviously biased. (2) SNPv induced by salt stress may be related to the methylation changes under salt stress. (3) SNPr may influence salt tolerance of plants by affecting the expression of salt-tolerance related genes.
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Affiliation(s)
- Xiaoge Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Anyang 455000, Henan, China
| | - Xuke Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Anyang 455000, Henan, China
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Anyang 455000, Henan, China
| | - Delong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Anyang 455000, Henan, China
| | - Zujun Yin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Anyang 455000, Henan, China
| | - Weili Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Anyang 455000, Henan, China
| | - Shuai Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Anyang 455000, Henan, China
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Anyang 455000, Henan, China
- * E-mail:
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Du D, Gao X, Geng J, Li Q, Li L, Lv Q, Li X. Identification of Key Proteins and Networks Related to Grain Development in Wheat (Triticum aestivum L.) by Comparative Transcription and Proteomic Analysis of Allelic Variants in TaGW2-6A. FRONTIERS IN PLANT SCIENCE 2016; 7:922. [PMID: 27446152 PMCID: PMC4923154 DOI: 10.3389/fpls.2016.00922] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/10/2016] [Indexed: 05/24/2023]
Abstract
In wheat, coding region allelic variants of TaGW2-6A are closely associated with grain width and weight, but the genetic mechanisms involved remain unclear. Thus, to obtain insights into the key functions regulated by TaGW2-6A during wheat grain development, we performed transcriptional and proteomic analyses of TaGW2-6A allelic variants. The transcription results showed that the TaGW2-6A allelic variants differed significantly by several orders of magnitude. Each allelic variant of TaGW2-6A reached its first transcription peak at 6 days after anthesis (DAA), but the insertion type TaGW2-6A allelic variant reached its second peak earlier than the normal type, i.e., at 12 DAA rather than 20 DAA. In total, we identified 228 differentially accumulated protein spots representing 138 unique proteins by two-dimensional gel electrophoresis and tandem MALDI-TOF/TOF-MS in these three stages. Based on the results, we found some key proteins that are closely related to wheat grain development. The results of this analysis improve our understanding of the genetic mechanisms related to TaGW2-6A during wheat grain development as well as providing insights into the biological processes involved in seed formation.
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