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Liao S, Xu Z, Fan X, Zhou Q, Liu X, Jiang C, Ma F, Wang Y, Wang T, Feng B. Identification and validation of two major QTL for grain number per spike on chromosomes 2B and 2D in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:147. [PMID: 38834870 DOI: 10.1007/s00122-024-04652-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/16/2024] [Indexed: 06/06/2024]
Abstract
KEY MESSAGE Major QTL for grain number per spike were identified on chromosomes 2B and 2D. Haplotypes and candidate genes of QGns.cib-2B.1 were analyzed. Grain number per spike (GNS) is one of the main components of wheat yield. Genetic dissection of their regulatory factors is essential to improve the yield potential. In present study, a recombinant inbred line population comprising 180 lines developed from the cross between a high GNS line W7268 and a cultivar Chuanyu12 was employed to identify quantitative trait loci (QTL) associated with GNS across six environments. Two major QTL, QGns.cib-2B.1 and QGns.cib-2D.1, were detected in at least four environments with the phenotypic variations of 12.99-27.07% and 8.50-13.79%, respectively. And significant interactions were observed between the two major QTL. In addition, QGns.cib-2B.1 is a QTL cluster for GNS, grain number per spikelet and fertile tiller number, and they were validated in different genetic backgrounds using Kompetitive Allele Specific PCR (KASP) markers. QGns.cib-2B.1 showed pleotropic effects on other yield-related traits including plant height, spike length, and spikelet number per spike, but did not significantly affect thousand grain weight which suggested that it might be potentially applicable in breeding program. Comparison analysis suggested that QGns.cib-2B.1 might be a novel QTL. Furthermore, haplotype analysis of QGns.cib-2B.1 indicated that it is a hot spot of artificial selection during wheat improvement. Based on the expression patterns, gene annotation, orthologs analysis and sequence variations, the candidate genes of QGns.cib-2B.1 were predicted. Collectively, the major QTL and KASP markers reported here provided a wealth of information for the genetic basis of GNS and grain yield improvement.
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Affiliation(s)
- Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanlin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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2
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Li Y, Hu J, Qu Y, Qiu D, Lin H, Du J, Hou L, Ma L, Wu Q, Zhou Y, Zhang H, Yang L, Liu H, Liu Z, Zhou Y, Li H. Alleles on locus chromosome 4B from different parents confer tiller number and the yield-associated traits in wheat. BMC PLANT BIOLOGY 2024; 24:454. [PMID: 38789943 PMCID: PMC11127307 DOI: 10.1186/s12870-024-05079-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/28/2024] [Indexed: 05/26/2024]
Abstract
Pleiotropy is frequently detected in agronomic traits of wheat (Triticum aestivum). A locus on chromosome 4B, QTn/Ptn/Sl/Sns/Al/Tgw/Gl/Gw.caas-4B, proved to show pleiotropic effects on tiller, spike, and grain traits using a recombinant inbred line (RIL) population of Qingxinmai × 041133. The allele from Qingxinmai increased tiller numbers, and the allele from line 041133 produced better performances of spike traits and grain traits. Another 52 QTL for the eight traits investigated were detected on 18 chromosomes, except for chromosomes 5D, 6D, and 7B. Several genes in the genomic interval of the locus on chromosome 4B were differentially expressed in crown and inflorescence samples between Qingxinmai and line 041133. The development of the KASP marker specific for the locus on chromosome 4B is useful for molecular marker-assisted selection in wheat breeding.
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Affiliation(s)
- Yahui Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinghuang Hu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunfeng Qu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Dan Qiu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huailong Lin
- Jiushenghe Seed Industry Co. Ltd, Changji, 831100, China
| | - Jiuyuan Du
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Lu Hou
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Lin Ma
- Datong Hui and Tu Autonomous County Agricultural Technology Extension Center, Xining, 810100, China
| | - Qiuhong Wu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Zhou
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongjun Zhang
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Yang
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwei Liu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yijun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China.
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Sakuma S, Yamashita Y, Suzuki T, Nasuda S. A Catalog of GNI-A1 Genes That Regulate Floret Fertility in a Diverse Bread Wheat Collection. PLANTS (BASEL, SWITZERLAND) 2024; 13:330. [PMID: 38337864 PMCID: PMC10857310 DOI: 10.3390/plants13030330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Modifying inflorescence architecture improves grain number and grain weight in bread wheat (Triticum aestivum). Allelic variation in Grain Number Increase 1 (GNI-A1) genes, encoding a homeodomain leucine zipper class I transcription factor, influences grain number and yield. However, allelic information about GNI-A1 in diverse germplasms remains limited. Here, we investigated GNI-A1 alleles in a panel of 252 diverse bread wheat accessions (NBRP core collection and HRO breeder's panel) by target resequencing. Cultivars carrying the reduced-function allele (105Y) were predominant in the NBRP panel, whereas the 105N functional allele was the major type in the HRO panel. Cultivars with the 105Y allele were distributed in Asian landraces but not in European genotypes. Association analysis demonstrated that floret fertility, together with grain size, were improved in cultivars in the NBRP core collection carrying the 105Y allele. These results imply that different alleles of GNI-A1 have been locally selected, with the 105Y allele selected in East Asia and the 105N allele selected in Europe.
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Affiliation(s)
- Shun Sakuma
- Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - Yoko Yamashita
- Central Agricultural Experiment Station, Hokkaido Research Organization, Naganuma, Hokkaido 069-1395, Japan; (Y.Y.); (T.S.)
| | - Takako Suzuki
- Central Agricultural Experiment Station, Hokkaido Research Organization, Naganuma, Hokkaido 069-1395, Japan; (Y.Y.); (T.S.)
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan;
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4
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Zhang Y, Shen C, Shi J, Shi J, Zhang D. Boosting Triticeae crop grain yield by manipulating molecular modules to regulate inflorescence architecture: insights and knowledge from other cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:17-35. [PMID: 37935244 DOI: 10.1093/jxb/erad386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
One of the challenges for global food security is to reliably and sustainably improve the grain yield of cereal crops. One solution is to modify the architecture of the grain-bearing inflorescence to optimize for grain number and size. Cereal inflorescences are complex structures, with determinacy, branching patterns, and spikelet/floret growth patterns that vary by species. Recent decades have witnessed rapid advancements in our understanding of the genetic regulation of inflorescence architecture in rice, maize, wheat, and barley. Here, we summarize current knowledge on key genetic factors underlying the different inflorescence morphologies of these crops and model plants (Arabidopsis and tomato), focusing particularly on the regulation of inflorescence meristem determinacy and spikelet meristem identity and determinacy. We also discuss strategies to identify and utilize these superior alleles to optimize inflorescence architecture and, ultimately, improve crop grain yield.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
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5
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Haq SAU, Bashir T, Roberts TH, Husaini AM. Ameliorating the effects of multiple stresses on agronomic traits in crops: modern biotechnological and omics approaches. Mol Biol Rep 2023; 51:41. [PMID: 38158512 DOI: 10.1007/s11033-023-09042-8] [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: 12/15/2022] [Accepted: 10/13/2023] [Indexed: 01/03/2024]
Abstract
While global climate change poses a significant environmental threat to agriculture, the increasing population is another big challenge to food security. To address this, developing crop varieties with increased productivity and tolerance to biotic and abiotic stresses is crucial. Breeders must identify traits to ensure higher and consistent yields under inconsistent environmental challenges, possess resilience against emerging biotic and abiotic stresses and satisfy customer demands for safer and more nutritious meals. With the advent of omics-based technologies, molecular tools are now integrated with breeding to understand the molecular genetics of genotype-based traits and develop better climate-smart crops. The rapid development of omics technologies offers an opportunity to generate novel datasets for crop species. Identifying genes and pathways responsible for significant agronomic traits has been made possible by integrating omics data with genetic and phenotypic information. This paper discusses the importance and use of omics-based strategies, including genomics, transcriptomics, proteomics and phenomics, for agricultural and horticultural crop improvement, which aligns with developing better adaptability in these crop species to the changing climate conditions.
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Affiliation(s)
- Syed Anam Ul Haq
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Tanzeel Bashir
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Thomas H Roberts
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, Sydney Institute of Agriculture, The University of Sydney, Eveleigh, Australia
| | - Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India.
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6
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Niu J, Ma S, Zheng S, Zhang C, Lu Y, Si Y, Tian S, Shi X, Liu X, Naeem MK, Sun H, Hu Y, Wu H, Cui Y, Chen C, Long W, Zhang Y, Gu M, Cui M, Lu Q, Zhou W, Peng J, Akhunov E, He F, Zhao S, Ling HQ. Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States. THE PLANT CELL 2023; 35:4199-4216. [PMID: 37647532 PMCID: PMC10689146 DOI: 10.1093/plcell/koad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023]
Abstract
Breeding has dramatically changed the plant architecture of wheat (Triticum aestivum), resulting in the development of high-yielding varieties adapted to modern farming systems. However, how wheat breeding shaped the genomic architecture of this crop remains poorly understood. Here, we performed a comprehensive comparative analysis of a whole-genome resequencing panel of 355 common wheat accessions (representing diverse landraces and modern cultivars from China and the United States) at the phenotypic and genomic levels. The genetic diversity of modern wheat cultivars was clearly reduced compared to landraces. Consistent with these genetic changes, most phenotypes of cultivars from China and the United States were significantly altered. Of the 21 agronomic traits investigated, 8 showed convergent changes between the 2 countries. Moreover, of the 207 loci associated with these 21 traits, more than half overlapped with genomic regions that showed evidence of selection. The distribution of selected loci between the Chinese and American cultivars suggests that breeding for increased productivity in these 2 regions was accomplished by pyramiding both shared and region-specific variants. This work provides a framework to understand the genetic architecture of the adaptation of wheat to diverse agricultural production environments, as well as guidelines for optimizing breeding strategies to design better wheat varieties.
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Affiliation(s)
- Jianqing Niu
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengwei Ma
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yaru Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoli Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muhammad Kashif Naeem
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunlin Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbo Long
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengjun Gu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Man Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiao Lu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjuan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhua Peng
- Huazhi Bio-tech Company Ltd., Changsha, Hunan 410125, China
| | - Eduard Akhunov
- Wheat Genetic Resources Center, Kansas State University, Manhattan, KS 66506, USA
| | - Fei He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shancen Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Hong-Qing Ling
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Si Y, Tian S, Niu J, Yu Z, Ma S, Lu Q, Wu H, Ling HQ, Zheng S. Dissection and validation of a promising QTL controlling spikelet number on 5B in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:240. [PMID: 37930446 DOI: 10.1007/s00122-023-04488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
KEY MESSAGE Five environmentally stable QTLs for spikelet number per spike and days to heading were identified using a high-genetic map containing 95,444 SNPs, among which QSns.ucas-5B was validated using residual heterozygous line at multiple environments. Spikelet number per spike (SNS) and days to heading (DTH) play pivotal roles in the improvement of wheat yield. In this study, a high-density genetic map for a recombinant inbred lines (RILs) population derived from Zhengnong 17 (ZN17) and Yangbaimai (YBM) was constructed using 95,444 single-nucleotide polymorphism (SNP) markers from the Wheat660K SNP array. Our study identified a total of five environmentally stable QTLs for SNS and DTH, one of which was named QSns.ucas-5B, with a physical interval of approximately 545.4-552.1 Mb on the 5BL chromosome arm. Importantly, the elite haplotype within QSns.ucas-5B showed a consistent and positive effect on SNS, grain number and weight per spike, without extending the days to heading. These findings provide a foundation for future efforts to map and clone the gene(s) responsible for QSns.ucas-5B and further indicate the potential application of the developed and validated InDel marker of QSns.ucas-5B for molecular breeding purposes, aimed at improving wheat grain yield.
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Affiliation(s)
- Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianqing Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhongqing Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Shengwei Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiao Lu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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8
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Rieu P, Arnoux-Courseaux M, Tichtinsky G, Parcy F. Thinking outside the F-box: how UFO controls angiosperm development. THE NEW PHYTOLOGIST 2023; 240:945-959. [PMID: 37664990 DOI: 10.1111/nph.19234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/19/2023] [Indexed: 09/05/2023]
Abstract
The formation of inflorescences and flowers is essential for the successful reproduction of angiosperms. In the past few decades, genetic studies have identified the LEAFY transcription factor and the UNUSUAL FLORAL ORGANS (UFO) F-box protein as two major regulators of flower development in a broad range of angiosperm species. Recent research has revealed that UFO acts as a transcriptional cofactor, redirecting the LEAFY floral regulator to novel cis-elements. In this review, we summarize the various roles of UFO across species, analyze past results in light of new discoveries and highlight the key questions that remain to be solved.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - Moïra Arnoux-Courseaux
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - Gabrielle Tichtinsky
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
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9
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Zhao C, Zhou J, Li C, You J, Liu Y, Tang H, Deng M, Xu Q, Zhang Y, Jiang Q, Chen G, Qi P, Jiang Y, Wang J, Li W, Pu Z, Chen G, Jiang Y, Zheng Z, Liu C, Zheng Y, Wei Y, Ma J. A major QTL simultaneously increases the number of spikelets per spike and thousand-kernel weight in a wheat line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:213. [PMID: 37740730 DOI: 10.1007/s00122-023-04459-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/31/2023] [Indexed: 09/25/2023]
Abstract
KEY MESSAGE A novel and stably expressed QTL QSNS.sicau-SSY-7A for spikelet number per spike in wheat without negative effects on thousand-kernel weight was identified and validated in different genetic backgrounds. Spikelet number per spike (SNS) is an important determinant of yield in wheat. In the present study, we combined bulked segregant analysis (BSA) and the wheat 660 K single-nucleotide polymorphism (SNP) array to rapidly identify genomic regions associated with SNS from a recombinant inbred line (RIL) population derived from a cross between the wheat lines S849-8 and SY95-71. A genetic map was constructed using Kompetitive Allele Specific PCR markers in the SNP-enriched region on the long arm of chromosome 7A. A major and stably expressed QTL, QSNS.sicau-SSY-7A, was detected in multiple environments. It was located in a 1.6 cM interval on chromosome arm 7AL flanked by the markers AX-109983514 and AX-109820548. This QTL explained 6.86-15.72% of the phenotypic variance, with LOD values ranging from 3.66 to 8.66. Several genes associated with plant growth and development were identified in the interval where QSNS.sicau-SSY-7A was located on the 'Chinese Spring' wheat and wild emmer reference genomes. Furthermore, the effects of QSNS.sicau-SSY-7A and WHEAT ORTHOLOG OFAPO1(WAPO1) on SNS were analyzed. Interestingly, QSNS.sicau-SSY-7A significantly increased SNS without negative effects on thousand-kernel weight, anthesis date and plant height, demonstrating its great potential for breeding aimed at improving grain yield. Taken together, these results indicate that QSNS.sicau-SSY-7A is a promising locus for yield improvement, and its linkage markers are helpful for fine mapping and molecular breeding.
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Affiliation(s)
- Conghao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jianing You
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy ofAgricultural Sciences, Chengdu, China
| | - Zhi Zheng
- CSIRO Agriculture and Food, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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10
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Qin R, Ma T, Cai Y, Shi X, Cheng J, Dong J, Wang C, Li S, Pan G, Guan Y, Zhang L, Yang S, Xu H, Zhao C, Sun H, Li X, Wu Y, Li J, Cui F. Characterization and fine mapping analysis of a major stable QTL qKnps-4A for kernel number per spike in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:211. [PMID: 37737910 DOI: 10.1007/s00122-023-04456-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023]
Abstract
KEY MESSAGE A major stable QTL for kernel number per spike was narrowed down to a 2.19-Mb region containing two potential candidate genes, and its effects on yield-related traits were characterized. Kernel number per spike (KNPS) in wheat is a key yield component. Dissection and characterization of major stable quantitative trait loci (QTLs) for KNPS would be of considerable value for the genetic improvement of yield potential using molecular breeding technology. We had previously reported a major stable QTL controlling KNPS, qKnps-4A. In the current study, primary fine-mapping analysis, based on the primary mapping population, located qKnps-4A to an interval of approximately 6.8-Mb from 649.0 to 655.8 Mb on chromosome 4A refering to 'Kenong 9204' genome. Further fine-mapping analysis based on a secondary mapping population narrowed qKnps-4A to an approximately 2.19-Mb interval from 653.72 to 655.91 Mb. Transcriptome sequencing, gene function annotation analysis and homologous gene related reports showed that TraesKN4A01HG38570 and TraesKN4A01HG38590 were most likely to be candidate genes of qKnps-4A. Phenotypic analysis based on paired near-isogenic lines in the target region showed that qKnps-4A increased KNPS mainly by increasing the number of central florets per spike. We also evaluated the effects of qKnps-4A on other yield-related traits. Moreover, we dissected the QTL cluster of qKnps-4A and qTkw-4A and proved that the phenotypic effects were probably due to close linkage of two or more genes rather than pleiotropic effects of a single gene. This study provides molecular marker resource for wheat molecular breeding designed to improve yield potential, and lay the foundation for gene functional analysis of qKnps-4A.
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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
| | - Tianhang Ma
- 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
| | - Xinyao Shi
- 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
| | - Jiajia Cheng
- 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
| | - Chenyang Wang
- 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
| | - Shihui Li
- 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
| | - Guoqing Pan
- 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
| | - Yuxiang Guan
- 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 Zhang
- 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
| | - Shuang 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
| | - 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
| | - 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
| | - Ximei Li
- 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
- Shandong Key Laboratory of Dryland Farming Technology, Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, 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.
| | - Junming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, 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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11
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Backhaus AE, Griffiths C, Vergara-Cruces A, Simmonds J, Lee R, Morris RJ, Uauy C. Delayed development of basal spikelets in wheat explains their increased floret abortion and rudimentary nature. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5088-5103. [PMID: 37338600 PMCID: PMC10498016 DOI: 10.1093/jxb/erad233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/15/2023] [Indexed: 06/21/2023]
Abstract
Large differences exist in the number of grains per spikelet across an individual wheat (Triticum aestivum L.) spike. The central spikelets produce the highest number of grains, while apical and basal spikelets are less productive, and the most basal spikelets are commonly only developed in rudimentary form. Basal spikelets are delayed in initiation, yet they continue to develop and produce florets. The precise timing or the cause of their abortion remains largely unknown. Here, we investigated the underlying causes of basal spikelet abortion using shading applications in the field. We found that basal spikelet abortion is likely to be the consequence of complete floret abortion, as both occur concurrently and have the same response to shading treatments. We detected no differences in assimilate availability across the spike. Instead, we show that the reduced developmental age of basal florets pre-anthesis is strongly associated with their increased abortion. Using the developmental age pre-abortion, we were able to predict final grain set per spikelet across the spike, alongside the characteristic gradient in the number of grains from basal to central spikelets. Future efforts to improve spikelet homogeneity across the spike could thus focus on improving basal spikelet establishment and increasing floret development rates pre-abortion.
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Affiliation(s)
| | - Cara Griffiths
- Plant Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | | | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Rebecca Lee
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Richard J Morris
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
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12
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Wang Y, Zeng Z, Li J, Zhao D, Zhao Y, Peng C, Lan C, Wang C. Identification and validation of new quantitative trait loci for spike-related traits in two RIL populations. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:64. [PMID: 37533603 PMCID: PMC10390419 DOI: 10.1007/s11032-023-01401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/19/2023] [Indexed: 08/04/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important cereal crops for ensuring food security worldwide. Identification of major quantitative trait loci (QTL) for spike-related traits is important for improvement of yield potential in wheat breeding. In this study, by using the wheat 55K single nucleotide polymorphism (SNP) array and diversity array technology (DArT), two recombinant inbred line populations derived from crosses avocet/chilero and avocet/huites were used to map QTL for kernel number per spike (KNS), total spikelet number per spike (TSS), fertile spikelet number per spike (FSS), and spike compactness (SC). Forty-two QTLs were identified on chromosomes 2A (4), 2B (3), 3A (2), 3B (7), 5A (11), 6A (4), 6B, and 7A (10), explaining 3.13-21.80% of the phenotypic variances. Twelve QTLs were detected in multi-environments on chromosomes 2A, 3B (2), 5A (4), 6A (3), 6B, and 7A, while four QTL clusters were detected on chromosomes 3A, 3B, 5A, and 7A. Two stable and new QTL clusters, QKns/Tss/Fss/SC.haust-5A and QKns/Tss/Fss.haust-7A, were detected in the physical intervals of 547.49-590.46 Mb and 511.54-516.15 Mb, accounting for 7.53-14.78% and 7.01-20.66% of the phenotypic variances, respectively. High-confidence annotated genes for QKns/Tss/Fss/SC.haust-5A and QKns/Tss/Fss.haust-7A were more highly expressed in spike development. The results provide new QTL and molecular markers for marker-assisted breeding in wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01401-4.
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Affiliation(s)
- Yuying Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Zhankui Zeng
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Jiachuang Li
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Dehui Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Yue Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Chen Peng
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Caixia Lan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
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13
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Li Z, Hu Y, Ma X, Da L, She J, Liu Y, Yi X, Cao Y, Xu W, Jiao Y, Su Z. WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:324-336. [PMID: 35660007 PMCID: PMC10626052 DOI: 10.1016/j.gpb.2022.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 03/16/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks. Here, using large-scale transcriptome data, we constructed co-expression networks for diploid, tetraploid, and hexaploid wheat species, and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors, named WheatCENet. WheatCENet is a platform for searching and comparing specific functional co-expression networks, as well as identifying the related functions of the genes clustered therein. Functional annotations like pathways, gene families, protein-protein interactions, microRNAs (miRNAs), and several lines of epigenome data are integrated into this platform, and Gene Ontology (GO) annotation, gene set enrichment analysis (GSEA), motif identification, and other useful tools are also included. Using WheatCENet, we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION 1 (WAPO1) has more co-expressed genes related to spike development in hexaploid wheat than its progenitors. We also found a novel motif of CCWWWWWWGG (CArG) specifically in the promoter region of WAPO-A1, suggesting that neofunctionalization of the WAPO-A1 gene affects spikelet development in hexaploid wheat. WheatCENet is useful for investigating co-expression networks and conducting other analyses, and thus facilitates comparative and functional genomic studies in wheat. WheatCENet is freely available at http://bioinformatics.cpolar.cn/WheatCENet and http://bioinformatics.cau.edu.cn/WheatCENet.
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Affiliation(s)
- Zhongqiu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiheng Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lingling Da
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiajie She
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xin Yi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yaxin Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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14
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Slafer GA, Foulkes MJ, Reynolds MP, Murchie EH, Carmo-Silva E, Flavell R, Gwyn J, Sawkins M, Griffiths S. A 'wiring diagram' for sink strength traits impacting wheat yield potential. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:40-71. [PMID: 36334052 PMCID: PMC9786893 DOI: 10.1093/jxb/erac410] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/04/2022] [Indexed: 05/17/2023]
Abstract
Identifying traits for improving sink strength is a bottleneck to increasing wheat yield. The interacting processes determining sink strength and yield potential are reviewed and visualized in a set of 'wiring diagrams', covering critical phases of development (and summarizing known underlying genetics). Using this framework, we reviewed and assembled the main traits determining sink strength and identified research gaps and potential hypotheses to be tested for achieving gains in sink strength. In pre-anthesis, grain number could be increased through: (i) enhanced spike growth associated with optimized floret development and/or a reduction in specific stem-internode lengths and (ii) improved fruiting efficiency through an accelerated rate of floret development, improved partitioning between spikes, or optimized spike cytokinin levels. In post-anthesis, grain, sink strength could be augmented through manipulation of grain size potential via ovary size and/or endosperm cell division and expansion. Prospects for improving spike vascular architecture to support all rapidly growing florets, enabling the improved flow of assimilate, are also discussed. Finally, we considered the prospects for enhancing grain weight realization in relation to genetic variation in stay-green traits as well as stem carbohydrate remobilization. The wiring diagrams provide a potential workspace for breeders and crop scientists to achieve yield gains in wheat and other field crops.
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Affiliation(s)
| | | | - Matthew P Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico, El Batan, Texcoco, Mexico
| | - Erik H Murchie
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, UK
| | | | - Richard Flavell
- International Wheat Yield Partnership, 1500 Research Parkway, College Station, TX 77843, USA
| | - Jeff Gwyn
- International Wheat Yield Partnership, 1500 Research Parkway, College Station, TX 77843, USA
| | - Mark Sawkins
- International Wheat Yield Partnership, 1500 Research Parkway, College Station, TX 77843, USA
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Ln, Norwich NR4 7UH, UK
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15
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Biomolecular Strategies for Vascular Bundle Development to Improve Crop Yield. Biomolecules 2022; 12:biom12121772. [PMID: 36551200 PMCID: PMC9775962 DOI: 10.3390/biom12121772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
The need to produce crops with higher yields is critical due to a growing global population, depletion of agricultural land, and severe climate change. Compared with the "source" and "sink" transport systems that have been studied a lot, the development and utilization of vascular bundles (conducting vessels in plants) are increasingly important. Due to the complexity of the vascular system, its structure, and its delicate and deep position in the plant body, the current research on model plants remains basic knowledge and has not been repeated for crops and applied to field production. In this review, we aim to summarize the current knowledge regarding biomolecular strategies of vascular bundles in transport systems (source-flow-sink), allocation, helping crop architecture establishment, and influence of the external environment. It is expected to help understand how to use sophisticated and advancing genetic engineering technology to improve the vascular system of crops to increase yield.
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16
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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17
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Gill HS, Halder J, Zhang J, Rana A, Kleinjan J, Amand PS, Bernardo A, Bai G, Sehgal SK. Whole-genome analysis of hard winter wheat germplasm identifies genomic regions associated with spike and kernel traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2953-2967. [PMID: 35939073 DOI: 10.1007/s00122-022-04160-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Genetic dissection of yield component traits including spike and kernel characteristics is essential for the continuous improvement in wheat yield. Genome-wide association studies (GWAS) have been frequently used to identify genetic determinants for spike and kernel-related traits in wheat, though none have been employed in hard winter wheat (HWW) which represents a major class in US wheat acreage. Further, most of these studies relied on assembled diversity panels instead of adapted breeding lines, limiting the transferability of results to practical wheat breeding. Here we assembled a population of advanced/elite breeding lines and well-adapted cultivars and evaluated over four environments for phenotypic analysis of spike and kernel traits. GWAS identified 17 significant multi-environment marker-trait associations (MTAs) for various traits, representing 12 putative quantitative trait loci (QTLs), with five QTLs affecting multiple traits. Four of these QTLs mapped on three chromosomes 1A, 5B, and 7A for spike length, number of spikelets per spike (NSPS), and kernel length are likely novel. Further, a highly significant QTL was detected on chromosome 7AS that has not been previously associated with NSPS and putative candidate genes were identified in this region. The allelic frequencies of important quantitative trait nucleotides (QTNs) were deduced in a larger set of 1,124 accessions which revealed the importance of identified MTAs in the US HWW breeding programs. The results from this study could be directly used by the breeders to select the lines with favorable alleles for making crosses, and reported markers will facilitate marker-assisted selection of stable QTLs for yield components in wheat breeding.
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Affiliation(s)
- Harsimardeep S Gill
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jinfeng Zhang
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Anshul Rana
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jonathan Kleinjan
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Paul St Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
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18
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Wittern LM, Barrero JM, Bovill WD, Verbyla KL, Hughes T, Swain SM, Steed G, Webb AAR, Gardner K, Greenland A, Jacobs J, Frohberg C, Schmidt RC, Cavanagh C, Rohde A, Davey MW, Hannah MA. Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat. Sci Rep 2022; 12:14229. [PMID: 35987959 PMCID: PMC9392761 DOI: 10.1038/s41598-022-18614-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractTwo homoeologous QTLs for number of spikelets per spike (SPS) were mapped on chromosomes 7AL and 7BL using two wheat MAGIC populations. Sets of lines contrasting for the QTL on 7AL were developed which allowed for the validation and fine mapping of the 7AL QTL and for the identification of a previously described candidate gene, WHEAT ORTHOLOG OF APO1 (WAPO1). Using transgenic overexpression in both a low and a high SPS line, we provide a functional validation for the role of this gene in determining SPS also in hexaploid wheat. We show that the expression levels of this gene positively correlate with SPS in multiple MAGIC founder lines under field conditions as well as in transgenic lines grown in the greenhouse. This work highlights the potential use of WAPO1 in hexaploid wheat for further yield increases. The impact of WAPO1 and SPS on yield depends on other genetic and environmental factors, hence, will require a finely balanced expression level to avoid the development of detrimental pleiotropic phenotypes.
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19
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Geyer M, Mohler V, Hartl L. Genetics of the Inverse Relationship between Grain Yield and Grain Protein Content in Common Wheat. PLANTS 2022; 11:plants11162146. [PMID: 36015449 PMCID: PMC9413592 DOI: 10.3390/plants11162146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022]
Abstract
Grain protein content (GPC) is one of the most important criteria to determine the quality of common wheat (Triticum aestivum). One of the major obstacles for bread wheat production is the negative correlation between GPC and grain yield (GY). Previous studies demonstrated that the deviation from this inverse relationship is highly heritable. However, little is known about the genetics controlling these deviations in common wheat. To fill this gap, we performed quantitative trait locus (QTL) analysis for GY, GPC, and four derived GY-GPC indices using an eight-way multiparent advanced generation intercross population comprising 394 lines. Interval mapping was conducted using phenotypic data from up to nine environments and genotypic data from a 20k single-nucleotide polymorphism array. The four indices were highly heritable (0.76–0.88) and showed distinct correlations to GY and GPC. Interval mapping revealed that GY, GPC, and GY-GPC indices were controlled by 6, 12, and 12 unique QTL, of which each explained only a small amount of phenotypic variance (R2 ≤ 10%). Ten of the 12 index QTL were independent of loci affecting GY and GPC. QTL regions harboured several candidate genes, including Rht-1, WAPO-A1, TaTEF-7A, and NRT2.6-7A. The study confirmed the usefulness of indices to mitigate the inverse GY-GPC relationship in breeding, though the selection method should reflect their polygenic inheritance.
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20
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White J, Sharma R, Balding D, Cockram J, Mackay IJ. Genome-wide association mapping of Hagberg falling number, protein content, test weight, and grain yield in U.K. wheat. CROP SCIENCE 2022; 62:965-981. [PMID: 35915786 PMCID: PMC9314726 DOI: 10.1002/csc2.20692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Association mapping using crop cultivars allows identification of genetic loci of direct relevance to breeding. Here, 150 U.K. wheat (Triticum aestivum L.) cultivars genotyped with 23,288 single nucleotide polymorphisms (SNPs) were used for genome-wide association studies (GWAS) using historical phenotypic data for grain protein content, Hagberg falling number (HFN), test weight, and grain yield. Power calculations indicated experimental design would enable detection of quantitative trait loci (QTL) explaining ≥20% of the variation (PVE) at a relatively high power of >80%, falling to 40% for detection of a SNP with an R2 ≥ .5 with the same QTL. Genome-wide association studies identified marker-trait associations for all four traits. For HFN (h 2 = .89), six QTL were identified, including a major locus on chromosome 7B explaining 49% PVE and reducing HFN by 44 s. For protein content (h 2 = 0.86), 10 QTL were found on chromosomes 1A, 2A, 2B, 3A, 3B, and 6B, together explaining 48.9% PVE. For test weight, five QTL were identified (one on 1B and four on 3B; 26.3% PVE). Finally, 14 loci were identified for grain yield (h 2 = 0.95) on eight chromosomes (1A, 2A, 2B, 2D, 3A, 5B, 6A, 6B; 68.1% PVE), of which five were located within 16 Mbp of genetic regions previously identified as under breeder selection in European wheat. Our study demonstrates the utility of exploiting historical crop datasets, identifying genomic targets for independent validation, and ultimately for wheat genetic improvement.
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Affiliation(s)
- Jon White
- Genetics and Breeding Dep.NIAB93 Lawrence Weaver RoadCambridge, CB3 0LEUK
- Institute of GeneticsUniv. College LondonLondon, WC1E 6BTUK
| | - Rajiv Sharma
- Scotland's Rural College (SRUC)Kings Buildings, West Mains RoadEdinburgh, EH9 3JGUK
| | - David Balding
- Institute of GeneticsUniv. College LondonLondon, WC1E 6BTUK
- Current address: Melbourne Integrative GenomicsUniv. of MelbourneMelbourneAustralia
| | - James Cockram
- Genetics and Breeding Dep.NIAB93 Lawrence Weaver RoadCambridge, CB3 0LEUK
| | - Ian J. Mackay
- Scotland's Rural College (SRUC)Kings Buildings, West Mains RoadEdinburgh, EH9 3JGUK
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21
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Chen Z, Ke W, He F, Chai L, Cheng X, Xu H, Wang X, Du D, Zhao Y, Chen X, Xing J, Xin M, Guo W, Hu Z, Su Z, Liu J, Peng H, Yao Y, Sun Q, Ni Z. A single nucleotide deletion in the third exon of FT-D1 increases the spikelet number and delays heading date in wheat (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:920-933. [PMID: 34978137 PMCID: PMC9055817 DOI: 10.1111/pbi.13773] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/02/2021] [Accepted: 12/24/2021] [Indexed: 05/31/2023]
Abstract
The spikelet number and heading date are two crucial and correlated traits for yield in wheat. Here, a quantitative trait locus (QTL) analysis was conducted in F8 recombinant inbred lines (RILs) derived from crossing two common wheats with different spikelet numbers. A total of 15 stable QTL influencing total spikelet number (TSN) and heading date (HD) were detected. Notably, FT-D1, a well-known flowering time gene in wheat, was located within the finely mapped interval of a major QTL on 7DS (QTsn/Hd.cau-7D). A causal indel of one G in the third exon of FT-D1 was significantly associated with total spikelet number and heading date. Consistently, CRISPR/Cas9 mutant lines with homozygous mutations in FT-D1 displayed an increase in total spikelet number and heading date when compared with wild type. Moreover, one simple and robust marker developed according to the polymorphic site of FT-D1 revealed that this one G indel had been preferentially selected to adapt to different environments. Collectively, these data provide further insights into the genetic basis of spikelet number and heading date, and the diagnostic marker of FT-D1 will be useful for marker-assisted pyramiding in wheat breeding.
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Affiliation(s)
- Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Fei He
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJCIC‐MCPCIC‐MCPNanjing Agricultural UniversityNanjingChina
| | - Huanwen Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Dejie Du
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Yidi Zhao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Xiyong Chen
- Hebei Crop Genetic Breeding LaboratoryInstitute of Cereal and Oil CropsHebei Academy of Agriculture and Forestry SciencesShijiazhuangChina
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Zhenqi Su
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
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22
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Katz A, Byrne P, Reid S, Bratschun S, Haley S, Pearce S. Identification and validation of a QTL for spikelet number on chromosome arm 6BL of common wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:17. [PMID: 37309457 PMCID: PMC10248590 DOI: 10.1007/s11032-022-01288-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
To provide food security for a growing world population, it will be necessary to increase yields of staple crops such as wheat (Triticum aestivum L.). Yield is a complex, polygenic trait influenced by grain weight and number, which are negatively correlated with one another. Spikelet number is an important determinant of grain number, but allelic variants impacting its expression are often associated with heading date, constraining their use in wheat germplasm that must be adapted for specific environments. Identification and characterization of genetic variants affecting spikelet number will increase selection efficiency through their deployment in breeding programs. In this study, a quantitative trait locus (QTL) on chromosome arm 6BL for spikelet number was identified and validated using an association mapping panel, a recombinant inbred line population, and seven derived heterogeneous inbred families. The superior allele, QSn.csu-6Bb, was associated with an increase of 0.248 to 0.808 spikelets per spike across multiple environments that varied for mean spikelet number. Despite epistatic interactions between QSn.csu-6B and three other loci (WAPO-A1, VRN-D3, and PPD-B1), genotypes with a greater number of superior alleles at these loci consistently exhibit higher spikelet number. The frequency of superior alleles at these loci varies among winter wheat varieties adapted to different latitudes of the US Great Plains, revealing opportunities for breeders to select for increased spikelet number using simple molecular markers. This work lays the foundation for the positional cloning of the genetic variant underlying the QSn.csu-6B QTL to strengthen our understanding of spikelet number determination in wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01288-7.
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Affiliation(s)
- Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Patrick Byrne
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Scott Reid
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Sarah Bratschun
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Scott Haley
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
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23
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Qiao L, Li H, Wang J, Zhao J, Zheng X, Wu B, Du W, Wang J, Zheng J. Analysis of Genetic Regions Related to Field Grain Number per Spike From Chinese Wheat Founder Parent Linfen 5064. FRONTIERS IN PLANT SCIENCE 2022; 12:808136. [PMID: 35069666 PMCID: PMC8769526 DOI: 10.3389/fpls.2021.808136] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Wheat founder parents have been important in the development of new wheat cultivars. Understanding the effects of specific genome regions on yield-related traits in founder variety derivatives can enable more efficient use of these genetic resources through molecular breeding. In this study, the genetic regions related to field grain number per spike (GNS) from the founder parent Linfen 5064 were analyzed using a doubled haploid (DH) population developed from a cross between Linfen 5064 and Nongda 3338. Quantitative trait loci (QTL) for five spike-related traits over nine experimental locations/years were identified, namely, total spikelet number per spike (TSS), base sterile spikelet number per spike (BSSS), top sterile spikelet number per spike (TSSS), fertile spikelet number per spike (FSS), and GNS. A total of 13 stable QTL explaining 3.91-19.51% of the phenotypic variation were found. The effect of six of these QTL, Qtss.saw-2B.1, Qtss.saw-2B.2, Qtss.saw-3B, Qfss.saw-2B.2, Qbsss.saw-5A.1, and Qgns.saw-1A, were verified by another DH population (Linfen 5064/Jinmai 47), which showed extreme significance (P < 0.05) in more than three environments. No homologs of reported grain number-related from grass species were found in the physical regions of Qtss.saw-2B.1 and Qtss.saw-3B, that indicating both of them are novel QTL, or possess novel-related genes. The positive alleles of Qtss.saw-2B.2 from Linfen 5064 have the larger effect on TSS (3.30%, 0.62) and have 66.89% in Chinese cultivars under long-term artificial selection. This study revealed three key regions for GNS in Linfen 5064 and provides insights into molecular marker-assisted breeding.
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Affiliation(s)
- Ling Qiao
- College of Agronomy, State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong, China
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Hanlin Li
- College of Agronomy, State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong, China
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jie Wang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bangbang Wu
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Weijun Du
- College of Agronomy, State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong, China
| | - Juanling Wang
- College of Agronomy, State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
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24
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Kong X, Wang F, Geng S, Guan J, Tao S, Jia M, Sun G, Wang Z, Wang K, Ye X, Ma J, Liu D, Wei Y, Zheng Y, Fu X, Mao L, Lan X, Li A. The wheat AGL6-like MADS-box gene is a master regulator for floral organ identity and a target for spikelet meristem development manipulation. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:75-88. [PMID: 34487615 PMCID: PMC8710900 DOI: 10.1111/pbi.13696] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/22/2021] [Indexed: 05/13/2023]
Abstract
The AGAMOUS-LIKE6 (AGL6)-like genes are ancient MADS-box genes and are functionally studied in a few model plants. The knowledge of these genes in wheat remains limited. Here, by studying a 'double homoeolog mutant' of the AGL6 gene in tetraploid wheat, we showed that AGL6 was required for the development of all four whorls of floral organs with dosage-dependent effect on floret fertility. Yeast two-hybrid analyses detected interactions of AGL6 with all classes of MADS-box proteins in the ABCDE model for floral organ development. AGL6 was found to interact with several additional proteins, including the G protein β and γ (DEP1) subunits. Analysis of the DEP1-B mutant showed a significant reduction in spikelet number per spike in tetraploid wheat, while overexpression of AGL6 in common wheat increased the spikelet number per spike and hence the grain number per spike. RNA-seq analysis identified the regulation of several meristem activity genes by AGL6, such as FUL2 and TaMADS55. Our work therefore extensively updated the wheat ABCDE model and proposed an alternative approach to improve wheat grain yield by manipulating the AGL6 gene.
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Affiliation(s)
- Xingchen Kong
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Fang Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Jiantao Guan
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Shu Tao
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Meiling Jia
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Guoliang Sun
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Zhenyu Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Ke Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xingguo Ye
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Jian Ma
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Dengcai Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yuming Wei
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Youliang Zheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xiangdong Fu
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xiujin Lan
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
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25
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Kuzay S, Lin H, Li C, Chen S, Woods DP, Zhang J, Lan T, von Korff M, Dubcovsky J. WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat. PLoS Genet 2022; 18:e1009747. [PMID: 35025863 PMCID: PMC8791482 DOI: 10.1371/journal.pgen.1009747] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/26/2022] [Accepted: 12/18/2021] [Indexed: 01/08/2023] Open
Abstract
Improving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high-resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 (WAPO-A1) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Results from this and our previous study show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheat varieties but is rare in durum wheat, where it might be particularly useful to improve grain yield.
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Affiliation(s)
- Saarah Kuzay
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Huiqiong Lin
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Chengxia Li
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Shisheng Chen
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| | - Daniel P. Woods
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Tianyu Lan
- Institute for Plant Genetics, Heinrich Heine University, Duesseldorf, Germany
| | - Maria von Korff
- Institute for Plant Genetics, Heinrich Heine University, Duesseldorf, Germany
- Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow’s Needs”, Heinrich Heine University, Duesseldorf, Germany
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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26
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Saini DK, Chopra Y, Singh J, Sandhu KS, Kumar A, Bazzer S, Srivastava P. Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:1. [PMID: 37309486 PMCID: PMC10248672 DOI: 10.1007/s11032-021-01272-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.
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Affiliation(s)
- Dinesh K. Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
| | - Anand Kumar
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, 202002 India
| | - Sumandeep Bazzer
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
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Mizuno N, Ishikawa G, Kojima H, Tougou M, Kiribuchi-Otobe C, Fujita M, Nakamura K. Genetic mechanisms determining grain number distribution along the spike and their effect on yield components in wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:62. [PMID: 37309314 PMCID: PMC10236116 DOI: 10.1007/s11032-021-01255-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/28/2021] [Indexed: 06/14/2023]
Abstract
The number of wheat grains is one of the major determinants of yield. Many quantitative trait loci (QTLs) and some causal genes such as GNI-A1 and WAPO-A1 that are associated with grain number per spike (GNS) have been identified, but the underlying mechanisms remain largely unknown. We analyzed QTLs for grain number and other related traits using 188 doubled haploid lines derived from the Japanese high-yield variety, Kitahonami, as a parent to elucidate the genetic mechanism determining grain number. The major QTLs for grain number at the apical, central, and basal parts of the spike were identified in different chromosomal regions. We considered GNI-A1 and WAPO-A1 as candidate genes controlling grain number at the central and basal parts of the spike, respectively. Kitahonami had the favorable 105Y allele of GNI-A1 and WAPO-A1b allele and unfavorable alleles of QTLs for grain number at the apical part of spikes. Pyramiding the favorable alleles of these QTLs significantly increased GNS without significantly reducing thousand-grain weight (TGW). In contrast, the accumulation of favorable alleles of QTLs for TGW significantly decreased GNS, whereas days to heading positively correlated with GNS. Late heading increased the spikelet number per spike, resulting in a higher GNS. Pyramiding of the QTLs for TGW and days to heading also altered the GNS. In conclusion, GNS is a complex trait controlled by many QTLs, and it is essential for breeding to design. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01255-8.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
| | - Hisayo Kojima
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
- Present Address: Headquarters, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8517 Japan
| | - Makoto Tougou
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
| | - Chikako Kiribuchi-Otobe
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
| | - Masaya Fujita
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518 Japan
- Present Address: Headquarters, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8517 Japan
| | - Kazuhiro Nakamura
- Present Address: Headquarters, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8517 Japan
- Present Address: Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka 833-0041 Japan
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Kaur B, Sandhu KS, Kamal R, Kaur K, Singh J, Röder MS, Muqaddasi QH. Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PLANTS 2021; 10:plants10101989. [PMID: 34685799 PMCID: PMC8541486 DOI: 10.3390/plants10101989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.
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Affiliation(s)
- Balwinder Kaur
- Everglades Research and Education Center, University of Florida, 3200 E. Palm Beach Rd., Belle Glade, FL 33430, USA;
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Kawalpreet Kaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
- Correspondence: or
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29
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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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30
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Corsi B, Obinu L, Zanella CM, Cutrupi S, Day R, Geyer M, Lillemo M, Lin M, Mazza L, Percival-Alwyn L, Stadlmeier M, Mohler V, Hartl L, Cockram J. Identification of eight QTL controlling multiple yield components in a German multi-parental wheat population, including Rht24, WAPO-A1, WAPO-B1 and genetic loci on chromosomes 5A and 6A. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1435-1454. [PMID: 33712876 PMCID: PMC8081691 DOI: 10.1007/s00122-021-03781-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/20/2021] [Indexed: 05/26/2023]
Abstract
KEY MESSAGE Quantitative trait locus (QTL) mapping of 15 yield component traits in a German multi-founder population identified eight QTL each controlling ≥2 phenotypes, including the genetic loci Rht24, WAPO-A1 and WAPO-B1. Grain yield in wheat (Triticum aestivum L.) is a polygenic trait representing the culmination of many developmental processes and their interactions with the environment. Toward maintaining genetic gains in yield potential, 'reductionist approaches' are commonly undertaken by which the genetic control of yield components, that collectively determine yield, are established. Here we use an eight-founder German multi-parental wheat population to investigate the genetic control and phenotypic trade-offs between 15 yield components. Increased grains per ear was significantly positively correlated with the number of fertile spikelets per ear and negatively correlated with the number of infertile spikelets. However, as increased grain number and fertile spikelet number per ear were significantly negatively correlated with thousand grain weight, sink strength limitations were evident. Genetic mapping identified 34 replicated quantitative trait loci (QTL) at two or more test environments, of which 24 resolved into eight loci each controlling two or more traits-termed here 'multi-trait QTL' (MT-QTL). These included MT-QTL associated with previously cloned genes controlling semi-dwarf plant stature, and with the genetic locus Reduced height 24 (Rht24) that further modulates plant height. Additionally, MT-QTL controlling spikelet number traits were located to chromosome 7A encompassing the gene WHEAT ORTHOLOG OF APO1 (WAPO-A1), and to its homoeologous location on chromosome 7B containing WAPO-B1. The genetic loci identified in this study, particularly those that potentially control multiple yield components, provide future opportunities for the targeted investigation of their underlying genes, gene networks and phenotypic trade-offs, in order to underpin further genetic gains in yield.
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Affiliation(s)
| | - Lia Obinu
- Department of Agriculture, University of Sassari, Viale Italia, 07100, Sassari, Italy
| | | | | | - Rob Day
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - Morten Lillemo
- Norwegian University of Life Sciences (NMBU), P.O. Box 5003, NO-1432, Ås, Norway
| | - Min Lin
- Norwegian University of Life Sciences (NMBU), P.O. Box 5003, NO-1432, Ås, Norway
| | | | | | - Melanie Stadlmeier
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
- Saatzucht Donau GesmbH and Co KG, Mendelweg 1, 4981, Reichersberg, Austria
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
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31
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Wang C, Yang X, Li G. Molecular Insights into Inflorescence Meristem Specification for Yield Potential in Cereal Crops. Int J Mol Sci 2021; 22:3508. [PMID: 33805287 PMCID: PMC8037405 DOI: 10.3390/ijms22073508] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
Flowering plants develop new organs throughout their life cycle. The vegetative shoot apical meristem (SAM) generates leaf whorls, branches and stems, whereas the reproductive SAM, called the inflorescence meristem (IM), forms florets arranged on a stem or an axis. In cereal crops, the inflorescence producing grains from fertilized florets makes the major yield contribution, which is determined by the numbers and structures of branches, spikelets and florets within the inflorescence. The developmental progression largely depends on the activity of IM. The proper regulations of IM size, specification and termination are outcomes of complex interactions between promoting and restricting factors/signals. Here, we focus on recent advances in molecular mechanisms underlying potential pathways of IM identification, maintenance and differentiation in cereal crops, including rice (Oryza sativa), maize (Zea mays), wheat (Triticum aestivum), and barley (Hordeum vulgare), highlighting the researches that have facilitated grain yield by, for example, modifying the number of inflorescence branches. Combinatorial functions of key regulators and crosstalk in IM determinacy and specification are summarized. This review delivers the knowledge to crop breeding applications aiming to the improvements in yield performance and productivity.
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Affiliation(s)
- Chengyu Wang
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
| | - Xiujuan Yang
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Campus, The University of Adelaide, Glen Osmond, SA 5064, Australia;
| | - Gang Li
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Campus, The University of Adelaide, Glen Osmond, SA 5064, Australia;
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32
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Muqaddasi QH, Kamal R, Mirdita V, Rodemann B, Ganal MW, Reif JC, Röder MS. Genome-Wide Association Studies and Prediction of Tan Spot ( Pyrenophora tritici-repentis) Infection in European Winter Wheat via Different Marker Platforms. Genes (Basel) 2021; 12:genes12040490. [PMID: 33801723 PMCID: PMC8103242 DOI: 10.3390/genes12040490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/17/2021] [Accepted: 03/25/2021] [Indexed: 11/22/2022] Open
Abstract
Tan spot, caused by the fungus Pyrenophoratritici-repentis (Ptr), is a severe foliar disease of wheat (Triticumaestivum L.). Improving genetic resistance is a durable strategy to reduce Ptr-related losses. Here, we dissected Ptr-infection’s genetic basis in 372 European wheat varieties via simple sequence repeats (SSRs) plus 35k and 90k single nucleotide polymorphism (SNP) marker platforms. In our phenotypic data analyses, Ptr infection showed a significant genotypic variance and a significant negative correlation with plant height. Genome-wide association studies revealed a highly quantitative nature of Ptr infection and identified two quantitative trait loci (QTL), viz., QTs.ipk-7A and QTs.ipk-7B, which imparted 21.23 and 5.84% of the genotypic variance, respectively. Besides, the Rht-D1 gene showed a strong allelic influence on the infection scores. Due to the complex genetic nature of the Ptr infection, the potential of genome-wide prediction (GP) was assessed via three different genetic models on individual and combined marker platforms. The GP results indicated that the marker density and marker platforms do not considerably impact prediction accuracy (~40–42%) and that higher-order epistatic interactions may not be highly pervasive. Our results provide a further understanding of Ptr-infection’s genetic nature, serve as a resource for marker-assisted breeding, and highlight the potential of genome-wide selection for improved Ptr resistance.
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Affiliation(s)
- Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, Germany; (R.K.); (J.C.R.); (M.S.R.)
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, D-06466 Stadt Seeland OT Gatersleben, Germany;
- Correspondence:
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, Germany; (R.K.); (J.C.R.); (M.S.R.)
| | - Vilson Mirdita
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, D-06466 Stadt Seeland OT Gatersleben, Germany;
| | - Bernd Rodemann
- Julius-Kühn-Institute (JKI), D-38104 Braunschweig, Germany;
| | - Martin W. Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, D-06466 Stadt Seeland OT Gatersleben, Germany;
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, Germany; (R.K.); (J.C.R.); (M.S.R.)
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, Germany; (R.K.); (J.C.R.); (M.S.R.)
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33
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Gao L, Meng C, Yi T, Xu K, Cao H, Zhang S, Yang X, Zhao Y. Genome-wide association study reveals the genetic basis of yield- and quality-related traits in wheat. BMC PLANT BIOLOGY 2021; 21:144. [PMID: 33740889 PMCID: PMC7980635 DOI: 10.1186/s12870-021-02925-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/11/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Identifying the loci and dissecting the genetic architecture underlying wheat yield- and quality-related traits are essential for wheat breeding. A genome-wide association study was conducted using a high-density 90 K SNP array to analyze the yield- and quality-related traits of 543 bread wheat varieties. RESULTS A total of 11,140 polymorphic SNPs were distributed on 21 chromosomes, including 270 significant SNPs associated with 25 yield- and quality-related traits. Additionally, 638 putative candidate genes were detected near the significant SNPs based on BLUP data, including three (TraesCS7A01G482000, TraesCS4B01G343700, and TraesCS6B01G295400) related to spikelet number per spike, diameter of the first internode, and grain volume. The three candidate genes were further analyzed using stage- and tissue- specific gene expression data derived from an RNA-seq analysis. These genes are promising candidates for enhancing yield- and quality-related traits in wheat. CONCLUSIONS The results of this study provide a new insight to understand the genetic basis of wheat yield and quality. Furthermore, the markers detected in this study may be applicable for marker-assisted selection in wheat breeding programs.
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Affiliation(s)
- Le Gao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Chengsheng Meng
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Tengfei Yi
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Ke Xu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Huiwen Cao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Shuhua Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Xueju Yang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000, Hebei, China.
| | - Yong Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000, Hebei, China.
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Brassac J, Muqaddasi QH, Plieske J, Ganal MW, Röder MS. Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike. Sci Rep 2021; 11:1585. [PMID: 33452357 PMCID: PMC7811022 DOI: 10.1038/s41598-020-80473-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/17/2020] [Indexed: 11/21/2022] Open
Abstract
Total spikelet number per spike (TSN) is a major component of spike architecture in wheat (Triticumaestivum L.). A major and consistent quantitative trait locus (QTL) was discovered for TSN in a doubled haploid spring wheat population grown in the field over 4 years. The QTL on chromosome 7B explained up to 20.5% of phenotypic variance. In its physical interval (7B: 6.37–21.67 Mb), the gene FLOWERINGLOCUST (FT-B1) emerged as candidate for the observed effect. In one of the parental lines, FT-B1 carried a non-synonymous substitution on position 19 of the coding sequence. This mutation modifying an aspartic acid (D) into a histidine (H) occurred in a highly conserved position. The mutation was observed with a frequency of ca. 68% in a set of 135 hexaploid wheat varieties and landraces, while it was not found in other plant species. FT-B1 only showed a minor effect on heading and flowering time (FT) which were dominated by a major QTL on chromosome 5A caused by segregation of the vernalization gene VRN-A1. Individuals carrying the FT-B1 allele with amino acid histidine had, on average, a higher number of spikelets (15.1) than individuals with the aspartic acid allele (14.3) independent of their VRN-A1 allele. We show that the effect of TSN is not mainly related to flowering time; however, the duration of pre-anthesis phases may play a major role.
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Affiliation(s)
- Jonathan Brassac
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr 3, 06466, Stadt Seeland OT Gatersleben, Germany.
| | - Quddoos H Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr 3, 06466, Stadt Seeland OT Gatersleben, Germany.,European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Jörg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr 3, 06466, Stadt Seeland OT Gatersleben, Germany
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35
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Nyine M, Adhikari E, Clinesmith M, Aiken R, Betzen B, Wang W, Davidson D, Yu Z, Guo Y, He F, Akhunova A, Jordan KW, Fritz AK, Akhunov E. The Haplotype-Based Analysis of Aegilops tauschii Introgression Into Hard Red Winter Wheat and Its Impact on Productivity Traits. FRONTIERS IN PLANT SCIENCE 2021; 12:716955. [PMID: 34484280 PMCID: PMC8416154 DOI: 10.3389/fpls.2021.716955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/20/2021] [Indexed: 05/13/2023]
Abstract
The introgression from wild relatives have a great potential to broaden the availability of beneficial allelic diversity for crop improvement in breeding programs. Here, we assessed the impact of the introgression from 21 diverse accessions of Aegilops tauschii, the diploid ancestor of the wheat D genome, into 6 hard red winter wheat cultivars on yield and yield component traits. We used 5.2 million imputed D genome SNPs identified by the whole-genome sequencing of parental lines and the sequence-based genotyping of introgression population, including 351 BC1F3:5 lines. Phenotyping data collected from the irrigated and non-irrigated field trials revealed that up to 23% of the introgression lines (ILs) produce more grain than the parents and check cultivars. Based on 16 yield stability statistics, the yield of 12 ILs (3.4%) was stable across treatments, years, and locations; 5 of these lines were also high yielding lines, producing 9.8% more grain than the average yield of check cultivars. The most significant SNP- and haplotype-trait associations were identified on chromosome arms 2DS and 6DL for the spikelet number per spike (SNS), on chromosome arms 2DS, 3DS, 5DS, and 7DS for grain length (GL) and on chromosome arms 1DL, 2DS, 6DL, and 7DS for grain width (GW). The introgression of haplotypes from A. tauschii parents was associated with an increase in SNS, which was positively correlated with a heading date (HD), whereas the haplotypes from hexaploid wheat parents were associated with an increase in GW. We show that the haplotypes on 2DS associated with an increase in the spikelet number and HD are linked with multiple introgressed alleles of Ppd-D1 identified by the whole-genome sequencing of A. tauschii parents. Meanwhile, some introgressed haplotypes exhibited significant pleiotropic effects with the direction of effects on the yield component traits being largely consistent with the previously reported trade-offs, there were haplotype combinations associated with the positive trends in yield. The characterized repertoire of the introgressed haplotypes derived from A. tauschii accessions with the combined positive effects on yield and yield component traits in elite germplasm provides a valuable source of alleles for improving the productivity of winter wheat by optimizing the contribution of component traits to yield.
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Affiliation(s)
- Moses Nyine
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Elina Adhikari
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Marshall Clinesmith
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Robert Aiken
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Bliss Betzen
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Wei Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Dwight Davidson
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Zitong Yu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Yuanwen Guo
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Alina Akhunova
- Integrated Genomics Facility, Kansas State University, Manhattan, KS, United States
| | - Katherine W. Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- United States Department of Agriculture, Agricultural Research Service Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Allan K. Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- *Correspondence: Eduard Akhunov
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36
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Lin Y, Zhou K, Hu H, Jiang X, Yu S, Wang Q, Li C, Ma J, Chen G, Yang Z, Liu Y. Multi-Locus Genome-Wide Association Study of Four Yield-Related Traits in Chinese Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2021; 12:665122. [PMID: 34484253 PMCID: PMC8415402 DOI: 10.3389/fpls.2021.665122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/20/2021] [Indexed: 05/13/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important crops in the world. Here, four yield-related traits, namely, spike length, spikelets number, tillers number, and thousand-kernel weight, were evaluated in 272 Chinese wheat landraces in multiple environments. Five multi-locus genome-wide association studies (FASTmrEMMA, ISIS EN-BLASSO, mrMLM, pKWmEB, and pLARmEB) were performed using 172,711 single-nucleotide polymorphisms (SNPs) to identify yield-related quantitative trait loci (QTL). A total of 27 robust QTL were identified by more than three models. Nine of these QTL were consistent with those in previous studies. The remaining 18 QTL may be novel. We identified a major QTL, QTkw.sicau-4B, with up to 18.78% of phenotypic variation explained. The developed kompetitive allele-specific polymerase chain reaction marker for QTkw.sicau-4B was validated in two recombinant inbred line populations with an average phenotypic difference of 16.07%. After combined homologous function annotation and expression analysis, TraesCS4B01G272300 was the most likely candidate gene for QTkw.sicau-4B. Our findings provide new insights into the genetic basis of yield-related traits and offer valuable QTL to breed wheat cultivars via marker-assisted selection.
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Affiliation(s)
- Yu Lin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kunyu Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haiyan Hu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaojun Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shifan Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Zisong Yang
- College of Resources and Environment, Aba Teachers University, Wenchuan, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Yaxi Liu, , orcid.org/0000-0001-6814-7218
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37
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Muqaddasi QH, Brassac J, Ebmeyer E, Kollers S, Korzun V, Argillier O, Stiewe G, Plieske J, Ganal MW, Röder MS. Prospects of GWAS and predictive breeding for European winter wheat's grain protein content, grain starch content, and grain hardness. Sci Rep 2020; 10:12541. [PMID: 32719416 PMCID: PMC7385145 DOI: 10.1038/s41598-020-69381-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023] Open
Abstract
Grain quality traits determine the classification of registered wheat (Triticum aestivum L.) varieties. Although environmental factors and crop management practices exert a considerable influence on wheat quality traits, a significant proportion of the variance is attributed to the genetic factors. To identify the underlying genetic factors of wheat quality parameters viz., grain protein content (GPC), grain starch content (GSC), and grain hardness (GH), we evaluated 372 diverse European wheat varieties in replicated field trials in up to eight environments. We observed that all of the investigated traits hold a wide and significant genetic variation, and a significant negative correlation exists between GPC and GSC plus grain yield. Our association analyses based on 26,694 high-quality single nucleotide polymorphic markers revealed a strong quantitative genetic nature of GPC and GSC with associations on groups 2, 3, and 6 chromosomes. The identification of known Puroindoline-b gene for GH provided a positive analytic proof for our studies. We report that a locus QGpc.ipk-6A controls both GPC and GSC with opposite allelic effects. Based on wheat's reference and pan-genome sequences, the physical characterization of two loci viz., QGpc.ipk-2B and QGpc.ipk-6A facilitated the identification of the candidate genes for GPC. Furthermore, by exploiting additive and epistatic interactions of loci, we evaluated the prospects of predictive breeding for the investigated traits that suggested its efficient use in the breeding programs.
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Affiliation(s)
- Quddoos H Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany.
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany.
| | - Jonathan Brassac
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | | | | | | | | | - Gunther Stiewe
- Syngenta Seeds GmbH, 32107, Bad Salzuflen, Germany
- SaKa Beteiligungsgesellschaft mbH, Albert-Einstein-Ring 5, 22761, Hamburg, Germany
| | - Jörg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
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38
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Cao S, Xu D, Hanif M, Xia X, He Z. Genetic architecture underpinning yield component traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1811-1823. [PMID: 32062676 DOI: 10.1007/s00122-020-03562-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/06/2020] [Indexed: 05/19/2023]
Abstract
Genetic atlas, reliable QTL and candidate genes of yield component traits in wheat were figured out, laying concrete foundations for map-based gene cloning and dissection of regulatory mechanisms underlying yield. Mining genetic loci for yield is challenging due to the polygenic nature, large influence of environment and complex relationship among yield component traits (YCT). Many genetic loci related to wheat yield have been identified, but its genetic architecture and key genetic loci for selection are largely unknown. Wheat yield potential can be determined by three YCT, thousand kernel weight, kernel number per spike and spike number. Here, we summarized the genetic loci underpinning YCT from QTL mapping, association analysis and homology-based gene cloning. The major loci determining yield-associated agronomic traits, such as flowering time and plant height, were also included in comparative analyses with those for YCT. We integrated yield-related genetic loci onto chromosomes based on their physical locations. To identify the major stable loci for YCT, 58 QTL-rich clusters (QRC) were defined based on their distribution on chromosomes. Candidate genes in each QRC were predicted according to gene annotation of the wheat reference genome and previous information on validation of those genes in other species. Finally, a technological route was proposed to take full advantage of the resultant resources for gene cloning, molecular marker-assisted breeding and dissection of molecular regulatory mechanisms underlying wheat yield.
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Affiliation(s)
- Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Mamoona Hanif
- 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
| | - 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), c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
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Chen Z, Cheng X, Chai L, Wang Z, Du D, Wang Z, Bian R, Zhao A, Xin M, Guo W, Hu Z, Peng H, Yao Y, Sun Q, Ni Z. Pleiotropic QTL influencing spikelet number and heading date in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1825-1838. [PMID: 32016554 DOI: 10.1007/s00122-020-03556-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/24/2020] [Indexed: 05/23/2023]
Abstract
Three pleiotropic QTL regions associated with spikelet number and heading date were identified, with FT-A1 considered the candidate gene for QTspn/Hd.cau-7A. Spikelet number traits and heading date (HD) play key roles in yield improvement of wheat and its wide adaptation to different environments. Here, we used a Recombinant Inbred Lines population derived from a cross between Yi5029 (5029) and Nongda4332 (4332) to construct a high-density genetic linkage map and identify quantitative trait loci (QTL) associated with total spikelet number per spike (TSPN), fertile spikelet number per spike (FSPN), sterile spikelet number per spike (SSPN) and HD. A total of 22 environmentally stable QTL for TSPN, FSPN, SSPN and HD were identified. Notably, three pleiotropic QTL regions for TSPN and HD were detected on chromosomes 2A, 7A and 7D. The QTL associated with TSPN and HD on chromosome 7AS was designated QTspn/Hd.cau-7A. Furthermore, the candidate gene FT-A1 located in the region of QTspn/Hd.cau-7A had a single-nucleotide polymorphism (T-G) within the third exon, which might be the cause of diversity in spikelet number and HD between the two parents. Additionally, we developed a semi-thermal asymmetric reverse PCR (STARP) marker to analyze the geographical distribution and evolution of FT-A1 (T or G) alleles. This study contributes to our understanding of the molecular mechanisms of the four traits (TSPN, FSPN, SSPN and HD) and provides further insights into the genetic relationship between spikelet number traits and HD in wheat.
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Affiliation(s)
- Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Xuejiao Cheng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zihao Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Dejie Du
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhihui Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Ruolin Bian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
- National Plant Gene Research Centre, Beijing, 100193, China.
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40
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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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