{"title":"Candidate gene analysis of rice grain shape based on genome-wide association study.","authors":"Wei Xin, Ning Chen, Jiaqi Wang, Yilei Liu, Yifeng Sun, Baojia Han, Xinghua Wang, Zijie Liu, Hualong Liu, Hongliang Zheng, Luomiao Yang, Detang Zou, Jingguo Wang","doi":"10.1007/s00122-024-04724-8","DOIUrl":null,"url":null,"abstract":"<p><strong>Key message: </strong>Thirteen QTLs associated with rice grain shape were localized by genome-wide association study. LOC_Os01g74020, the putative candidate gene in the co-localized QTL-qGSE1.2 interval, was identified and validated. Grain shape (GS) is a key trait that affects yield and quality of rice. Identifying and analyzing GS-related genes and elucidating the physiological, biochemical and molecular mechanisms are important for rice breeding. In this study, genome-wide association studies (GWAS) were conducted based on 1, 795, 076 single-nucleotide polymorphisms (SNPs) and three GS-related traits, grain length (GL), grain width (GW) and thousand-grain weight (TGW), in a natural population which comprised 374 rice varieties. A total of 13 quantitative trait locus (QTLs) related to GL, GW and TGW were identified, respectively, of which two QTLs (qGSE1.2 and qGSE5.3) were associated with both GL and TGW. A known key GS regulatory gene, GW5, was present in the interval of qGSE5.3. Based on the qRT-PCR results, LOC_Os01g74020 (OsGSE1.2) was identified as a GS candidate gene. Functional analysis of OsGSE1.2 showed that glume cell width and GW were significantly reduced, and that glume cell length, GL, TGW and single-plant yield were significantly increased in OsGSE1.2 knockout lines than those of wild type. OsGSE1.2 affects rice grain length by suppressing the elongation of glume cell and is a novel GS regulatory gene. These findings laid the foundation for molecular breeding to improve rice GS and increase rice yield and profitability.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 10","pages":"241"},"PeriodicalIF":4.4000,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Theoretical and Applied Genetics","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1007/s00122-024-04724-8","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRONOMY","Score":null,"Total":0}
引用次数: 0
Abstract
Key message: Thirteen QTLs associated with rice grain shape were localized by genome-wide association study. LOC_Os01g74020, the putative candidate gene in the co-localized QTL-qGSE1.2 interval, was identified and validated. Grain shape (GS) is a key trait that affects yield and quality of rice. Identifying and analyzing GS-related genes and elucidating the physiological, biochemical and molecular mechanisms are important for rice breeding. In this study, genome-wide association studies (GWAS) were conducted based on 1, 795, 076 single-nucleotide polymorphisms (SNPs) and three GS-related traits, grain length (GL), grain width (GW) and thousand-grain weight (TGW), in a natural population which comprised 374 rice varieties. A total of 13 quantitative trait locus (QTLs) related to GL, GW and TGW were identified, respectively, of which two QTLs (qGSE1.2 and qGSE5.3) were associated with both GL and TGW. A known key GS regulatory gene, GW5, was present in the interval of qGSE5.3. Based on the qRT-PCR results, LOC_Os01g74020 (OsGSE1.2) was identified as a GS candidate gene. Functional analysis of OsGSE1.2 showed that glume cell width and GW were significantly reduced, and that glume cell length, GL, TGW and single-plant yield were significantly increased in OsGSE1.2 knockout lines than those of wild type. OsGSE1.2 affects rice grain length by suppressing the elongation of glume cell and is a novel GS regulatory gene. These findings laid the foundation for molecular breeding to improve rice GS and increase rice yield and profitability.
期刊介绍:
Theoretical and Applied Genetics publishes original research and review articles in all key areas of modern plant genetics, plant genomics and plant biotechnology. All work needs to have a clear genetic component and significant impact on plant breeding. Theoretical considerations are only accepted in combination with new experimental data and/or if they indicate a relevant application in plant genetics or breeding. Emphasizing the practical, the journal focuses on research into leading crop plants and articles presenting innovative approaches.