Genome-Wide Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice

作     者：LV Yang WANG Yueying Noushin JAHAN HU Haitao CHEN Ping SHANG Lianguang LIN Haiyan DONG Guojun HU Jiang GAO Zhenyu QIAN Qian ZHANG Yu GUO Longbiao 

作者机构：State Key Lab for Rice Biology China National Rice Research Institute Hangzhou 310006 China Tobacoo Research Institute Chinese Academy of Agricultural Sciences Qingdao 266101 China 

出 版 物：《Rice science》 (水稻科学（英文版）)

年 卷 期：2019年第26卷第6期

页      面：384-392页

核心收录：

学科分类：09[农学] 

基　　金：supported by the Natural Science Foundation of China(Grant Nos.31461143014,31771778 and 31801336) the National Key Research and Development Program of China(Grant No.2016YFD0100902-07) the China Postdoctoral Science Foundation(Grant No.2018M641556) the Zhejiang Provincial Natural Science Foundation of China(Grant No.LGN19C130006) 

主　　题：candidate gene grain shape genome-wide association study haplotype rice single nucleotide polymorphism 

摘      要：Excavating single nucleotide polymorphisms (SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study (GWAS) can provide a theoretical basis for discovery and utilization of excellent genetic resources in rice. Based on 16 352 SNPs, 161 natural indica rice varieties with various grain sizes in southern China were used for GWAS of grain shape-related traits, referring to grain length (GL), grain width (GW), 1000-grain weight (TGW), and grain length/width (GLW). Phenotypic statistics showed that coefficient of variation values for these four traits GL, GW, TGW and GLW were 9.92%, 9.09%, 20.20% and 16.38%, respectively. Each trait showed a normal distribution, and there was a certain correlation between these traits. Through general linear model correlation analysis, a total of 38 significant loci were identified, and a range of 100 kb upstream and downstream of the significant loci was identified as the candidate interval. On chromosome 3, GS3 and qGL3 were found to regulate GL. On chromosome 6, TGW6 and GW6a were found to regulate TGW. Also, some QTLs related to grain shape were found on chromosomes 5 and 9. Besides that, using sequenced 3K-germplasm resources, we found that there are 22 overlapped varieties between these two natural populations. Twenty-six SNPs and fourteen haplotypes were identified in five regions of GS3 genes. The detection of multiple candidate genes/QTLs within the candidate interval is beneficial for further excavation of superior rice genetic resources.