广西水稻地方品种核心种质芽期耐盐性全基因组关联分析  

Genome wide association study of salt tolerance at the germination stage for core Germplasm of rice landrace in Guangxi,China

作　　者：夏秀忠[1] 张宗琼[1] 杨行海[1] 荘洁 曾宇[2] 邓国富[2] 宋国显 黄欲晓 农保选[1] 李丹婷[1] XIA Xiu-Zhong;ZHANG Zong-Qiong;YANG Xing-Hai;ZHUANG Jie;ZENG Yu;DENG Guo-Fu;SONG Guo-Xian;HUANG Yu-Xiao;NONG Bao-Xuang;LI Dan-Ting(Rice Research Institute,Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding,Nanning 530007,Guangxi,China;Guangxi Academy of Agricultural Sciences,Nanning 530007,Guangxi,China;Qinzhou Institute of Agricultural Sciences,Qinzhou 535000,Guangxi,China)

机构地区：[1]广西农业科学院水稻研究所/广西水稻遗传育种重点实验室,广西南宁530007 [2]广西农业科学院,广西南宁530007 [3]钦州市农业科学研究所,广西钦州535000

出　　处：《作物学报》2022年第8期2007-2015,共9页Acta Agronomica Sinica

基　　金：水稻生物学国家重点实验室开放课题(170102);广西重大科技创新基地开放课题(2018-05-Z06-CX04);广西农业科学院发展基金项目(桂农科2021JM07,桂农科2021JM49),广西农业科学院基本科研业务专项(桂农科2021YT030)资助。

摘　　要：水稻属盐敏感的作物,盐胁迫会导致产量显著减少。我国盐渍地总面积大,并且呈迅速增长趋势,因此,筛选水稻耐盐种质,培育耐盐水稻品种十分必要。本研究在1.5%NaCl盐胁迫条件下评价419份广西水稻地方品种核心种质种子芽期的相对盐害率,并利用全基因组关联分析鉴定耐盐位点。研究结果表明:盐胁迫下,种子芽期平均发芽率为57.67%,显著低于对照92.55%,且夏皮罗-威尔克检验(0.9301)不符合正态分布。基于208,993个SNP标记,将419份核心种质资源分为6个亚群,利用一般线性模型(general linear model,GLM)和混合线性模型(mixed linear model,MLM)分析分别获得129个和1个显著关联SNP,分布在1号、2号、3号、4号、5号、6号、8号、9号和12号染色体上。在14个与水稻耐盐性显著关联区域,有13个区域与前人定位或克隆的耐盐基因重叠。显著关联区域Chr.8:10,564,948~10,733,175为首次报道,命名为qGR8。qGR8区域内含有53个基因,其中34个经转录组数据比对获得表达谱,比对结果推测LOC_Os08g17370为候选基因,该基因为跨膜9超家族成员,在耐盐亲本的根部和叶部上调表达,可能为qGR8区域内水稻芽期耐盐的新基因。这些研究结果为耐盐新基因的克隆奠定基础,为培育耐盐水稻品种提供新的基因资源。Rice is a salt-sensitive crop,and salt stress can cause significant reduction in rice yield.China’s total saline area is large and growing rapidly.Therefore,it is necessary to screen for the salt-tolerant rice germplasm and cultivate these varieties.In this study,we evaluated the relative salt damage rate of 419 core germplasm of Guangxi rice landraces at seed germination stage under 1.5%NaCl salt stress,and identified the salt-tolerant loci by whole-genome association analysis.The results showed that the average germination rate under salt stress was 57.67%,which was significantly 92.55%lower than that of control group,and the Shapiro-Wilk test(0.9301)found that the distribution did not conform to normal distribution.Based on 208,993 SNP markers,419core germplasm was divided into 6 subgroups.We used general linear model(GLM)and mixed linear model(MLM)analysis to identify 129 and 1 significantly associated SNPs,respectively,which were distributed on chromosomes 1,2,3,4,5,6,8,9,and 12.Among the 14 regions that were significantly associated with rice salt tolerance,13 regions overlapped with previously identified or cloned salt tolerance genes.The significantly associated region Chr.8:10,564,948–10,733,175 was reported for the first time and named q GR8.There were 53 genes in qGR8 region,34 of which were compared with transcriptome data to obtain the expression profiles.We compared the expression profiles and speculated that LOC_Os08g17370 was a candidate gene.This gene is a member of transmembrane 9 superfamily and is up-regulated in roots and leaves of salt-tolerant parent.Thus,this gene might be a novel salt-tolerant gene in q GR8 region at germination stage in rice.These results lay a foundation for cloning new genes of salt-tolerant and provide new genetic resources for breeding salt-tolerant rice varieties.

关 键 词：水稻 核心种质 芽期 耐盐 全基因组关联分析 

分 类 号：S511[农业科学—作物学]