Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs.
Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs.
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DOI：
10.1111/pbi.12722
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发表时间：
2017-11
影响因子：
13.8
通讯作者：
Lin Z
中科院分区：
文献类型：
--
作者：
Huang C;Nie X;Shen C;You C;Li W;Zhao W;Zhang X;Lin Z
Gossypium hirsutum L.中国是世界上最大的棉花生产国和消费国之一。为了研究中国高地棉农艺性状的遗传结构，收集了一个包含503份陆地棉种质的全国性群体，对16个农艺性状进行了全基因组关联研究（GWAS）。从2012年到2013年，在四个地方种植这些种质进行表型分析。使用CottonSNP63K阵列和基于该阵列的已发表的高密度图谱进行基因分型。基于11975个定量多态性单核苷酸多态性（SNP）将503份陆地棉种质分为3个亚群。通过比较3个遗传亚群体、7个地理分布区和4个育种时期的遗传结构和表型变异，发现地理分布区和育种时期不是遗传结构的决定因素。此外，尽管3个亚群体具有不同的遗传背景，但它们之间没有明显的表型分化。共鉴定出324个SNPs和160个候选数量性状位点（QTL）区域与16个农艺性状显著相关。建立了QTL多重效应和性状间关联的网络。38个相关区域具有控制多个性状的多效性效应。推测一个候选基因Gh_D08G2376控制衣分（LP）。该GWAS是中国首次利用高地棉高分辨率SNPs综合研究农艺性状的报告，为棉花遗传研究和育种提供了基础资源。
Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton‐producing and cotton‐consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome‐wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high‐density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single‐nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty‐eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high‐resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.
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DOI：
10.1093/dnares/dsw016
发表时间：
2016-06
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Li X;Jin X;Wang H;Zhang X;Lin Z
通讯作者：
Lin Z
影响因子：
16.6
作者：
Crowell S;Korniliev P;Falcão A;Ismail A;Gregorio G;Mezey J;McCouch S
通讯作者：
McCouch S
影响因子：
4.4
作者：
Fang DD;Jenkins JN;Deng DD;McCarty JC;Li P;Wu J
通讯作者：
Wu J
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
46.9
作者：
Li, Fuguang;Fan, Guangyi;Yu, Shuxun
通讯作者：
Yu, Shuxun