Mei Hongxian, Zhu Xiefei, Zhang Tianzhen
National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, China ; Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China.
National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, China.
PLoS One. 2013 Dec 26;8(12):e82193. doi: 10.1371/journal.pone.0082193. eCollection 2013.
Linkage disequilibrium based association mapping is a powerful tool for dissecting the genetic basis underlying complex traits. In this study, an association mapping panel consisting of 356 representative Upland cotton cultivars was constructed, evaluated in three environments and genotyped using 381 SSRs to detect molecular markers associated with lint yield and its components. The results showed that abundant phenotypic and moderate genetic diversities existed within this germplasm panel. The population could be divided into two subpopulations, and weak relatedness was detected between pair-wise accessions. LD decayed to the background (r(2) = 0.1182, P ≤ 0.01), r(2) = 0.1 and r(2) = 0.2 level within 12-13 cM, 17-18 cM and 3-4 cM, respectively, providing the potential for association mapping of agronomically important traits in Chinese Upland cotton. A total of 55 marker-trait associations were detected between 26 SSRs and seven lint yield traits, based on a mixed linear model (MLM) and Bonferroni correction (P ≤ 0.05/145, -log10 P ≥ 3.46). Of which 41 could be detected in more than one environment and 17 markers were simultaneously associated with two or more traits. Many associations were consistent with QTLs identified by linkage mapping in previous reports. Phenotypic values of alleles of each loci in 41 stably detected associations were compared, and 23 favorable alleles were identified. Population frequency of each favorable allele in historically released cultivar groups was also evaluated. The QTLs detected in this study will be helpful in further understanding the genetic basis of lint yield and its components, and the favorable alleles may facilitate future high-yield breeding by genomic selection in Upland cotton.
基于连锁不平衡的关联作图是剖析复杂性状遗传基础的有力工具。本研究构建了一个由356个代表性陆地棉品种组成的关联作图群体，在三种环境下进行评估，并使用381个SSR进行基因分型，以检测与皮棉产量及其构成因素相关的分子标记。结果表明，该种质群体存在丰富的表型多样性和中等程度的遗传多样性。群体可分为两个亚群，成对材料间亲缘关系较弱。连锁不平衡分别在12 - 13 cM、17 - 18 cM和3 - 4 cM内衰减至背景水平（r² = 0.1182，P ≤ 0.01）、r² = 0.1和r² = 0.2水平，为中国陆地棉重要农艺性状的关联作图提供了潜力。基于混合线性模型（MLM）和Bonferroni校正（P ≤ 0.05/145，-log10 P ≥ 3.46），在26个SSR与7个皮棉产量性状之间共检测到55个标记 - 性状关联。其中41个在多个环境中均可检测到，17个标记同时与两个或更多性状相关。许多关联与先前报道中通过连锁作图鉴定的QTL一致。比较了41个稳定检测到的关联中每个位点等位基因的表型值，鉴定出了23个有利等位基因。还评估了每个有利等位基因在历史上发布的品种群体中的群体频率。本研究中检测到的QTL将有助于进一步了解皮棉产量及其构成因素的遗传基础，有利等位基因可能有助于未来陆地棉通过基因组选择进行高产育种。
