棉花资源群体结构的推测与纤维品质的关联分析
首发时间:2010-03-31
摘要:关联分析是利用连锁不平衡(linkage disequilibrium, LD)检测自然群体中影响表型的基因位点及其等位变异的方法,而材料的基因组血统与分子亲缘关系的推测则是关联分析和提高育种效率的基础。本研究利用均匀分布于26条染色体上的132个SSR标记, 对经挑选的92份栽培棉材料的基因组变异进行扫描, 利用混合模型分析该群体的遗传结构。当指定7个亚群时(K=7),似然值达到最大,该群体分为亚洲棉组(Cluster 5)、海岛棉组(Cluster 7)、陆地棉1组-3组(Cluster 2、Cluster 4和Cluster 6)、混合血统组(Cluster 1和Cluster 3)。组群间的Kullback-Leibler和Q值矩阵显示了7个组群的遗传组成和材料间的分子亲缘关系。采用TASSEL软件的GLM (general linear model)方法对5个品质性状2年×3重复的观测值进行标记与性状的关联分析,结果表明:该群体中累计有21个位点与性状相关,一些标记同时与2个或多个性状相关联, 可能是性状相关乃至一因多效的遗传基础。本研究将为育种材料的利用、标记辅助选择及下一步候选基因关联作图提供参考信息。
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Inferring Population Structure and Association Analysis of Fiber Quality in Cultivated Cotton
Abstract:Association analysis is a method for detecting QTLs as well as their alleles based on linkage disequilibrium (LD) in natural population; meanwhile, the inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association analysis. One hundred and thirty-two SSR loci, evenly distributed in 26 chromosomes, were assayed for polymorphism among 92 cultivated cotton accessions which represent the high genetic diversity. The identified 494 alleles served as raw data for estimating population structure based on the ADMIXTURE model. Specifying seven subpopulations (K = 7) led to a maximum likelihood value. Therefore, this natural population was inferred to be composed of 7 subpopulations, which were arboreum (Cluster 5), barbadense (Cluster 7), hirsutum (Cluster 2, Cluster 4 and Cluster 6), and mixture (Cluster 1 and Cluster 3). The Kullback-Leibler distance of pairwise subpopulation was also inferred as (92 × 7) Q matrices, which gave a detailed percentage of genetic composition of seven subpopulations and molecular relatedness of each accession. The association analysis between SSR loci and 5 fiber quality traits (2 years × 3 replicate) was performed by using TASSEL GLM (general linear model) program. Twenty one SSR loci associated with the traits were screened out from this cultivated population. There were a few loci associated with two or more traits simultaneously, which might be the genetic reason of correlation among traits or pleiotropic phenomena. These results would provide some referenced information for the utilization of these accessions, for marker assisted selection (MAS), for the upcoming association studies of some candidate genes.
Keywords: Cultivated cotton Simple-sequence repeat (SSR) Population structure Association analysis
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