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本研究利用121个分布于棉花全基因组的SSR标记,对187份国外棉花种质材料和31份新疆本地棉花品种进行遗传多样性、群体遗传结构和连锁不平衡分析。结果表明:218份材料共检测到284个SSR等位变异,等位基因变异数在2~9之间,遗传多样性指数平均为0.402,PIC值平均为0.355。基于STRUCTURE分析,218份材料可被划分为三个亚群(POP-1/2/3)。AMOVA分析表明,14.6%的变异来源于亚群间,85.4%的变异来源于亚群内。连锁不平衡(linkage disequilibrium,LD)分析显示,r2≥0.05(p<0.01)的条件下,10.18%的SSR位点组合存在显著的LD,整体LD水平不高,共线性位点间存在LD的比例高于非共线性位点,表明位点间的连锁对LD有重要影响。在r2=0.1时(p<0.05),LD最大遗传距离为34.7 c M,当r2=0.2时,LD最大遗传距离为9 c M。进一步对Chr.3、Chr.11、Chr.23和Chr.24共4个染色体的LD衰减距离进行分析,发现Chr.3和Chr.11具有较高的LD衰减距离。LD分析结果表明本研究群体可用于标记——性状关联分析,并且对单个染色体LD的评估将提供重要的参考。
In this study, using 121 SSR markers distributed in the genome of cotton, genetic diversity, population genetic structure and linkage disequilibrium analysis of 187 foreign cotton germplasm materials and 31 Xinjiang native cotton varieties were analyzed. The results showed that a total of 284 SSR alleles were detected in 218 cultivars, the allelic variation was between 2 and 9, the average genetic diversity index was 0.402, and the average PIC was 0.355. Based on the STRUCTURE analysis, 218 pieces of material can be divided into three subpopulations (POP-1/2/3). AMOVA analysis showed that 14.6% of the variation was from subpopulations and 85.4% of the variation was from subpopulations. Link disequilibrium (LD) analysis showed that there was significant LD at the combination of 10.18% of SSR loci under the condition of r2≥0.05 (p <0.01), the overall LD level was not high, and there was LD The proportion was higher than that of the non-colinearity loci, indicating that the linkage between the loci had an important influence on LD. At r2 = 0.1 (p <0.05), the maximum genetic distance of LD was 34.7 cM, and the maximum genetic distance of LD was 9 cM when r2 = 0.2. Further analysis of the LD attenuation distances of 4 Chr.3, Chr.11, Chr.23 and Chr.24 chromosomes showed that Chr.3 and Chr.11 had higher LD decay distance. The results of LD analysis indicated that this study population could be used for marker-trait correlation analysis and would provide an important reference for the evaluation of single chromosome LD.