Analysis of the genetic structure and diversity of upland cotton groups in different planting areas based on SNP markers
Analysis of the genetic structure and diversity of upland cotton groups in different planting areas based on SNP markers
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基于SNP标记的不同种植区陆地棉类群遗传结构及多样性分析
DOI：
10.1016/j.gene.2021.146042
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发表时间：
2021
期刊：
影响因子：
3.5
通讯作者：
JuyunZheng
中科院分区：
文献类型：
--
作者：
JungduoWang;ZeliangZhang;ZhaolongGong;YajunLiang;XiantaoAi;ZhiweiSang;JiangpingGuo;XueyuanLi;JuyunZheng
通过对陆地棉种质资源的遗传多样性、亲缘关系和群体遗传结构的分析，可以更好地了解陆地棉的起源和进化。毛发生物多样性。本研究利用从世界各地收集的273份陆地棉优良品种资源，特别是从中国获得的1313331个SNP分子标记，用MEGAX软件构建每个样本的系统发育树，用混合软件进行群体结构分析，用EIGENSOFT软件进行主成分分析，用SPAGeDi进行亲缘关系估计。ADMIXATION软件将试验棉花群体划分为16个亚类，粗毛棉样本按产地大致可聚为一类，但样本间存在一定的重叠特征。将试验群体按来源划分为6个类群，计算遗传多样性指数(H)，所得结果(0.306)与中国等人收集的种质资源接近。群体4具有较高的遗传多样性水平(0.390)。棉花群体内的遗传分化程度较低(群体分化指数在0.02368~0.10664之间)。棉花品种间的遗传距离在0.000332651~0.562664014之间，平均为0.25240429。本研究的结果可能为挖掘优秀等位基因并将其用于后续的关联分析提供依据。
Genetic diversity, kinship and population genetic structure analyses ofGossypium hirsutumgermplasm can provide a better understanding of the origin and evolution ofG. hirsutumbiodiversity. In this study, adopt 273 elite upland cotton cultivar accessions collected from around the world, and especially from China to get 1,313,331 SNP molecular markers, it were used to construct a phylogenetic tree of each sample using MEGAX, to perform population structure analysis by ADMIXTURE software and principal component analysis (PCA) by EIGENSOFT software, and to estimate relatedness using SPAGeDi. ADMIXTURE software divided the experimental cotton population into 16 subgroups, and theGossypium hirsutumsamples could be roughly clustered according to source place, but there were some overlapping characteristics among samples. The experimental cotton population was divided into six groups according to source to calculate the genetic diversity index (H), and the obtained value (0.306) was close to that for germplasm collected by others in China. Cluster 4 had a relatively high genetic diversity level (0.390). The degrees of genetic differentiation within the experimental cotton population groups were low (the population differentiation indexes ranged from 0.02368 to 0.10664). The genetic distance among cotton accessions varied from 0.000332651 to 0.562664014, with an average of 0.25240429. The results of this study may provide a basis for mining elite alleles and using them for subsequent association analysis.