基于SNP和InDel标记的巴西木薯遗传多样性与群体遗传结构分析

Genetic diversity and population structure analysis by SNP and InDel markers of cassava in Brazil

为了对巴西木薯种质资源进行遗传多样性、亲缘关系和群体遗传结构分析,本研究利用了7946个SNPs和1997个InDels分子标记,通过ADMIXTURE软件进行群体结构分析、GCTA软件进行主成分分析。结果显示,巴西木薯被划分为9个亚群。这与利用PHYLIP进行的聚类分析结果大概一致,其中亚群1、亚群2、亚群4、亚群6和亚群8能较好地分别聚在一起,而其他亚群中的样品大致能聚在一起,且样品间有一定的交叉。巴西木薯种质资源遗传多样性指数(0.274)高于中国、尼日利亚等,其中巴西木薯亚群5具有相对较高的遗传多样性水平(0.29)。巴西木薯各亚群的群体遗传分化程度较低(群体分化指数在0.03~0.15之间),但高于中国木薯种质资源的群体分化指数。各木薯材料间的遗传距离变幅为0.084~0.297,平均遗传距离为0.228。本研究结果可为后续关联分析发掘优良等位基因及引种提供依据。

As a typical tropical crop,cassava(Manihot esculenta Crantz)has the characteristics of drought resistance,barren resistance,high biomass and so on.In addition to being used for food and forage,it can also be used for production,processing and starch extraction.Due to highly heterozygous cassava genome,breeding is more difficult.Enriching the genetic diversity of cassava germplasm,comprehensively evaluating its genetic background and traits,and discovering superior alleles that control excellent traits are of great significance for cassava breeding in the future.In order to analyze the genetic diversity,genetic relationship and population structure of cassava germplasm in Brazil,7946 SNPs and 1997 InDels molecular markers were used.Population structure analysis was performed by ADMIXTURE software,and principal component analysis was performed by GCTA software.Brazilian cassava was divided into nine subgroups,and was roughly consistent with the results of cluster analysis using PHYLIP.Among them,subgroup 1,subgroup 2,subgroup 4,subgroup 6,and subgroup 8 could be clustered together respectively,while the samples of other subgroups could be roughly clustered,and there was a certain cross between the samples.The genetic diversity of cassava germplasm in Brazil(0.274)was higher than the genetic diversity level of cassava germplasm in China and Nigeria.Subgroup 5 of Brazil cassava had a relatively high genetic diversity(0.29).The genetic differentiation of subgroups was low(the genetic differentiation vary from 0.03 to 0.15),but higher than domestic cassava germplasm.The genetic distance between cassava accessions varied from 0.084 to 0.297,with the average of 0.228.The results of this study can provide a basis for subsequent association analysis to identify great alleles and introduction.