基于SNP分子标记的95个热带亚热带玉米自交系遗传多样性分析

Genetic diversity analysis of 95 tropical and subtropical maize inbred lines based on SNP molecular markers

  • 摘要: 【目的】对95个热带亚热带血缘玉米自交系的群体结构和遗传多样性进行分析,为热带亚热带血缘种质的创新和精准利用提供参考。【方法】利用10K玉米SNP育种芯片对95个玉米自交系进行全基因组分型扫描,所得数据进行质控后利用PowerMarker V3.25计算遗传多样性指标,利用MEGA X计算遗传距离并采用邻接法进行聚类分析,使用R包计算群体间遗传分化系数(Fst)并进行非度量多维尺度(NMDS)分析。【结果】从95个玉米自交系中检测到7812个高质量SNP分子标记位点,分布于玉米10条染色体上。95个自交系间的遗传距离变化范围为0.001~0.482,平均值为0.356。根据遗传距离信息将95个玉米自交系划分为A、B、C 3个类群,A群有5个自交系,B群有17个自交系,C群有73个自交系;C群又可分为5个亚群,每个亚群均有各自代表性的自交系材料,聚类分析结果与育种实践基本吻合。基于SNP分子标记位点进行统计,95个玉米自交系的平均杂合率为1.4%,基因多样性均值为0.3718,杂合度难测值均值为0.0139,最小等位基因频率均值为0.2886,多态信息含量均值为0.3004。A群的Fst(0.1491)最高,B群和C群的Fst(0.1422和0.1400)接近。NMDS分析也将95个自交系分成3个群,与聚类分析结果相对应。【结论】95个热带亚热带玉米种质具有较丰富的遗传多样性,被划分为3个类群,其中C群可划分为5个亚群,进一步明确了各自交系间的遗传亲缘关系。

     

    Abstract: 【Objective】The population structure and genetic diversity of 95 tropical and subtropical maize inbred lines were analyzed,which would provide reference for the innovation and precise utilization of tropical and subtropical germplasms. 【Method】A 10K maize SNP breeding chip was used to perform whole genome typing scans on 95 maize inbred lines. After quality control,genetic diversity indicators were calculated using PowerMarker V3.25 software,genetic distance were performed using MEGA X software,cluster analysis was conducted by neighbor-joining method, the genetic differentiation coefficient between populations(Fst) was calculated by R package and nonmetric multidimensional scaling(NMDS) was analyzed. 【Result】A total of 7812 high-quality SNP molecular marker loci were detected from 95 maize inbred lines,distributed on 10 maize chromosomes. The genetic distance variation among the 95 inbred lines was 0.001-0.482,with an average genetic similarity of 0.36. Based on genetic distance information,95 maize inbred lines were classified into A, B and C major populations. Population A included 5 inbred lines,population B included 17 inbred lines,while population C included 73 inbred lines. Population C could be further divided into 5 subgroups,each with its own representative inbred line material. The overall cluster analysis results were consistent with breeding practice experience. Based on these SNP molecular marker loci,statistics showed that the average heterozygosity rate of 95 maize inbred lines was 1.4%,the average gene diversity was 0.3718, the average observed heterozygosity was 0.0139, the minimum allele frequency evaluation was 0.2886,the average polymorphic information content was 0.3004. The highest Fst was in population A(0.1491),while the Fst of populations B(0.1422) and C(0.1400) were close. NMDS analysis divided 95 inbred lines into 3 groups,corresponding to the results of cluster analysis. 【Conclusion】The 95 tropical and subtropical maize germplasms have relatively rich genetic diversity and are classified into three major populations, among which population C can be further divided into 5 subgroups. This further clarifies the genetic kinship among the inbred lines.

     

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