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

【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(F_st) 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 F_st was in population A（0.1491）,while the F_st 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.