Genetic characterization of elite tropical, subtropical and temperate maize germplasm based on genome-wide SNP markers

The genetic characteristics of maize ( Zea mays L.) germplasm are helpful to understand their genetic diversity and heterotic group, as well as provide a reference for germplasm improvement and GWAS. A total of 241 maize inbreds including tropical, subtropical, and temperate maize, were selected from the global maize germplasm in the study. Genetic diversity, population structure, genetic relationship, and LD were analyzed using the Affymetrix SNP56K chip. Finally, 20,586 high-quality SNP markers were screened out which detected a total of 41,172 allelic variants among materials, the average gene diversity was 0.3779 and the average PIC was 0.3002. There were greater genetic differences between different germplasm sources, the genetic diversity of China & USA maize was higher than that of CIMMYT & Thailand maize. Based on model analysis, cluster analysis, and PCA, a consistent population structure was got that the materials were firstly divided into tropical & subtropical maize and temperate maize; then, the latter was furtherly divided into three subgroups named SS, NSS, and TSPT, and the remaining inbreeds were classified into Mixed groups. The results were consistent with domestic major results as well as their pedigree information. The LD decay distance of temperate maize was greater than tropical & subtropical maize. This study further confirmed that there exists population stratification among tropical, subtropical, and temperate maize germplasm, but the specific stratification results may be different by using different materials, markers, and analysis methods. In addition, the genetic difference between temperate maize and tropical & subtropical maize is certainly great, the latter will continue to play an important role in maize breeding in China.