Microsatellite-based genetic diversity evaluation of Zea mays L. accessions from different geographical origins

Abstract

The purpose of this study was to investigate genetic diversity and the structure of 51 maize (Zea mays L.) accessions originating from Kazakhstan, China, and Europe using simple sequence repeat (SSR) markers. A total of 21 highly polymorphic SSR markers were applied to genotype 255 individuals, enabling a comprehensive assessment of allelic variation and genetic relationships. The number of alleles per locus ranged from 1.0 to 2.7, with a mean of 1.517, while expected heterozygosity (uHe) averaged 0.192, indicating moderate genetic diversity across accessions. Genetic diversity analysis by geographic origin revealed that European accessions exhibited the highest allelic richness (Na = 5.9) and genetic diversity, followed by the Chinese and Kazakhstani groups. Despite these differences, all groups showed 100% polymorphism, confirming the high informativeness of the selected SSR markers. Polymorphic information content (PIC) values ranged from 0.446 to 0.884, with an average of 0.712, indicating that markers such as phi047, bnlg1520, and umc2189 are highly informative. Analysis of molecular variance (AMOVA) demonstrated that 70% of the total genetic variation was attributable to differences among accessions, indicating strong genetic differentiation (Fst = 0.702) and limited gene flow (Nm = 0.212). Cluster analysis, principal coordinate analysis, and STRUCTURE results consistently revealed clear genetic separation of Chinese accessions, while European and Kazakhstani accessions showed closer genetic relationships and partial admixture. Overall, the findings highlight substantial genetic diversity and distinct population structure among maize accessions, providing valuable insights for germplasm conservation and for selecting genetically diverse parental lines in breeding programs.