Genetic diversity analysis of nationally approved maize varieties in different ecological regions

Analyzing the genetic diversity of maize varieties approved at the national level across different ecological regions reveals patterns of genetic differentiation among regional germplasms. This provides a theoretical basis for elite germplasm screening and region-specific variety breeding. In this study, 273 nationally approved common maize varieties were analyzed. Sixteen field phenotypic traits and genetic variation parameters based on 40 SSR markers were statistically evaluated. Cluster analysis and association analysis of phenotypic and genotypic data were conducted to explore the relationships among phenotypes, genotypes, and environmental factors in common maize. The results showed significant differences in growth period and regional trial yield across ecological regions, with <italic>F</italic> values of 2484.95 and 472.83, respectively. Genetic diversity was relatively high in the Xi-Nan spring-sowing region (XN), with a gene diversity index of 0.72. Phenotypic clustering divided 325 variety records into four groups: Group X1 mainly included varieties from the Dong-Hua-Bei (DHB) and Xi-Bei (XB) spring-sowing regions; Group X2 was dominated by varieties from the Bei-Fang (BF) early-maturity spring-sowing region; Group X3 included varieties from the XN region; and Group X4 mostly comprised varieties from the Huang-Huai-Hai (HHH) summer-sowing and Dong-Nan (DN) spring-sowing regions. Phenotypic differentiation among ecological regions followed clear trends: DHB and XB varieties were characterized by medium-late maturity and tall stalks; BF by early maturity and medium short stalks; XN by medium maturity and medium stalks; and HHH and DN by early maturity and medium stalks. Notably, XN, HHH, and DN regions experienced relatively high disease pressure. Principal component analysis (PCA) of phenotypic traits showed that the first two components explained 69.0% of the total variance, with clear group separation, supporting the validity of the phenotypic classifications. Genotypic clustering also divided the 273 varieties into four groups. In Group Y1, the predominant heterosis patterns were Reid × X and Improved Reid × X; in Group Y2, X × Tangsipingtou (Huangzaosi-derived lines); and in Group Y4, Improved Reid × Tangsipingtou. Genotypic PCA demonstrated a cumulative contribution of 57.9% from the first two components, with clear intra-group cohesion and significant inter-group differentiation, confirming the reliability of the genotypic groupings. Association analysis between genotypes and phenotypes revealed a weak correlation, likely due to the design objectives of molecular marker selection. Maize varieties from different ecological regions in China exhibit distinct regional differentiation in field performance and parental heterosis groups, resulting in a well-defined correspondence among ecological zones, trait expression, and genetic background. This pattern reflects region-specific breeding goals that prioritize yield stability and efficient resource utilization.