Integrating Multi-Environment Phenotypes and Genome-Wide Variation to Evaluate Diversity and Identify Representative...

To facilitate the innovation and efficient utilization of specialty maize germplasm, this study aimed to systematically evaluate a panel of 222 inbred lines. The objective was to comprehensively characterize phenotypic variation, genetic diversity, and genotype-phenotype associations to screen for representative germplasm resources.

We integrated Best Linear Unbiased Prediction (BLUP) values derived from multi-environment field trials with high-density whole-genome single-nucleotide polymorphism (SNP) data. Population structure and genetic diversity were analyzed, Mantel tests were conducted to assess genotype-phenotype correspondence, and a genome-wide association study (GWAS) was performed to identify significant loci.

The population exhibited substantial phenotypic variation, particularly in plant height and tassel traits, with distinct morphological differentiations among specialty types. Genetic diversity analyses revealed varying diversity levels among subpopulations. While Mantel tests indicated a weak overall genotype-phenotype correspondence, specific traits showed significant associations with genetic distance. GWAS successfully identified significant loci associated with plant height and tassel traits. Furthermore, population structure analysis revealed distinct genetic stratification corresponding to specialty types, albeit with a certain degree of admixture.

By integrating multi-dimensional phenotypic and genomic profiles, a panel of highly diverse and representative candidate germplasm was identified. These findings provide a crucial theoretical basis for specialty maize breeding and the optimized utilization of germplasm resources.