From Diversity to Discovery: Genome-Wide Insights into the Genetic Landscape of Tropical Maize DH Lines

Abstract Understanding the extent and structure of genetic diversity within breeding populations is essential for sustaining long-term genetic gain in maize improvement programs. In this study, a panel of 2,555 maize doubled haploid (DH) lines representing diverse genetic backgrounds was genotyped using 3305 high-quality single nucleotide polymorphism (SNP) markers to assess genome-wide diversity, population structure, and relatedness. The SNPs were distributed across all ten chromosomes, with varying marker densities among genomic regions. Diversity indices revealed moderate polymorphism, with mean gene diversity (0.38) and polymorphic information content (0.30), while the minor allele frequency ranged from 0.04 to 0.50. The low observed heterozygosity (0.04) and high fixation index (0.89) confirmed the expected homozygosity of DH lines. Population structure analysis using sparse non-negative matrix factorization (sNMF) and principal coordinate analysis (PCoA) consistently identified two major genetic clusters corresponding to the established heterotic groups used in CIMMYT’s tropical maize breeding pipelines. The Analysis of Molecular Variance (AMOVA) indicated that 36% of genetic variation occurred among populations, 58% among individuals within populations, and 6% within individuals (P = 0.001), confirming significant population differentiation and high within-group diversity. These results demonstrate that the DH panel represents a genetically diverse and well-structured population with limited relatedness among lines. The distinct clustering by heterotic group, coupled with substantial within-group variation, provides a strong foundation for genome-wide association studies, genomic selection, and allele mining for complex adaptive traits. The panel’s diversity and structure make it an invaluable genomic resource for dissecting trait architecture and accelerating genetic gain in tropical maize breeding programs targeting sub-Saharan Africa and similar environments. Competing Interest Statement The authors have declared no competing interest.