List of traits and their measurements.

Soybean (Glycine max) is one of the world’s most important oilseed crops and has adapted to various environmental conditions. Yields of soybeans in Nigeria are notably low due to different production constraints, including the limited availability of improved varieties and the slow replacement rate of old varieties with new and high-yielding ones. Ensuring high genetic diversity in the working germplasm is among the primary factors for the success of breeding programs in identifying high-yielding and well-adapted improved varieties. This study aimed to assess the genetic diversity and population structure of 45 soybean breeding lines of the International Institute of Tropical Agriculture soybean breeding program at the advanced evaluation stage based on phenotypic traits and SNP markers to support breeding strategies. Field trials were conducted in 2022 across three International Institute of Tropical Agriculture stations in Nigeria using a 5 × 9 alpha-lattice design with three replications. The collected yield and yield component data were subjected to analysis of variance, mean comparison, principal component analyses, and cluster analyses using R software. The genotypes were further assessed using 10,630 SNP markers obtained from DArTseq genotyping. The combined analysis of variance revealed a significant genotype × location interaction for grain yield and a highly significant difference in days to 50% flowering and days to 95% maturity. The genotypes G02, G10, G11, G01, and G24 were significantly superior in grain yield. Principal component analysis showed that the first three components explained 64.8% of total variation, with major contributions from traits such as lodging score, hundred seed weight, plant height, nodulation, and days to 50% flowering. Hierarchical clustering grouped the genotypes into five clusters, highlighting desirable traits such as high yield, early maturity, and lodging tolerance. SNP-based population structure grouped the genotypes into three distinct subpopulations. The SNP markers showed average observed heterozygosity, expected heterozygosity, minor allele frequency, and polymorphic information content of 0.08, 0.27, 0.20, and 0.22, respectively, which showed the existence of considerable genetic variation among the studied genotypes.