Abstract
BACKGROUND: Soybean (Glycine max) is a globally important crop, yet its genetic diversity remains underutilized in breeding programs, particularly in emerging production regions such as Kazakhstan. As Kazakhstan expands its soybean cultivation, a detailed understanding of the genetic diversity and population structure of both local and international germplasm is critical for developing regionally adapted cultivars. RESULTS: This study analyzed 694 soybean accessions - including landraces, modern cultivars, and wild relatives (Glycine soja) - using 80,971 high-quality SNPs obtained via whole-genome resequencing. Population structure analysis, PCA, and phylogenetic clustering consistently distinguished wild from cultivated groups and identified transitional genotypes bridging the two. Kazakhstan's accessions showed closest genetic similarity to European and North American cultivars, reflecting historical cultivar exchange and breeding for temperate adaptation. However, Kazakhstan's accessions exhibited the lowest within-group diversity, underscoring a narrow genetic base. CONCLUSIONS: These findings reveal the genetic structure and evolutionary relationships within a global soybean collection and highlight the limited genetic diversity of Kazakhstan's germplasm. The results suggest two complementary breeding strategies for Kazakhstan: (1) broadening the genetic base through the introduction of diverse foreign and wild germplasm, and (2) increasing the frequency of favorable alleles already present in locally adapted lines. This integrated approach can support the development of high-performing, resilient cultivars tailored to Kazakhstan's agricultural environments.