Legume Genomics and Genetics 2026, Vol.17, No.1, 49-67 http://cropscipublisher.com/index.php/lgg 59 2025). Similarly, SNP-based studies in Southern Africa and Central Europe revealed low F_ST among introduced temperate lines and modest overall molecular diversity, reflecting intensive germplasm exchange but also high redundancy and shared pedigrees (Haupt and Schmid, 2019; Tsindi et al., 2023). When core collections are derived from such global datasets, population-structure analysis is essential not only for defining clusters and admixture patterns, but also for guiding sampling so that both major groups and admixed genotypes are proportionally represented. In SNP-driven USDA core construction, for instance, structure analysis showed that optimization algorithms tend to favor admixed accessions, which can efficiently capture allelic variation from multiple ancestral groups in a limited number of entries (Figure 3) (Satyawan and Tasma, 2021). Figure 3 Population structure analysis of global soybean core germplasm (Adopted from Satyawan and Tasma, 2021) 6.3 Applications of core germplasm resources in molecular breeding Core and mini-core collections genotyped with dense SNP markers serve as powerful diversity panels for molecular breeding, enabling efficient trait discovery, allele mining, and pre-breeding. Because they retain most of the allelic richness and phenotypic range of the base collection, these panels are ideal for genome-wide association studies (GWAS) targeting complex traits such as seed protein and oil content, flowering time, and stress tolerance (Jo et al., 2023). The SoySNP50K-genotyped USDA collection has already supported large-scale GWAS that identified and refined major loci controlling seed composition traits, including narrowing a chromosome-20 region for protein/oil to a handful of candidate genes and confirming many previously mapped QTL (Bandillo et al., 2015). Similarly, wild soybean core subsets have been used to map loci for days to flowering and maturity, revealing allelic variation at E-genes that can be introgressed into cultivars to broaden adaptation (Jo et al., 2023). Trait-specific “integrated applied core collections” composed of accessions with documented resistance to cold, drought, salinity, soybean cyst nematode, and viral diseases provide ready-to-use donor sets for marker-assisted backcrossing and pyramiding of multiple resistance genes (Li et al., 2023). Beyond gene discovery, SNP-anchored core collections help breeders rationalize crossing schemes and widen genetic bases in targeted environments. Objective-driven cores assembled for Central European or Southern African conditions, for example, combine environmentally pre-adapted accessions with maximum molecular diversity, creating tailored panels for phenotyping under local climates and for identifying parental combinations that optimize heterogeneity while avoiding close relatedness (Tsindi et al., 2023). In countries with emerging soybean industries such as Kazakhstan, structure and diversity analyses of local versus global germplasm suggest dual strategies: introgressing novel alleles from wild and exotic sources to broaden the base, while simultaneously increasing the frequency of favorable alleles already present in adapted lines (Zatybekov et al., 2025). At a global scale, SNP-based core populations that maintain haplotype diversity and LD structure are also central to genomic
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