The Genetic Diversity of Old and Modern Accessions of Glycine max Revealed by Genotyping-by-Sequencing (GBS)

Soybean (Glycine max (L.) Merr.) is one of the most widely cultivated grain legumes worldwide. A genetic analysis of soybean samples around the world is essential for effective breeding programs and the development of genomic and marker-assisted selection. This study investigated the genetic diversity of soybean accessions from the VIR collection, one of the world’s largest seed banks. The sample consisted of 163 soybean (G. max) varieties. The study was conducted using Genotyping-by-Sequencing (GBS) technology. The aim of the study was to evaluate temporal changes in genetic diversity, population structure, and linkage disequilibrium in cultivated soybean. The material was divided according to two criteria: (1) three chronological groups of varieties, Group I (before 1959), Group II (1960–1989), and Group III (after 1990), and (2) regional characteristics. Linkage disequilibrium (LD) decay analysis revealed differences among chronological groups, with the longest LD decay distance observed in early accessions developed before 1959 and shorter LD decay distances in later groups. Nei’s gene diversity showed only slight differences among chronological groups, with a moderate decreasing trend in more recent accessions. Key loci were defined as SNPs showing the largest allele frequency differences between chronological groups and located within or near annotated genes. The results highlight the importance of comprehensive genomic analysis for the conservation and efficient utilization of genetic resources, as well as for the development of soybean breeding strategies in the future.