Molecular diversity analysis and development of a core set in wheat using array-based SNP markers

Landrace collections from decades represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Repatriating wheat landraces and integrating them into modern breeding programs represents a crucial step toward restoring eroded genetic diversity. Here, we study genetic diversity and population structure of 828 landraces along with 100 cultivars. Genetic diversity using SNPs in the present study demonstrated B genome with the highest SNP density, followed by A and D. Chromosome 2B was the most densely covered, while 4D was the least, showing known differences in the evolution of the hexaploid wheat genome. Estimates of genome-wide diversity showed slightly higher gene diversity as well as PIC in the B and D genomes compared to A. Slightly negative Tajima’s D values, interpreted comparatively, were consistent with a relatively stable demographic history and weaker recent selection pressure in landraces compared to cultivars and lower nucleotide diversity in landraces than improved genotypes. Transitions were more common than transversions, with Ts/Tv ratios exceeding two across the genomes, which supported the reliability of the SNP set. STRUCTURE identified two major genetic clusters (K = 2) while BIC based DAPC inferred K = 6 indicating that the wheat germplasm collection exhibits hierarchical population structure, with K = 2 representing the primary level of genetic differentiation while higher values of K describe progressively finer-scale subdivision. AMOVA confirmed that most variation is within groups rather than between them. LD decay was fastest in the A genome and slowest in the B genome. A core collection was also constructed based on maximization, that comprised of 25% of accessions, retained 99.74% of alleles and showed similar or greater diversity than the full set. Together, these results show that repatriated Indian landraces contain significant and structured genetic variation. They offer a well-defined core resource for future association studies, pre-breeding, and improving climate-resilient wheat.