Functional gene diversity and zone-targeted genotype prioritization using trait-diagnostic KASP markers in bread wheat (Triticum aestivum L.)

Functional gene diversity is essential for adaptation and sustained genetic improvement in bread wheat. In this study, 40 KASP assays targeting 40 functional SNPs across 35 genes linked to adaptation, stress resilience, quality, and yield were used to quantify allelic variation and develop a strategy for region-specific genotype deployment. Functional diversity and population structure were assessed in 178 wheat genotypes, including genetic stocks (80), released varieties (72), and landraces (26). High-throughput KASP assays classified all loci as favourable or unfavourable. Phylogenetic, principal coordinate, and Bayesian STRUCTURE analyses consistently identified two major subpopulations: a founder-centric group fixed for productivity- and disease-resistance alleles, and a recombination-driven group enriched for adaptive and stress-resilience alleles. Among trait categories, adaptation-related loci showed the highest mean gene diversity (He = 0.420), while loci linked to yield and quality had lower polymorphism, indicating strong directional selection during breeding. Landraces had the highest proportion of rare favourable alleles (mean = 9.35), highlighting their importance as reservoirs of underutilized functional variation for pre-breeding. The complementary distribution of alleles between founder- and recombination-derived groups reflected the combined effects of historical selection and introgression on the genomic structure of Indian wheat. Using this functional genomic dataset, a rule-based, zone-weighted suitability scoring model was developed to integrate allele states with breeding priorities across India’s five wheat production zones. This model enabled quantitative, zone-specific genotype prioritization and identification of regionally adapted donors with complementary adaptive alleles. The strategy turned functional markers into practical tools for strategic allele deployment and established a scalable decision-support system for precision breeding.