Advancing rust resistance in elite wheat with haplotype mapping and a novel introgression strategy

Wheat production is continually threatened by stripe and leaf rust, because virulent races rapidly overcome single race specific genes; durable, broad spectrum resistance is needed. Adult plant resistance (APR) provides partial, stable resistance from many minor effect loci acting additively; pleiotropic loci like Lr34/Yr18 and Lr46/Yr29 add durability. We utilised an elite Australian panel (OzWheat=589) and a diverse landrace panel (Vavilov=295), genotyped ~30K SNPs, and phenotyped for stripe and leaf rust infection across environments. Linkage disequilibrium partitioning defined 7,659 genome-wide haploblocks. To prioritise robust signals, we ranked haploblocks by haplotype effect variance and examined the top 100 per trait. For stripe rust, 52/100 were significant, with 32 identified in both panels; for leaf rust, 50/100 were significant, 29 of which were also detected in Vavilov. Several intervals co-localised with APR regions (e.g. Lr46/Yr29, Yr39), whereas one 7BL interval intersected seedling gene Lr14a. To translate mapping into breeding decisions, we developed an introgression fitness index that quantifies the value of bringing resistant haplotypes into an elite background. Using elite cultivar Scepter as a case study, we applied a genetic algorithm to select 50 complementary donor parents that collectively carry desirable haplotypes absent from Scepter. Forward simulations indicated that pyramiding these haplotypes can substantially increase resistance while maintaining the elite genomic background. This study demonstrates the utility of haplotype-informed mapping to bridge exotic and elite diversity and provides practical breeding tools, including haplotype catalogues and a novel introgression selection index to accelerate breeding of rust-resistant wheat with extensibility to other crops and complex traits.