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 multiple minor-effect loci acting additively; pleiotropic loci such as Lr34/Yr18 and Lr46/Yr29 add durability. We used an elite Australian panel (OzWheat=589) and a diverse landrace panel (Vavilov=295), genotyped with ∼30 000 single nucleotide polymorphisms (SNPs) and phenotyped across environments. Linkage disequilibrium partitioning defined 7659 genome-wide haploblocks. To prioritize 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 shared across panels; for leaf rust, 50 were significant, with 29 also detected in Vavilov. Several intervals co-localized with APR regions (Lr46/Yr29), and one 7BL interval intersected the seedling gene Lr14a. To translate mapping into breeding decisions, we developed an introgression fitness index to quantify the value of resistant haplotypes in elite backgrounds. Using the elite cultivar Scepter, we applied a genetic algorithm to select 50 donor parents carrying desirable haplotypes. Simulations showed that pyramiding these haplotypes can enhance resistance while maintaining the elite genomic background. This study provides practical breeding tools, including a haplotype catalogue and a novel selection index to accelerate rust-resistant wheat development.