Discovering putative novel stem rust resistance loci in wheat genetic resources

Stem rust (SR), caused by Puccinia graminis f. sp. tritici (Pgt), poses a threat to wheat production in Germany. This study evaluated 200 plant genetic resources (PGR) and 50 elite lines across four field environments. Multi-environment genome-wide association mapping based on PGR accessions revealed 1942 marker-trait associations (MTAs), grouped into eight quantitative trait loci (QTLs), which explained 0.84%-28.19% of phenotypic variance. Three of these QTL, QSr1B_1.47_67.79, QSr4A_716.31_716.32, and QSr7D_171.80_174.34, harbor five haplotypes that have likely not been used in breeding. Five representative MTAs (Chr1B:25506861, Chr1B:17349639, Chr1B:67755088, Chr4A:716319007, and Chr7D:171807054) represent these five putative novel haplotypes, and together they conservatively explained 2.40%-7.03% of the phenotypic variance. Four genotypes carrying all favorable alleles of the representative MTAs were identified as potential donor lines for future breeding. Within eight QTL regions, 44 candidate genes were prioritized. These findings provide new insights into the genetic architecture of SR resistance and highlight promising targets for marker-assisted prebreeding.