Genetic Architecture of Complex Resistance to Wheat Rusts Using Nested Association Mapping

Rust diseases affect wheat grain production significantly and are important threats to future food security worldwide. The rust pathogens can evolve into new virulent strains over time and thus present new threats to the crop. In this study, a wheat nested association mapping (WNAM) population with 1122 lines, including nine recombinant inbred line (RIL) families sharing one common parent (PBW343) was generated. This WNAM is the largest publicly available genetic resource platform to dissect the genetic architecture of resistances to stem rust (Sr), yellow rust (Yr) and leaf rust (Lr) using joint linkage analysis. The ten parental lines and their derived WNAM population showed a wide range of genetic and phenotypic variation, particularly for Sr resistance. The consensus map was constructed with 777 polymorphic DArT markers, which were polymorphic in at least three WNAM families. In total, there were 34 QTL related to adult plant resistance (APR) to Sr, Yr, and Lr with 9, 18, and 7 QTL located on A, B and D genomes, respectively. Twenty of 34 QTL had pleiotropic effects on Sr, Yr and Lr resistances. Four QTL were located at same chromosomes region as well characterized APR genes (Sr31/Sr26, Lr46/Yr29/Sr58, Sr2/Yr30/Lr27, and Sr57/Yr18/Lr34); and 12 previously reported QTL were validated. Seventeen QTL are reported for the first time, three (q1AL, q1BS-1, and q1DS-2) of which showed high sequence similarity to various resistance genes encoding proteins that recognize pathogen effectors or their modified host targets. Two novel QTL, q1AL and q1BS-1 had pleiotropic effects on Sr, Yr and Lr resistances. For Sr, 65.7% of the resistance alleles were contributed by non-PBW343, and the performance of WNAM founders could be predicted by the estimated additive effects of Sr resistance QTL (R²=0.41). Novel pleiotropic QTL identified in this study will advance the genetic research for wheat rusts, and will provide valuable resources for genomics-assisted breeding.