Genomic exploration of durable wheat rust resistance by integrating data from multiple worldwide populations

Global wheat (Triticum aestivum L.) production faces significant challenges due to the destructive nature of leaf (Puccinia triticina; leaf rust [Lr]), stem (Puccinia graminis; stem rust [Sr]), and stripe (Puccinia striiformis; stripe rust [Yr]) rust diseases. Despite ongoing efforts to develop resistant varieties, these diseases remain a persistent challenge due to their highly evolving nature. Overcoming these challenges requires the identification and deployment of genetically diverse resistance genes in future cultivars. This study explored durable resistance against rust diseases by integrating data from five global populations. The populations exhibit diverse origins and were phenotypically evaluated in 16, 13, and 19 global field experiments, with total phenotypic observations of 12,694, 10,725, and 16,281 for Lr, Sr, and Yr, respectively. Field experiments showed moderate heritability of 0.43, 0.62, and 0.41 for Lr, Sr, and Yr, respectively. Genetic correlations were moderate among experiments for the same disease (0.34–0.59), but low among the three diseases (<0.21). The meta-genome-wide association studies (metaGWAS) analysis identified 19 quantitative trait loci (QTLs) associated with the resistance to Lr, 17 with the resistance to Sr, and five with the resistance to Yr. Six QTLs controlling resistance to more than one rust disease were also identified. Additionally, the study unveiled 13 potentially new QTLs (five for Lr and Yr each and three for Yr), contributing valuable insights into the genetic basis of wheat rust resistance. The integration of diverse populations and environments through metaGWAS enhanced the detection of stable QTL. This research provides breeders with additional resistance loci to combat rust pathogens.