The pan-NLRome and diversity of Watkins wheat provide genetic resources for improving disease resistance and adaptation

The nucleotide-binding domain leucine-rich repeat (NLR) receptor proteins play pivotal roles in plant disease resistance due to their extensive genetic diversity driven by long-term co-evolution with pathogens. In this study, we present a comprehensive wheat pan-NLRome containing 8056 NLR genes, which display remarkable diversity in gene structure, nucleotide variation, and presence-absence polymorphisms across the A.E. Watkins landrace collection. Comparative analysis between the landraces and modern cultivars revealed that 1316 NLRs were gained, and 1179 NLRs were lost during wheat breeding. Furthermore, we identified 221 spatial pairs of NLR genes in the genome, which show co-evolutionary patterns similar to those of physical NLR pairs. Finally, we identified 1710 candidate NLR genes potentially involved in resistance to various diseases or environmental adaptation. Overall, our study establishes a comprehensive and diversified NLR gene resource that will facilitate the discovery and utilization of genes for disease resistance and climate adaptation in wheat.