Plant disease resistance is typically conferred by nucleotide-binding site leucine-rich repeats (NLR) proteins; however, the diversity of NLR genes in spinach has remained largely unexplored. We identified 2, 549 NLR genes across 19 Spinacia assemblies of cultivated spinach and its two wild species, and constructed a comprehensive pan-NLRome, which was categorized into six subfamilies, and the most frequent NLR class was CC-NBARC-LRR. The pan-NLRome consists of 186 NLR families, comprising 38. 7% core, 51. 1% dispensable and 10. 2% private families. By integrating pan-NLRome with k -mer-based genome-wide association studies (GWAS), we developed a novel pipeline for rapid identification of disease resistance genes. Using this approach, we directly pinpointed a candidate gene, Te17S24XXChr1ₙlr42, for the RPF1 locus, which confers resistance to spinach downy mildew pathogen races 1–7, 9, 11, 13, 15, 16, 18, and 20. In contrast, a single-genome-based method identified four candidate genes, which required further analysis confirm the final gene. The Spinacia pan-NLRome serves as an invaluable resource for exploring NLR gene evolution and plant disease resistance mechanisms. Our developed pipeline offers a reliable and efficient strategy for cloning resistance genes across multiple crops.
She et al. (Tue,) studied this question.