Pan-NLRome analysis uncovers genetic diversity and evolutionary dynamics among rice, maize and sorghum

Nucleotide-binding leucine-rich repeat (NLR) genes constitute one of the largest families of plant immune receptors and are central to crop disease resistance. Rice (Oryza sativa L.), maize (Zea mays L.), and sorghum (Sorghum bicolor (L.) Moench) are major crops underpinning global food security, and enhancing their immunity is critical for yield stability. Here, we conducted a comprehensive analysis of NLR repertoires across 75 genomes from these three grass crops, identifying 24,944 genes that exhibit extensive intra- and interspecific variation. The crops share broadly comparable domain architectures of NLR genes, despite their differences in gene number and genomic clustering pattern. We detected 68 integrated domains, revealing high diversity and pronounced lineage specificity. The pan-NLR profiles of the three crops were generally similar, with strong lineage-restricted expansion of NLR gene families. Cross-species comparisons revealed distinct proportions of common gene and lineage-specific genes between the crops, suggesting divergent evolutionary trajectories. Widespread presence/absence variation of NLR genes was identified within each crop, with an enrichment in clustered loci. NLRs, especially clustered ones, were significantly enriched in disease-resistance quantitative trait locus (QTL) hotspots, supporting their critical role in crop disease resistance. Notably, conserved Rp1-D clusters co-localized with resistance QTLs in the three crops, underscoring functional conservation and the translational potential of cross-species NLR studies. Collectively, these findings provide new insights into the genetic diversity and evolutionary dynamics of NLRs in three major grass crops and provide a valuable genomic resource for enhancing crop disease resistance.