Genome-wide prediction of cloned disease resistance homologues across the Oryza genus.

The wild relatives of rice (Oryza sativa L.) represent reservoirs of genetic diversity and potential sources of novel pest and disease resistance. The recent availability of high-quality Oryza genome assemblies has enabled greater exploration of this diversity across the genus. This study aimed to identify and characterize novel disease resistance gene candidates across these wild species. A total of 24 assembled Oryza genomes and proteomes from both wild and cultivated species were analyzed. Putative homologues to functionally validated, cloned disease resistance (CDR) genes in rice were identified using basic local alignment searches with BLASTp and designated into classes with RGAugury. Homologue characterization analyses, including physical distribution, clustering, gene duplication, phylogenies, and domain structure for NBS-LRR (NLR)-like homologues, were also conducted. A total of 2460 homologues to CDR genes were identified. Homologue abundance was generally highest in cultivated rices, followed by wild AA species and non-AA taxa, with no clear relationship to genome or chromosome size. In allotetraploids, CDR homologues were more abundant in CC sub-genomes, consistent with broader patterns of preferential gene retention. Most homologues were designated as NLRs or receptor-like kinases, which were also the gene classes most frequently associated with duplication. Atypical resistance genes were often designated as singletons or segmental genes. Nucleotide-binding site domain analyses revealed conserved motifs across the genus. Discordance between gene phylogenies and the Oryza species tree suggests complex evolutionary histories across resistance-associated gene families. Overall, this study provides an insight into disease resistance gene diversity across the Oryza genus and highlights loci that warrant further investigation for future rice breeding.