Comparative genome assemblies reveal distinct allelic and structural variation at blast resistance loci in rice CT21375‐F4‐4 and Moroberekan

Rice blast, caused by Magnaporthe oryzae, remains a major constraint to rice (Oryza sativa L.) production, and durable resistance will require broader use of genetic diversity beyond commonly studied elite cultivars. We present chromosome-scale genome assemblies of two agronomically significant but genetically divergent rice cultivars: CT21375-F4-4 (hereafter, CT21) and Moroberekan. Despite their genetic divergence, both cultivars show consistently strong resistance to blast under multiyear field conditions. We combined field phenotyping with genome-wide protein-to-genome alignment, predicted proteome comparisons, nucleotide-binding leucine-rich repeat (NLR) annotation, and locus-specific analyses of cloned blast resistance genes to examine resistance-associated genomic variation in these cultivars. The cultivars contained similar numbers and overall subtype compositions of NLR loci, but differed markedly in their correspondence to characterized blast resistance genes. CT21 contained multiple exact or near-exact matches to cloned blast resistance genes and alleles, whereas Moroberekan contained fewer exact matches and was characterized predominantly by high-identity but divergent homologs, suggesting the presence of divergent alleles or resistance architectures that are not well represented by the cloned gene repertoire. Locus-specific analyses further confirmed that high sequence similarity alone does not reliably predict resistance function, and revealed structural variation, including duplication within the Pish NLR cluster in CT21. These results demonstrate that comparable blast resistance phenotypes can occur in cultivars with distinct allelic and structural architectures at known resistance loci. The assemblies and comparative framework developed here provide resources for identifying resistance diversity that may be overlooked by reference gene or marker-based analyses and for prioritizing candidate loci for functional validation and rice improvement.