A multi‐race blast resistance locus identified and validated in US elite rice via association and biparental mapping

Rice blast, caused by Magnaporthe oryzae (syn. Pyricularia oryzae), remains a major disease in US rice (Oryza sativa L.) production, highlighting the need for additional resistance loci and continued development of blast-resistant rice varieties. We evaluated 258 US elite long-grain breeding lines for resistance to four M. oryzae strains representing blast races IB-1, IB-17, IB-49, and IE1K and conducted a genome-wide association study using 543,136 single-nucleotide polymorphisms. Thirteen significant loci were detected, including three multi-race resistance loci. The strongest locus, qBlast4.1, overlapped the Pi63 region and conferred resistance to IB-1, IB-49, and IE1K. A second locus, qBlast12.1, located near the Pita gene cluster, contributed resistance to IB-1 and IB-17. qBlast4.1 and qBlast12.1 explained up to 38% and 56% of phenotypic variation, respectively, and jointly accounted for 74% of the variation for IB-1. Both loci were validated in a recombinant inbred line population. Additional screening with eight M. oryzae strains demonstrated complementary resistance profiles for qBlast4.1 and qBlast12.1. These results show that qBlast4.1 confers resistance to multiple blast races. Together, qBlast4.1 and qBlast12.1 provide valuable targets for marker-assisted breeding. Resistant alleles at both loci were present in only 6.4% of elite breeding lines, highlighting substantial opportunities for resistance allele pyramiding.