High-resolution genetic mapping of a novel bacterial blight resistance gene xa-45(t) identified from Oryza glaberrima and transferred to Oryza sativa

A novel recessive bacterial blight resistance locus designated as a xa-45(t) was identified from Oryza glaberrima accession IRGC 102600B, transferred to O. sativa and mapped to the long arm of chromosome 8 using ddRAD sequencing approach. The identified QTL spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. An STS marker developed from the locus LOC_Os08g42410 was found co-segregating with the trait and will be useful for marker-assisted transfer of this recessive resistance gene in breeding programs. Bacterial blight, caused by Xanthomonas oryzae pv. oryzae, is one of the major constraints of rice productivity in Southeast Asia. In spite of having 44 bacterial blight resistance genes from cultivated rice and wild species, the durability of resistance is always at stake due to the continually evolving nature of the pathogen and lack of suitable chemical control. Here, we report high-resolution genetic mapping of a novel bacterial blight resistance gene tentatively designated as a xa-45(t) from an introgression line derived from Oryza glaberrima accession IRGC 102600B. This introgression line was crossed with the susceptible rice indica cultivar cv. Pusa 44 to generate F₂ and F_2:3 populations for inheritance and mapping studies. The inheritance studies revealed the presence of single recessive locus controlling resistance to the Xanthomonas pathotype seven. A high-density linkage map was constructed using double-digest restriction-associated DNA sequencing of 96 F₂ populations along with the parents. The QTL mapping identified a major locus on the long arm of rice chromosome 8 with a LOD score of 33.22 between the SNP markers C8.26737175 and C8.26818765. The peak marker, C8.26810477, explains 49.8% of the total phenotypic variance and was positioned at 202.90 cM on the linkage map. This major locus spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. A co-segregating STS marker was developed from the LOC_Os08g42410 for efficient transfer of this novel gene to elite cultivars.