Fine mapping and Candidate Gene Identification of a Novel Rice Bacterial Blight Resistance Gene Xa51(t) from Yunnan Landrace Haonuoyang

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae ( Xoo ) is one of the most severe limitations on rice production. The most renewable strategy to combat this disease is the spread of host plant resistance. In a previous study, we identified an introgression line (H197) derived from the Yunnan landrace rice variety Haonuoyang that possesses extensive resistance to Xoo . To analyze the inheritance of resistance in Haonuoyang and to identify genomic regions Linked to BB resistance, an F₂ population stemmed from a cross between H197 and Jingang 30 was utilized to verify and fine-map the BB resistance-related gene in H197. The observation of a 3:1 phenotypic ratio (resistant: susceptible) in the F ₂ population suggests that a single dominant gene controls the resistance in H197. In the F₃ generation, the constructed bulks, consisting of 47 resistant and 47 susceptible lines, were genotyped using SLAF-seq a high-throughput reduced-representation genome sequencing approach. This has enabled the discovery and analysis of thousands (40K) of single nucleotide polymorphism (SNP) markers at the genome level. By compound interval mapping, a main locus was identified between SNP markers Chr11.28863864 and Chr11.28894443, and the locus was named Xa51(t) . Five putatively expressed genes were identified within the genomic region between the two markers flanking Xa51(t) . Based on cloning and sequence comparison of these genes in the parents, Os11g47910 (encoding a GRAS domain-containing protein) was found to be the most candidate gene for BB resistance. A 250-bp deletion at the 3’end of the gene was detected between Haonuoyang and Jingang30. The association of Os11g47910 with BB resistance was further confirmed by sequence-based DNA marker analysis in the RIL population. A co-segregating PCR-based(Kompetitive Allele Specific PCR)KASP marker was developed for marker-assisted breeding. The cloning of this novel BB resistance gene Xa51(t) not only enriched the molecular mechanism study of rice disease resistance but also expanded the genetic basis of resistance breeding by tapping excellent gene resources from Yunnan local rice landraces, laying a solid foundation for efficient marker-assisted breeding of durable disease-resistant rice varieties.