Fine mapping and sequence analysis reveal a promising candidate gene encoding a novel NB-ARC domain derived from wild rice (Oryza officinalis) that confers bacterial blight resistance.

Bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious constraints in rice production. The most sustainable strategy to combat the disease is the deployment of host plant resistance. Earlier, we identified an introgression line, IR 75084-15-3-B-B, derived from Oryza officinalis possessing broad-spectrum resistance against Xoo. In order to understand the inheritance of resistance in the O. officinalis accession and identify genomic region(s) associated with resistance, a recombinant inbred line (RIL) mapping population was developed from the cross Samba Mahsuri (susceptible to bacterial blight) × IR 75084-15-3-B-B (resistant to bacterial blight). The F2 population derived from the cross segregated in a phenotypic ratio of 3: 1 (resistant susceptible) implying that resistance in IR 75084-15-3-B-B is controlled by a single dominant gene/quantitative trait locus (QTL). In the F7 generation, a set of 47 homozygous resistant lines and 47 homozygous susceptible lines was used to study the association between phenotypic data obtained through screening with Xoo and genotypic data obtained through analysis of 7K rice single-nucleotide polymorphism (SNP) chip. Through composite interval mapping, a major locus was detected in the midst of two flanking SNP markers, viz., Chr11.27817978 and Chr11.27994133, on chromosome 11L with a logarithm of the odds (LOD) score of 10.21 and 35.93% of phenotypic variation, and the locus has been named Xa48t. In silico search in the genomic region between the two markers flanking Xa48t identified 10 putatively expressed genes located in the region of interest. The quantitative expression and DNA sequence analysis of these genes from contrasting parents identified the Os11g0687900 encoding an NB-ARC domain-containing protein as the most promising gene associated with resistance. Interestingly, a 16-bp insertion was noticed in the untranslated region (UTR) of the gene in the resistant parent, IR 75084-15-3-B-B, which was absent in Samba Mahsuri. The association of Os11g0687900 with resistance phenotype was further established by sequence-based DNA marker analysis in the RIL population. A co-segregating PCR-based INDEL marker, Marker_Xa48, has been developed for use in the marker-assisted breeding of Xa48t.

Identification and fine mapping of a new bacterial blight resistance gene, Xa43(t), in Zhangpu wild rice (Oryza rufipogon).

Bacterial blight (BB) is currently considered one of the most serious rice diseases and is caused by Xanthomonas oryzae pv. oryzae (Xoo). Numerous studies have shown that breeding resistant rice varieties is one of the most effective methods to prevent BB, and it is important to identify and isolate more BB resistance (R) genes from different rice resources. Using a map-based approach, we identified a new QTL/gene, Xa43(t), from ZhangPu wild rice, which was highly resistant to the BB isolate PX099. We performed bulked segregant analysis combined with candidate gene prediction to identify the candidate gene. The Xa43(t) gene was narrowed down to a 29-kb region containing four putative genes. More importantly, the candidate gene Xa43(t) did not affect the main agronomic traits of rice. We also identified a widely applicable molecular marker, namely Inde1-18, which co-segregates with the Xa43(t) gene. The Xa43(t) gene is a new broad-spectrum BB resistance gene without identified alleles and has good application prospects for rice disease resistance breeding.

Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm.

BACKGROUND: A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines. Rice diversity panels can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. This study was conducted to identify loci associated to BB resistance, new genetic donors and useful molecular markers for marker-assisted breeding. RESULTS: A genome-wide association study (GWAS) of BB resistance using a diverse panel of 285 rice accessions was performed to identify loci that are associated with resistance to nine Xoo strains from the Philippines, representative of eight global races. Single nucleotide polymorphisms (SNPs) associated with differential resistance were identified in the diverse panel and a subset of 198 indica accessions. Strong associations were found for novel SNPs linked with known bacterial blight resistance Xa genes, from which high utility markers for tracking and selection of resistance genes in breeding programs were designed. Furthermore, significant associations of SNPs in chromosomes 6, 9, 11, and 12 did not overlap with known resistance loci and hence might prove to be novel sources of resistance. Detailed analysis revealed haplotypes that correlated with resistance and analysis of putative resistance alleles identified resistant genotypes as potential donors of new resistance genes. CONCLUSIONS: The results of the GWAS validated known genes underlying resistance and identified novel loci that provide useful targets for further investigation. SNP markers and genetic donors identified in this study will help plant breeders in improving and diversifying resistance to BB.