Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major factor causing rice yield loss in most rice-cultivating countries, especially in Asia.


The deployment of cultivars with resistance to BB is the most effective method to control the disease. However, the evolution of new Xoo or pathotypes altered by single-gene-dependent mutations often results in breakdown of resistance. Thus, efforts to identify novel R-genes with sustainable BB resistance are urgently needed. In this study, we identified three quantitative trait loci (QTLs) on chromosomes 1, 4, and 11, from an F2 population of 493 individuals derived from a cross between IR73571-3B-11-3-K3 and Ilpum using a 7K SNP chip. Of these QTLs, one major QTL, qBB_11, on chromosome 11 explained 61.58% of the total phenotypic variance in the population, with an LOD value of 113.59, based on SNPs 11964077 and 11985463. The single major R-gene, with recessive gene action, was designated xa44(t) and was narrowed down to a 120-kb segment flanked within 28.00 Mbp to 28.12 Mbp. Of nine ORFs present in the target region, two ORFs revealed significantly different expression levels of the candidate genes. These candidate genes (Os11g0690066 and Os11g0690466) are described as “serine/threonine protein kinase domain containing protein” and “hypothetical protein,” respectively. The results will be useful to further understand BB resistance mechanisms and provide new sources of resistance, together with DNA markers for MAS breeding to improve BB resistance in rice.





Fig. 2 Linkage map and QTL analysis using F2 mapping population. a Genetic linkage map of the 12 chromosomes based on 1954 SNP markers segregating in the P6/Ilpum 493 F2plants. Black dots beside chromosomes 1, 4, and 11 represent the positions of detected QTLs. b The LOD profile and additive effect of major QTL analyzed by inclusive composite interval mapping on chromosome 11. The SNP location was positioned in the whole genome. The positive additive effect was derived from the susceptible parent Ilpum, whereas the negative value was related to the resistant parent. The dotted line is LOD threshold calculated by 1000 permutations.