Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a worldwide rice disease. QTL providing BB resistance were identified using a set of introgression lines (ILs) derived from a cross between Teqing and Lemont, and 3924 evenly distributed SNP markers developed from the two parents. After inoculating three Xoo pathotypes, CII, CIV and CV, seven major BB resistance-associated QTL were detected. The alleles at all loci with improved BB resistance were from the Teqing background. Four QTL resistance to CII and CIV were identified in the reciprocal backgrounds across 2 years. Six QTL conferring resistance to CV identified in Teqing background were not detected in Lemont background, indicating that genetic background had a strong effect on the BB resistance-associated QTL. Based on the interactions of 27 significant digenic QTL pairs among the seven main-effect QTL, the QTL were divided into three strain-specific groups. Genotype analyses of resistant ILs suggest that rice lines with a high level of resistance to BB can be achieved by pyramiding R gene(s) and QTL that interact with R gene(s).
