Bacterial blight (BB), which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is an important rice disease responsible for significant yield losses. In the rice-growing regions of South China where BB outbreaks are common, the resistance of cultivars with BB resistance genes Xa4 and Xa21 has been lost because of rapid changes in the Xoo population structure and virulence. In this study, 421 diverse rice accessions were evaluated regarding their resistance to two Xoo strains, namely GD1358 (C5) and Ⅳ, which are prevalent pathotypes in South China and overcame the resistance of Xa4 and Xa21, respectively. Using the 4.8mio filtered SNP dataset, we conducted a genome-wide association study, which identified 13 loci associated with BB resistance, including eight new quantitative trait loci (QTL) and five QTL harboring known BB resistance genes: Xa3/Xa26, xa5, Xa35(t), Xa36(t), Xa40, Xa43(t), and xa44(t). Intriguingly, a steep peak was detected on chromosomes 5 and 11. Six QTL including three new ones, were distributed on chromosome 11, whereas a new QTL qBB5.1 and a known QTL were detected on chromosome 5. Haplotype analyses indicated that the LOC_Os05g01610 (OsPRAF2) gene within the qBB5.1 region, which encodes a PRAF protein, is associated with BB resistance. Furthermore, OsPRAF2 knockout lines generated using the CRISPR-Cpf1 system were significantly more resistant to Xoo strains than the wild-type plants. Our results provide researchers and breeders with useful information regarding QTL and gene resources, which may be relevant for developing new BB-resistant rice cultivars.

Bacterial blight (BB), which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most destructive bacterial diseases of rice (Oryza sativa L.). During plant defense responses, microRNAs (miRNAs) play important roles in regulating disease resistance. However, the functions of miRNAs in the interaction between rice and Xoo remain relatively uncharacterized. In this study, we compared the miRNA profiles of the BB resistant rice introgression line F329 and its susceptible recurrent parent Huang-Hua-Zhan (HHZ) at multiple time points after inoculation with Xoo. A total of 538 known and 312 novel miRNAs were identified, among which only 17 and 26 were responsive to Xoo infection in F329 and HHZ, respectively. Compared with the expression levels in HHZ, 37 up-regulated and 53 down-regulated miRNAs were detected in F329. The predicted target genes for the miRNAs differentially expressed between F329 and HHZ were revealed to be associated with flavonoid synthesis, the reactive oxygen species regulatory pathway, plant hormone signal transduction, defense responses, and growth and development. Additionally, the patterns of interactions between osa-miR390-3p, novel_miR_104, novel_miR_238, osa-miR166k-5p, osa-miR529b, and osa-miR167h-3p and their target genes were further validated by quantitative real-time PCR. Furthermore, we overexpressed osa-miR167h-3p in transgenic plants and proved that this miRNA positively regulates the resistance of rice to BB. These results provide novel information regarding the miRNA-based molecular mechanisms underlying the disease resistance of rice. The data presented herein may be useful for engineering rice BB resistance via miRNAs.