Integrating image-based phenotyping and QTL mapping to enhance genetic resistance and accelerate breeding for bacterial grain rot resistance in rice

Bacterial grain rot (BGR), caused by Burkholderia glumae, is a major disease that reduces the yield of rice (Oryza sativa L.), thereby threatening food security. Conventional phenotypic analysis methods face limitations in objectively evaluating disease resistance and understanding the genetic basis. In this study, we integrated image-based phenotypic analysis with QTL mapping to screen for QTLs and candidate genes associated with B. glumae resistance. B. glumae was inoculated into 189 recombinant inbred lines (RILs) derived from Kele (resistant) and IS592BB (susceptible), followed by visualization and quantitative analysis using DAB staining. Phenotypic parameters, including the field resistance score, ratio of diseased spikelets (%), DAB staining intensity, and ratio of diseased area (%), were measured and used for QTL mapping. On chromosome 1, within Chr01_24592710-Chr01_37274755, four QTLs-qFRS1 [LOD: 5.98, phenotype variation explained (PVE): 15.41%], qRDS1 (LOD: 5.29, PVE: 18.56%), qQDS1 (LOD: 9.58, PVE: 22.02%), and qRDA1 (LOD: 8.44, PVE: 31.51%)-were identified as overlapping. After fine-mapping we narrow down Chr01_33472174-Chr01_33838140 and a total of 16 candidate genes were screened this region. Among which OsBGq1 was found to encode a nucleotide-binding LRR receptor (NLR) domain. OsBGq1 expression increased significantly upon B. glumae infection. Additionally, RILs Kele type of Chr01_33472174-Chr01_33838140 presented increased ROS-scavenging enzyme activity and phytoalexin accumulation upon B. glumae infection, contributing to increased resistance. The integration of DAB-based quantitative phenotyping with QTL mapping is proposed to provide a more objective indicator for identifying genes associated with resistance to BGR.