Pyramiding resistance to bacterial grain rot and bacterial leaf blight in rice using novel CAPS/dCAPS markers

Bacterial grain rot (BGR), caused by Burkholderia glumae, is a major constraint in rice production, particularly under high temperature and humidity. However, effective molecular markers for BGR resistance remain to be developed. Thus, we aimed to identify quantitative trait loci (QTLs) associated with BGR resistance and develop molecular markers to facilitate marker-assisted selection (MAS). Kele (xa5, resistant to BGR) and IS592BB (Xa3, Xa21, susceptible to BGR), we constructed Kele/IS592BB recombinant inbred lines (KIRILs) to map QTLs associated with resistance to BGR. Based on the identified QTLs, we developed CAPS and dCAPS markers, which were subsequently validated in the Kele/IS592BB//IS592BB backcrossing inbred lines. Five QTLs were detected: qRBG(RDA)1 [logarithm of odds (LOD): 16.4, phenotypic variation explained (PVE): 37.0%] and qRBG(RDS)1 (LOD: 19.1, PVE: 44.4%) on chromosome 1; qRBG(RDS)3 (LOD: 4.2, PVE: 8.2%) on chromosome 3; and qRBG(RDA)6 (LOD: 3.5, PVE: 6.3%) and qRBG(RDS)6 (LOD: 4.7, PVE: 12.3%) on chromosome 6. Based on the flanking sequences of these loci, two cleaved amplified polymorphic sequences (CAPS) and four derived CAPS (dCAPS) markers were developed. Marker-assisted selection using these markers resulted in BGR-resistant lines with less than 30% infected grain ratio and lesion area. Among the selected lines, KIBIL84 (Kele/IS592BB//IS592BB backcross inbred line) exhibited strong resistance to BGR and harbored a pyramided gene combination (Xa3+xa5+Xa21) for resistance to bacterial leaf blight (BLB). Under BLB pressure, KIBIL84 showed reduced lesion length (1.2 cm) and lesion area (5.2%). In addition, it demonstrated improved aboveground growth under field conditions compared with its parental lines, suggesting a positive relationship with yield potential. These findings indicate that the developed markers are effective for screening BGR resistance and that KIBIL84 is a promising breeding material for improving resistance to multiple bacterial diseases in rice.