Identification of QTLs for Blast, Bacterial Blight, and Planthopper Resistance Using SNP-Based Linkage Maps from Two Recombinant Inbred Rice Lines

Rice is the most significant global food security. Several biotic factors limit rice production, breeding biotic-resistant rice has, therefore, become an increasingly important goal. Two elite rice lines, IR71033-121-15 (IR71033) and IR57514-PMI-5-B-1-2 (IR57514), provide potential genes for biotic stress resistance traits. In this study, genotyping by sequencing (GBS) for single nucleotide polymorphism (SNP)-based linkage map construction was used to detect quantitative trait loci (QTLs) for blast (BL), bacterial blight (BB), whitebacked planthopper (WBPH), and brown planthopper (BPH) resistance. IR71033 was derived from Oryza minuta and carried BL, BB, WBPH, and BPH resistance QTLs. IR57514 is a well-adapted rainfed lowland line that carries BL and BB resistance QTLs. Two sets of recombinant inbred line (RIL) populations derived from crosses of KDML105 × IR71033 and KDML105 × IR57514 were used to dissect the genetic basis of disease and insect pest resistance. The RIL populations were evaluated for BL, BB, WBPH, and BPH resistance from 2016 to 2018 at four rice research centers in Thailand. From these, we identified a large number of SNPs through GBS and constructed high-resolution linkage maps. By combining phenotypic evaluation with the GBS data, a total of 24 QTLs on four chromosomes were detected that confered pest resistance and explained 7.3% - 61.4% of the phenotypic variance. These findings should facilitate identifying novel resistance genes and applying marker-assisted selection for resistance to the four major rice pests investigated here. These strategies will improve the resilience and reliability of rice varieties adapted to the low-yielding environment of rainfed lowland areas worldwide.