QTL-Seq Approach Identified Pi63 Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum”

Abstract

Rice blast (BL) caused by Magnaporthe oryzae is a fungal disease causing significant yield losses in rice production worldwide. To overcome the breakdown of resistance by the rapid adaptation of pathogens, identifying resistance (R) genes or QTLs in indigenous rice, which harbors the R genes that co-evolved with the local pathogen race, is necessary. In this study, a recombinant inbred line (RIL) population derived from a cross between RD6 and Phaladum (PLD) was used to map quantitative trait loci (QTL) for BL resistance through a QTL-seq approach. A single QTL (qBLchr4) associated with BL resistance at the seedling and maximum tillering stages was mapped on the long arm of chromosome 4. Five genes, LOC_Os04g0616600, LOC_Os04g0617900 (OsGLP4-1), LOC_Os04g0619600 (OsRLCK161), LOC_Os04g0620800 (Pi63), and LOC_Os04g0621500, were considered the candidate genes representing qBLchr4. Subsequently, the Kompetitive Allele-Specific PCR (KASP) markers specific for the SNP variant and position of each gene were designed for validation in the mapping population. These markers showed the high phenotypic variance explained (PVE) values in all testing methods and/or environments, signifying the major effect of qBLchr4. Among these markers, the Pi63-KASP marker explained the highest and most stable phenotypic variation across all testing methods and/or environments, with 84.18%, 80.34%, and 23.43% in the upland short row (USR) method, Sila environment, and Mueang environment, respectively. Therefore, Pi63 was suggested to be the strongest candidate gene. These results represent the potential utility of future BL resistance breeding and/or pyramiding using marker-assisted selection (MAS).