Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping

Abstract

Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.

Marker-assisted selection in rice breeding programs in Hokkaido

“…Previously, we identified the blast resistant gene Pi-cd on chromosome 11 as a major genetic factor in the local rice population in Hokkaido (Fig. 3F), although it may be derived from a rice variety Cody from USA (Shinada et al 2015b). The Pi-cd locus is distributed specifically in tropical japonica (upland) rice varieties over the world and might be introgressed from wild relative O. meridionalis (Fujino et al 2019c).…”

“…The rice variety Kitakurin was registered in 2014 and exhibits good eating quality and vigorous resistance to rice blast (http://www.pref.hokkaido.lg.jp/ns/nsk/kome/index3.htm). Pi-cd plays a major role in blast resistance in Kitakurin (Fujino et al 2019c, Shinada et al 2015b.…”

Role of the rice blast resistance gene Pi‐cd in rice (Oryza sativa) breeding programmes

“…Previously, we identified a blast resistance gene, Pi‐cd , on chromosome 11 as a major genetic factor in the local population in Hokkaido, Japan (Shinada et al., 2015). Hokkaido is the northernmost region of Japan and one of the northern limits of rice cultivation in the world (Fujino, Hirayama, & Kaji, 2019; Fujino, Obara, & Ikegaya, 2019).…”

“…Hokkaido is the northernmost region of Japan and one of the northern limits of rice cultivation in the world (Fujino, Hirayama, & Kaji, 2019; Fujino, Obara, & Ikegaya, 2019). According to the pedigree of the varieties, Pi‐cd was transferred into the local population from the rice variety 'Cody' from America via the variety 'Kitaake', which was registered in 1984 (Shinada et al., 2015). Furthermore, characterization of the genome sequence around the Pi‐cd locus demonstrated that Pi‐cd may have originated from Oryza meridionalis (Fujino, Hirayama, Obara, & Ikegaya, 2019).…”

“…The rice variety 'Kitakurin' was registered in 2014 and exhibits good eating quality and strong resistance to rice blast. Pi‐cd in 'Kitakurin' plays a major role in its blast resistance (Fujino, Hirayama, Obara, et al, 2019; Shinada et al., 2015). Pi‐cd is only one of the exploited blast resistance genes and has been used for blast resistance in rice‐breeding programmes in Hokkaido (Shinada et al., 2015).…”