Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties

Abstract

Temperate japonica rice varieties exhibit wide variation in the phenotypes of several important agronomic traits, including disease resistance, pre-harvest sprouting resistance, plant architecture, and grain quality, indicating the presence of genes contributing to favorable agronomic traits. However, gene mapping and molecular breeding has been hampered as a result of the low genetic diversity among cultivars and scarcity of polymorphic DNA markers. Single nucleotide polymorphism (SNP)-based kompetitive allele-specific PCR (KASP) markers allow high-throughput genotyping for marker-assisted selection and quantitative trait loci (QTL) mapping within closely related populations. Previously, we identified 740,566 SNPs and developed 771 KASP markers for Korean temperate japonica rice varieties. However, additional markers were needed to provide sufficient genome coverage to support breeding programs. In this study, the 740,566 SNPs were categorized according to their predicted impacts on gene function. The high-impact, moderate-impact, modifier, and low-impact groups contained 703 (0.1%), 20,179 (2.7%), 699,866 (94.5%), and 19,818 (2.7%) SNPs, respectively. A subset of 357 SNPs from the high-impact group was selected for initial KASP marker development, resulting in 283 polymorphic KASP markers. After incorporation of the 283 markers with the 771 existing markers in a physical map, additional markers were developed to fill genomic regions with large gaps between markers, and 171 polymorphic KASP markers were successfully developed from 284 SNPs. Overall, a set of 1225 KASP markers was produced. The markers were evenly distributed across the rice genome, with average marker density of 3.3 KASP markers per Mbp. The 1225 KASP markers will facilitate QTL/gene mapping and marker-assisted selection in temperate japonica rice breeding programs.

Genomic Variation in Korean japonica Rice Varieties

“…We previously analyzed genome resequencing data from 13 Korean temperate japonica rice varieties and discovered 740,566 SNPs, from which we developed 1225 KASP markers [16][17][18]. These markers were successfully used for QTL mapping of several important traits and MABB within Korean temperate japonica varieties [19][20][21][22].…”

Investigation of Imidazolinone Herbicide Resistance Gene with KASP Markers for Japonica/Geng Rice Varieties in the Huanghuaihai Region of China

“…KASP can be used for accurate biallelic genotyping of target SNPs due to its accuracy, specificity, flexibility, low cost and high efficiency [ 43 ]. Additionally, the combination of multiple high-throughput sequences and KASP can compensate for the shortcomings of both methods and plays an important role in germplasm resource identification, marker-assisted breeding, genetic map construction and QTL mapping [ 33 , 44 , 45 ]. In this study, we developed four KASP markers based on OsALS1 variations, which facilitated the screening of Japonica / Geng rice in the Huanghuaihai region.…”

Recent Advances in Rice Varietal Development for Durable Resistance to Biotic and Abiotic Stresses through Marker-Assisted Gene Pyramiding

“…KASP markers were effectively employed in rice cultivars for genetic map building and QTL analyses of disease resistance and pre-harvest sprouting resistance. For example, genetic maps were built using the KASP 205, 158 and 175 markers with three populations of F 2 generations from crosses between Junam and Nampyeong [47,48]. Among these markers, SSR markers are highly prioritized in breeding programs due to their abundance, co-dominance and highly polymorphic nature [26].…”