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.
Highlights
Cultivated rice (Oryza sativa L.) is one of the most important crop species worldwide, providing food for more than half the global population
The 1225 kompetitive allele-specific PCR (KASP) marker set, which comprises 454 markers developed in this study and 771 markers developed previously, offers comprehensive genome coverage and will prove useful in breeding programs for temperate japonica rice varieties
283 and 171 markers were polymorphic, respectively, in the tested japonica rice varieties. These markers were combined with 771 KASP markers that we developed previously, resulting in a set of 1225 polymorphic KASP markers for high-throughput Single nucleotide polymorphism (SNP) genotyping in temperate japonica rice (Table 4 and Figure 3)
Summary
Cultivated rice (Oryza sativa L.) is one of the most important crop species worldwide, providing food for more than half the global population. Several types of molecular markers with high levels of polymorphism between indica and japonica cultivars have been developed, but the polymorphism of those markers within the japonica group is lower than within the indica group [2,3,5]. Despite this low level of marker diversity, phenotypic differences in agronomic traits are apparent among closely related japonica rice varieties [6,7]. The identification of genome sequence variants and the development of efficient high-throughput markers are required for genetic analysis and molecular breeding of temperate japonica rice varieties
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