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Single Nucleotide Polymorphism (SNP) Discovery and Kompetitive Allele-Specific PCR (KASP) Marker Development with Korean Japonica Rice Varieties
Plant Breed. Biotech. 2018;6:391-403
Published online December 1, 2018
© 2018 Korean Society of Breeding Science.

Kyeong-Seong Cheon1, Jeongho Baek1, Young-il Cho2, Young-Min Jeong2, Youn-Young Lee2, Jun Oh1,Yong Jae Won3, Do-Yu Kang1, Hyoja Oh1, Song Lim Kim1, Inchan Choi1, In Sun Yoon1, Kyung-Hwan Kim1,Jung-Heon Han1, Hyeonso Ji1*

1Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
2Seed Industry Promotion Center, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Gimje 54324, Korea
3Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration (RDA), Suwon 16429, Korea
Correspondence to: Hyeonso Ji,, Tel: +82-63-238-4657, Fax: +82-63-238-4654
Received October 19, 2018; Revised October 24, 2018; Accepted October 24, 2018.
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Genome resequencing by next-generation sequencing technology can reveal numerous single nucleotide polymorphisms (SNPs) within a closely-related cultivar group, which would enable the development of sufficient SNP markers for mapping and the identification of useful genes present in the cultivar group. We analyzed genome sequence data from 13 Korean japonica rice varieties and discovered 740,566 SNPs. The SNPs were distributed at 100-kbp intervals throughout the rice genome, although the SNP density was uneven among the chromosomes. Of the 740,566 SNPs, 1,014 SNP sites were selected on the basis of polymorphism information content (PIC) value higher than 0.4 per 200-kbp interval, and 506 of these SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers. The 506 KASP markers were tested for genotyping with the 13 sequenced Korean japonica rice varieties, and polymorphisms were detected in 400 KASP markers (79.1%) which would be suitable for genetic analysis and molecular breeding. Additionally, a genetic map comprising 205 KASP markers was successfully constructed with 188 F2 progenies derived from a cross between the varieties, Junam and Nampyeong. In a phylogenetic analysis with 81 KASP markers, 13 Korean japonica varieties showed close genetic relationships and were divided into three groups. More KASP markers are being developed and these markers will be utilized in gene mapping, quantitative trait locus (QTL) analysis, marker-assisted selection and other strategies relevant to crop improvement.
Keywords : Korean japonica rice, Resequencing, SNP, Kompetitive Alelle-Specific PCR (KASP) marker, Genotyping

December 2018, 6 (4)
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