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

Kyeong-Seong Cheon; Young-Min Jeong; Hyoja Oh; Jun Oh; Do-Yu Kang; Nyunhee Kim; Eungyeong Lee; Jeongho Baek; Song Lim Kim; Inchan Choi; In Sun Yoon; Kyung-Hwan Kim; Yong Jae Won; Young-il Cho; Jung-Heon Han; Hyeonso Ji

doi:10.3390/plants9111531

Plants (Nov 2020)

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

Kyeong-Seong Cheon,
Young-Min Jeong,
Hyoja Oh,
Jun Oh,
Do-Yu Kang,
Nyunhee Kim,
Eungyeong Lee,
Jeongho Baek,
Song Lim Kim,
Inchan Choi,
In Sun Yoon,
Kyung-Hwan Kim,
Yong Jae Won,
Young-il Cho,
Jung-Heon Han,
Hyeonso Ji

Affiliations

Kyeong-Seong Cheon: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Young-Min Jeong: Seed Industry Promotion Center, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Gimje 54324, Korea
Hyoja Oh: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Jun Oh: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Do-Yu Kang: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Nyunhee Kim: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Eungyeong Lee: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Jeongho Baek: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Song Lim Kim: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Inchan Choi: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
In Sun Yoon: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Kyung-Hwan Kim: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Yong Jae Won: Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Korea
Young-il Cho: Seed Business Team, Department of Seed Services, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Iksan 54667, Korea
Jung-Heon Han: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
Hyeonso Ji: Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea

DOI: https://doi.org/10.3390/plants9111531
Journal volume & issue: Vol. 9, no. 11
p. 1531

Abstract

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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.

Published in Plants

ISSN: 2223-7747 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Botany
Website: http://www.mdpi.com/journal/plants

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