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Journal article
Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties
Plants (Basel), v 9(11), pp 1-14
10 Nov 2020
PMID: 33182649
Featured in Collection : UN Sustainable Development Goals @ Drexel
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.
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Details
- Title
- Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties
- Creators
- Kyeong-Seong Cheon - RDA (United States)Young-Min Jeong - Fdn Agri Tech Commercializat Transfer FACT, Seed Ind Promot Ctr, Gimje 54324, South KoreaHyoja Oh - RDA (United States)Jun Oh - RDA (United States)Do-Yu Kang - RDA (United States)Nyunhee Kim - RDA (United States)Eungyeong Lee - RDA (United States)Jeongho Baek - RDA (United States)Song Lim Kim - RDA (United States)Inchan Choi - RDA (United States)In Sun Yoon - RDA (United States)Kyung-Hwan Kim - RDA (United States)Yong Jae Won - RDA (United States)Young-il Cho - Fdn Agri Tech Commercializat & Transfer FACT, Dept Seed Serv, Seed Business Team, Iksan 54667, South KoreaJung-Heon Han - RDA (United States)Hyeonso Ji - RDA (United States)
- Publication Details
- Plants (Basel), v 9(11), pp 1-14
- Publisher
- Mdpi
- Number of pages
- 14
- Grant note
- PJ01323401 / Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center); Rural Development Administration (RDA) Rural Development Administration, Republic of Korea; Rural Development Administration (RDA)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Mechanical Engineering and Mechanics
- Web of Science ID
- WOS:000593769900001
- Scopus ID
- 2-s2.0-85095987599
- Other Identifier
- 991020547447604721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Plant Sciences