Next Article in Journal
Overexpression of a Cytosolic 6-Phosphogluconate Dehydrogenase Gene Enhances the Resistance of Rice to Nilaparvata lugens
Previous Article in Journal
Nutrients Leaching in Response to Long-Term Fertigation and Broadcast Nitrogen in Blueberry Production
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Plants
Volume 9
Issue 11
10.3390/plants9111531
plants-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

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

by
Kyeong-Seong Cheon
1,
Young-Min Jeong
2,
Hyoja Oh
1,
Jun Oh
1,
Do-Yu Kang
1,
Nyunhee Kim
1,
Eungyeong Lee
1,
Jeongho Baek
1,
Song Lim Kim
1,
Inchan Choi
1,
In Sun Yoon
1,
Kyung-Hwan Kim
1,
Yong Jae Won
3,
Young-il Cho
4,
Jung-Heon Han
1 and
Hyeonso Ji
1,*
1
Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea
2
Seed Industry Promotion Center, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Gimje 54324, Korea
3
Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Korea
4
Seed Business Team, Department of Seed Services, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Iksan 54667, Korea
*
Author to whom correspondence should be addressed.
Plants 2020, 9(11), 1531; https://doi.org/10.3390/plants9111531
Submission received: 23 September 2020 / Revised: 4 November 2020 / Accepted: 7 November 2020 / Published: 10 November 2020
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
Browse Figures
Versions Notes

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.
Keywords: temperate japonica rice; SNP; high-throughput genotyping; KASP temperate japonica rice; SNP; high-throughput genotyping; KASP

Share and Cite

MDPI and ACS Style

Cheon, K.-S.; Jeong, Y.-M.; Oh, H.; Oh, J.; Kang, D.-Y.; Kim, N.; Lee, E.; Baek, J.; Kim, S.L.; Choi, I.; et al. Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties. Plants 2020, 9, 1531. https://doi.org/10.3390/plants9111531

AMA Style

Cheon K-S, Jeong Y-M, Oh H, Oh J, Kang D-Y, Kim N, Lee E, Baek J, Kim SL, Choi I, et al. Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties. Plants. 2020; 9(11):1531. https://doi.org/10.3390/plants9111531

Chicago/Turabian Style

Cheon, Kyeong-Seong, Young-Min Jeong, Hyoja Oh, Jun Oh, Do-Yu Kang, Nyunhee Kim, Eungyeong Lee, Jeongho Baek, Song Lim Kim, Inchan Choi, and et al. 2020. "Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties" Plants 9, no. 11: 1531. https://doi.org/10.3390/plants9111531

APA Style

Cheon, K.-S., Jeong, Y.-M., Oh, H., Oh, J., Kang, D.-Y., Kim, N., Lee, E., Baek, J., Kim, S. L., Choi, I., Yoon, I. S., Kim, K.-H., Won, Y. J., Cho, Y.-i., Han, J.-H., & Ji, H. (2020). Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties. Plants, 9(11), 1531. https://doi.org/10.3390/plants9111531

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop