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Kompetitive Allele-Specific PCR Marker Development and Quantitative Trait Locus Mapping for Bakanae Disease Resistance in Korean Japonica Rice Varieties
Plant Breed. Biotech. 2019;7:208-219
Published online September 1, 2019
© 2019 Korean Society of Breeding Science.

Kyeong-Seong Cheon1, Young-Min Jeong2, Youn-Young Lee2, Jun Oh1, Do-Yu Kang1, Hyoja Oh1, Song Lim Kim1, Nyunhee Kim1, Eungyeong Lee1, Jeongho Baek1, Inchan Choi1, Kyung-Hwan Kim1, Yong Jae Won3, In Sun Yoon1, Young-il Cho2, 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
Corresponding author: *Hyeonso Ji,, Tel: +82-63-238-4657, Fax: +82-63-238-4654
Received August 2, 2019; Revised August 12, 2019; Accepted August 12, 2019.
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.
High-throughput molecular markers with high genotyping accuracy will be helpful for genetic analysis, mapping of interesting genes, and rice breeding program. To develop high-throughput and cost-effective molecular markers for Korean japonica rice varieties, which are closely-related genetically, we designed kompetitive allele-specific polymerase chain reaction (KASP) assays from the sequence data of 13 Korean japonica rice varieties. Of the 504 new KASP assays, 371 (73.6%) showed polymorphisms among the tested varieties. In addition to the 400 previously developed KASP markers, this resulted in 771 KASP markers being applicable for Korean japonica rice varieties. These KASP markers were used to map the quantitative trait loci (QTLs) for rice bakanae disease (BD) resistance. From the results of QTL mapping and determination of the mortality rate of BD in two F2:F3 populations, a major QTL, qFfR1-1, and a novel QTL, qFfR6, were revealed on chromosome 1 in the Junam/Nampyeong F2:F3 population and on chromosome 6 in the Saenuri/Nampyeong F2:F3 population, respectively. Further, the insertion/deletion markers in the qFfR1-1 region were developed to select BD-resistant japonica rice varieties. The 771 developed KASP markers will accelerate the molecular breeding in Korean japonica rice varieties, and the detected QTLs will be helpful in identifying candidate genes for BD resistance.
Keywords : High-throughput, KASP marker, Genetic map, Quantitative trait loci, Bakanae disease

September 2019, 7 (3)
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  • Plant Molecular Breeding Center
      No PJ01323401
  • Rural Development Administration

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