Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice
The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, a...
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MDPI AG
2022-04-01
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| Online Access: | https://www.mdpi.com/2073-4425/13/5/794 |
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| author | Chaewon Lee Kyeong-Seong Cheon Yunji Shin Hyoja Oh Young-Min Jeong Hoon Jang Yong-Chan Park Kyung-Yun Kim Hang-Chul Cho Yong-Jae Won Jeongho Baek Young-Soon Cha Song-Lim Kim Kyung-Hwan Kim Hyeonso Ji |
| author_facet | Chaewon Lee Kyeong-Seong Cheon Yunji Shin Hyoja Oh Young-Min Jeong Hoon Jang Yong-Chan Park Kyung-Yun Kim Hang-Chul Cho Yong-Jae Won Jeongho Baek Young-Soon Cha Song-Lim Kim Kyung-Hwan Kim Hyeonso Ji |
| author_sort | Chaewon Lee |
| collection | DOAJ |
| description | The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for <i>japonica</i> and 1339 SNPs informative for <i>indica</i>, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F<sub>8</sub> recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection. |
| first_indexed | 2024-03-10T03:50:05Z |
| format | Article |
| id | doaj.art-37a93063dc3442ac8dfc6121038db72e |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T03:50:05Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-37a93063dc3442ac8dfc6121038db72e2023-11-23T11:09:31ZengMDPI AGGenes2073-44252022-04-0113579410.3390/genes13050794Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in RiceChaewon Lee0Kyeong-Seong Cheon1Yunji Shin2Hyoja Oh3Young-Min Jeong4Hoon Jang5Yong-Chan Park6Kyung-Yun Kim7Hang-Chul Cho8Yong-Jae Won9Jeongho Baek10Young-Soon Cha11Song-Lim Kim12Kyung-Hwan Kim13Hyeonso Ji14Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, KoreaDivision of Forest Tree Improvement and Biotechnology, Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, KoreaSeed Industry Promotion Center, Korea Agriculture Technology Promotion Agency (KOAT), Gimje 54324, KoreaCELEMICS, Seoul 08506, KoreaCELEMICS, Seoul 08506, KoreaINSILICOGEN, Yongin 16954, KoreaINSILICOGEN, Yongin 16954, KoreaCheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, KoreaThe development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for <i>japonica</i> and 1339 SNPs informative for <i>indica</i>, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F<sub>8</sub> recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection.https://www.mdpi.com/2073-4425/13/5/794genotypingpreharvest sproutingQTLriceSNPtarget capture sequencing |
| spellingShingle | Chaewon Lee Kyeong-Seong Cheon Yunji Shin Hyoja Oh Young-Min Jeong Hoon Jang Yong-Chan Park Kyung-Yun Kim Hang-Chul Cho Yong-Jae Won Jeongho Baek Young-Soon Cha Song-Lim Kim Kyung-Hwan Kim Hyeonso Ji Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice Genes genotyping preharvest sprouting QTL rice SNP target capture sequencing |
| title | Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice |
| title_full | Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice |
| title_fullStr | Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice |
| title_full_unstemmed | Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice |
| title_short | Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice |
| title_sort | development and application of a target capture sequencing snp genotyping platform in rice |
| topic | genotyping preharvest sprouting QTL rice SNP target capture sequencing |
| url | https://www.mdpi.com/2073-4425/13/5/794 |
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