Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage
We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their...
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MDPI AG
2021-04-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/11/4/318 |
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| author | Tae-Ho Ham Yebin Kwon Yoonjung Lee Jisu Choi Joohyun Lee |
| author_facet | Tae-Ho Ham Yebin Kwon Yoonjung Lee Jisu Choi Joohyun Lee |
| author_sort | Tae-Ho Ham |
| collection | DOAJ |
| description | We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs. |
| first_indexed | 2024-03-10T12:37:03Z |
| format | Article |
| id | doaj.art-c19f43d0650f47e8b570da4f62a7fbe8 |
| institution | Directory Open Access Journal |
| issn | 2077-0472 |
| language | English |
| last_indexed | 2024-03-10T12:37:03Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agriculture |
| spelling | doaj.art-c19f43d0650f47e8b570da4f62a7fbe82023-11-21T14:13:44ZengMDPI AGAgriculture2077-04722021-04-0111431810.3390/agriculture11040318Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling StageTae-Ho Ham0Yebin Kwon1Yoonjung Lee2Jisu Choi3Joohyun Lee4Department of Crop Science, Konkuk University, Seoul 05029, KoreaDepartment of Crop Science, Konkuk University, Seoul 05029, KoreaDepartment of Crop Science, Konkuk University, Seoul 05029, KoreaDepartment of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50434, KoreaDepartment of Crop Science, Konkuk University, Seoul 05029, KoreaWe conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.https://www.mdpi.com/2077-0472/11/4/318GWAScold toleranceseedlingrice |
| spellingShingle | Tae-Ho Ham Yebin Kwon Yoonjung Lee Jisu Choi Joohyun Lee Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage Agriculture GWAS cold tolerance seedling rice |
| title | Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage |
| title_full | Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage |
| title_fullStr | Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage |
| title_full_unstemmed | Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage |
| title_short | Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage |
| title_sort | genome wide association study reveals the genetic basis of cold tolerance in rice at the seedling stage |
| topic | GWAS cold tolerance seedling rice |
| url | https://www.mdpi.com/2077-0472/11/4/318 |
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