Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage
Abstract Cold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this s...
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2021
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oai:doaj.org-article:c721d4e2083b412f8a2e44021421e2972021-11-28T12:38:13ZAssociation Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage10.1186/s12284-021-00538-01939-84251939-8433https://doaj.org/article/c721d4e2083b412f8a2e44021421e2972021-11-01T00:00:00Zhttps://doi.org/10.1186/s12284-021-00538-0https://doaj.org/toc/1939-8425https://doaj.org/toc/1939-8433Abstract Cold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1–3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice.Dan WangZhuo LiuYinghui XiaoXionglun LiuYue ChenZhuo ZhangHouxiang KangXuli WangSu JiangShasha PengXinqiu TanDeyong ZhangYong LiuGuo-Liang WangChenggang LiSpringerOpenarticleRiceCold toleranceBud burst stageGenome-wide association studyPlant cultureSB1-1110ENRice, Vol 14, Iss 1, Pp 1-11 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Rice Cold tolerance Bud burst stage Genome-wide association study Plant culture SB1-1110 |
| spellingShingle |
Rice Cold tolerance Bud burst stage Genome-wide association study Plant culture SB1-1110 Dan Wang Zhuo Liu Yinghui Xiao Xionglun Liu Yue Chen Zhuo Zhang Houxiang Kang Xuli Wang Su Jiang Shasha Peng Xinqiu Tan Deyong Zhang Yong Liu Guo-Liang Wang Chenggang Li Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage |
| description |
Abstract Cold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1–3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice. |
| format |
article |
| author |
Dan Wang Zhuo Liu Yinghui Xiao Xionglun Liu Yue Chen Zhuo Zhang Houxiang Kang Xuli Wang Su Jiang Shasha Peng Xinqiu Tan Deyong Zhang Yong Liu Guo-Liang Wang Chenggang Li |
| author_facet |
Dan Wang Zhuo Liu Yinghui Xiao Xionglun Liu Yue Chen Zhuo Zhang Houxiang Kang Xuli Wang Su Jiang Shasha Peng Xinqiu Tan Deyong Zhang Yong Liu Guo-Liang Wang Chenggang Li |
| author_sort |
Dan Wang |
| title |
Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage |
| title_short |
Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage |
| title_full |
Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage |
| title_fullStr |
Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage |
| title_full_unstemmed |
Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage |
| title_sort |
association mapping and functional analysis of rice cold tolerance qtls at the bud burst stage |
| publisher |
SpringerOpen |
| publishDate |
2021 |
| url |
https://doaj.org/article/c721d4e2083b412f8a2e44021421e297 |
| work_keys_str_mv |
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1718407919245983744 |