Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding
Upland rice is a distinctive drought‐aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought‐aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical u...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2024
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| Acceso en línea: | https://hdl.handle.net/10568/163891 |
| _version_ | 1855514640219373568 |
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| author | Wang, Yulong Jiang, Conghui Zhang, Xingtan Yan, Huimin Yin, Zhigang Sun, Xingming Gao, Fenghua Zhao, Yan Liu, Wei Han, Shichen Zhang, Jingjing Zhang, Yage Zhang, Zhanying Zhang, Hongliang Li, Jinjie Xie, Xianzhi Zhao, Quanzhi Wang, Xiaoning Ye, Guoyou Li, Junzhou Ming, Ray Li, Zichao |
| author_browse | Gao, Fenghua Han, Shichen Jiang, Conghui Li, Jinjie Li, Junzhou Li, Zichao Liu, Wei Ming, Ray Sun, Xingming Wang, Xiaoning Wang, Yulong Xie, Xianzhi Yan, Huimin Ye, Guoyou Yin, Zhigang Zhang, Hongliang Zhang, Jingjing Zhang, Xingtan Zhang, Yage Zhang, Zhanying Zhao, Quanzhi Zhao, Yan |
| author_facet | Wang, Yulong Jiang, Conghui Zhang, Xingtan Yan, Huimin Yin, Zhigang Sun, Xingming Gao, Fenghua Zhao, Yan Liu, Wei Han, Shichen Zhang, Jingjing Zhang, Yage Zhang, Zhanying Zhang, Hongliang Li, Jinjie Xie, Xianzhi Zhao, Quanzhi Wang, Xiaoning Ye, Guoyou Li, Junzhou Ming, Ray Li, Zichao |
| author_sort | Wang, Yulong |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Upland rice is a distinctive drought‐aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought‐aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high‐quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought‐resistant rice and the “blue revolution” in agriculture. |
| format | Journal Article |
| id | CGSpace163891 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1638912024-12-22T05:44:44Z Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding Wang, Yulong Jiang, Conghui Zhang, Xingtan Yan, Huimin Yin, Zhigang Sun, Xingming Gao, Fenghua Zhao, Yan Liu, Wei Han, Shichen Zhang, Jingjing Zhang, Yage Zhang, Zhanying Zhang, Hongliang Li, Jinjie Xie, Xianzhi Zhao, Quanzhi Wang, Xiaoning Ye, Guoyou Li, Junzhou Ming, Ray Li, Zichao Upland rice is a distinctive drought‐aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought‐aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high‐quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought‐resistant rice and the “blue revolution” in agriculture. 2024-03 2024-12-19T12:53:10Z 2024-12-19T12:53:10Z Journal Article https://hdl.handle.net/10568/163891 en Open Access Wiley Wang, Yulong; Jiang, Conghui; Zhang, Xingtan; Yan, Huimin; Yin, Zhigang; Sun, Xingming; Gao, Fenghua; Zhao, Yan; Liu, Wei; Han, Shichen; Zhang, Jingjing; Zhang, Yage; Zhang, Zhanying; Zhang, Hongliang; Li, Jinjie; Xie, Xianzhi; Zhao, Quanzhi; Wang, Xiaoning; Ye, Guoyou; Li, Junzhou; Ming, Ray and Li, Zichao. 2024. Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding. Plant Biotechnology Journal, Volume 22 no. 3 p. 662-677 |
| spellingShingle | Wang, Yulong Jiang, Conghui Zhang, Xingtan Yan, Huimin Yin, Zhigang Sun, Xingming Gao, Fenghua Zhao, Yan Liu, Wei Han, Shichen Zhang, Jingjing Zhang, Yage Zhang, Zhanying Zhang, Hongliang Li, Jinjie Xie, Xianzhi Zhao, Quanzhi Wang, Xiaoning Ye, Guoyou Li, Junzhou Ming, Ray Li, Zichao Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding |
| title | Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding |
| title_full | Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding |
| title_fullStr | Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding |
| title_full_unstemmed | Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding |
| title_short | Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding |
| title_sort | upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding |
| url | https://hdl.handle.net/10568/163891 |
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