Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet
Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Compara...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/129215 |
| _version_ | 1855541180997042176 |
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| author | Haidong Yan Min Sun Zhongren Zhang Yarong Jin Ailing Zhang Chuang Lin Bingchao Wu Min He Bin Xu Jing Wang Peng Qin Mendieta, J.P. Gang Nie Jianping Wang Jones, Christopher S. Guangyan Feng Srivastava, R.K. Xinquan Zhang Bombarely, A. Dan Luo Long Jin Yuanying Peng Xiaoshan Wang Yang Ji Shilin Tian Linkai Huang |
| author_browse | Ailing Zhang Bin Xu Bingchao Wu Bombarely, A. Chuang Lin Dan Luo Gang Nie Guangyan Feng Haidong Yan Jianping Wang Jing Wang Jones, Christopher S. Linkai Huang Long Jin Mendieta, J.P. Min He Min Sun Peng Qin Shilin Tian Srivastava, R.K. Xiaoshan Wang Xinquan Zhang Yang Ji Yarong Jin Yuanying Peng Zhongren Zhang |
| author_facet | Haidong Yan Min Sun Zhongren Zhang Yarong Jin Ailing Zhang Chuang Lin Bingchao Wu Min He Bin Xu Jing Wang Peng Qin Mendieta, J.P. Gang Nie Jianping Wang Jones, Christopher S. Guangyan Feng Srivastava, R.K. Xinquan Zhang Bombarely, A. Dan Luo Long Jin Yuanying Peng Xiaoshan Wang Yang Ji Shilin Tian Linkai Huang |
| author_sort | Haidong Yan |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate. |
| format | Journal Article |
| id | CGSpace129215 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1292152025-08-21T15:39:31Z Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet Haidong Yan Min Sun Zhongren Zhang Yarong Jin Ailing Zhang Chuang Lin Bingchao Wu Min He Bin Xu Jing Wang Peng Qin Mendieta, J.P. Gang Nie Jianping Wang Jones, Christopher S. Guangyan Feng Srivastava, R.K. Xinquan Zhang Bombarely, A. Dan Luo Long Jin Yuanying Peng Xiaoshan Wang Yang Ji Shilin Tian Linkai Huang millets pearl millet heat tolerance Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate. 2023-03 2023-03-07T14:09:04Z 2023-03-07T14:09:04Z Journal Article https://hdl.handle.net/10568/129215 en Open Access Springer Haidong Yan, Min Sun, Zhongren Zhang, Yarong Jin, Ailing Zhang, Chuang Lin, Bingchao Wu, Min He, Bin Xu, Jing Wang, Peng Qin, Mendieta, J.P., Gang Nie, Jianping Wang, Jones, C.S., Guangyan Feng, Srivastava, R.K., Xinquan Zhang, Bombarely, A., Dan Luo, Long Jin, Yuanying Peng, Xiaoshan Wang, Yang Ji, Shilin Tian and Linkai Huang. 2023. Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nature Genetics 55:507–518. |
| spellingShingle | millets pearl millet heat tolerance Haidong Yan Min Sun Zhongren Zhang Yarong Jin Ailing Zhang Chuang Lin Bingchao Wu Min He Bin Xu Jing Wang Peng Qin Mendieta, J.P. Gang Nie Jianping Wang Jones, Christopher S. Guangyan Feng Srivastava, R.K. Xinquan Zhang Bombarely, A. Dan Luo Long Jin Yuanying Peng Xiaoshan Wang Yang Ji Shilin Tian Linkai Huang Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet |
| title | Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet |
| title_full | Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet |
| title_fullStr | Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet |
| title_full_unstemmed | Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet |
| title_short | Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet |
| title_sort | pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet |
| topic | millets pearl millet heat tolerance |
| url | https://hdl.handle.net/10568/129215 |
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