A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of <i>Populus davidiana</i>
Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the <i>Populus davidiana</i> southwest population in East Asia has differentiated from other populations in the range....
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| Format: | Article |
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MDPI AG
2023-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/4/821 |
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| author | Dandan Zhao Jianguo Zhang Nan Hui Li Wang Yang Tian Wanning Ni Jinhua Long Li Jiang Yi Li Songfeng Diao Jinhua Li Luke R. Tembrock Zhiqiang Wu Zhaoshan Wang |
| author_facet | Dandan Zhao Jianguo Zhang Nan Hui Li Wang Yang Tian Wanning Ni Jinhua Long Li Jiang Yi Li Songfeng Diao Jinhua Li Luke R. Tembrock Zhiqiang Wu Zhaoshan Wang |
| author_sort | Dandan Zhao |
| collection | DOAJ |
| description | Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the <i>Populus davidiana</i> southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of <i>P. davidiana</i> in the Yunnan–Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 <i>P. davidiana</i> samples from three regions across the species range. Our results showed that the uplift of the Qinghai–Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of <i>P. davidiana</i>. Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of <i>P. davidiana</i> adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region. |
| first_indexed | 2024-03-11T04:59:52Z |
| format | Article |
| id | doaj.art-351f1df9191f40ffae2868231dbf7c34 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T04:59:52Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-351f1df9191f40ffae2868231dbf7c342023-11-17T19:22:56ZengMDPI AGGenes2073-44252023-03-0114482110.3390/genes14040821A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of <i>Populus davidiana</i>Dandan Zhao0Jianguo Zhang1Nan Hui2Li Wang3Yang Tian4Wanning Ni5Jinhua Long6Li Jiang7Yi Li8Songfeng Diao9Jinhua Li10Luke R. Tembrock11Zhiqiang Wu12Zhaoshan Wang13State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaDepartment of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USAShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, ChinaIdentifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the <i>Populus davidiana</i> southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of <i>P. davidiana</i> in the Yunnan–Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 <i>P. davidiana</i> samples from three regions across the species range. Our results showed that the uplift of the Qinghai–Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of <i>P. davidiana</i>. Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of <i>P. davidiana</i> adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region.https://www.mdpi.com/2073-4425/14/4/821whole-genome re-sequencingancestral-state base (ASB)derived base (DB)linked selectiondemographic histories |
| spellingShingle | Dandan Zhao Jianguo Zhang Nan Hui Li Wang Yang Tian Wanning Ni Jinhua Long Li Jiang Yi Li Songfeng Diao Jinhua Li Luke R. Tembrock Zhiqiang Wu Zhaoshan Wang A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of <i>Populus davidiana</i> Genes whole-genome re-sequencing ancestral-state base (ASB) derived base (DB) linked selection demographic histories |
| title | A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of <i>Populus davidiana</i> |
| title_full | A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of <i>Populus davidiana</i> |
| title_fullStr | A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of <i>Populus davidiana</i> |
| title_full_unstemmed | A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of <i>Populus davidiana</i> |
| title_short | A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of <i>Populus davidiana</i> |
| title_sort | genomic quantitative study on the contribution of the ancestral state bases relative to derived bases in the divergence and local adaptation of i populus davidiana i |
| topic | whole-genome re-sequencing ancestral-state base (ASB) derived base (DB) linked selection demographic histories |
| url | https://www.mdpi.com/2073-4425/14/4/821 |
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