Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogonandO. punctata), to b...
| 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/10568/163971 |
| _version_ | 1855542015232573440 |
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| author | Zhou, Yong Yu, Zhichao Chebotarov, Dmytro Chougule, Kapeel Lu, Zhenyuan Rivera, Luis F. Kathiresan, Nagarajan Al-Bader, Noor Mohammed, Nahed Alsantely, Aseel Mussurova, Saule Santos, João Thimma, Manjula Troukhan, Maxim Fornasiero, Alice Green, Carl D. Copetti, Dario Kudrna, David Llaca, Victor Lorieux, Mathias Zuccolo, Andrea Ware, Doreen McNally, Kenneth Zhang, Jianwei Wing, Rod A. |
| author_browse | Al-Bader, Noor Alsantely, Aseel Chebotarov, Dmytro Chougule, Kapeel Copetti, Dario Fornasiero, Alice Green, Carl D. Kathiresan, Nagarajan Kudrna, David Llaca, Victor Lorieux, Mathias Lu, Zhenyuan McNally, Kenneth Mohammed, Nahed Mussurova, Saule Rivera, Luis F. Santos, João Thimma, Manjula Troukhan, Maxim Ware, Doreen Wing, Rod A. Yu, Zhichao Zhang, Jianwei Zhou, Yong Zuccolo, Andrea |
| author_facet | Zhou, Yong Yu, Zhichao Chebotarov, Dmytro Chougule, Kapeel Lu, Zhenyuan Rivera, Luis F. Kathiresan, Nagarajan Al-Bader, Noor Mohammed, Nahed Alsantely, Aseel Mussurova, Saule Santos, João Thimma, Manjula Troukhan, Maxim Fornasiero, Alice Green, Carl D. Copetti, Dario Kudrna, David Llaca, Victor Lorieux, Mathias Zuccolo, Andrea Ware, Doreen McNally, Kenneth Zhang, Jianwei Wing, Rod A. |
| author_sort | Zhou, Yong |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogonandO. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of theO. sativacv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance. |
| format | Journal Article |
| id | CGSpace163971 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1639712024-12-19T14:13:43Z Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice Zhou, Yong Yu, Zhichao Chebotarov, Dmytro Chougule, Kapeel Lu, Zhenyuan Rivera, Luis F. Kathiresan, Nagarajan Al-Bader, Noor Mohammed, Nahed Alsantely, Aseel Mussurova, Saule Santos, João Thimma, Manjula Troukhan, Maxim Fornasiero, Alice Green, Carl D. Copetti, Dario Kudrna, David Llaca, Victor Lorieux, Mathias Zuccolo, Andrea Ware, Doreen McNally, Kenneth Zhang, Jianwei Wing, Rod A. genetic diversity oryza sativa wild relatives plants gene expression linkage disequilibrium crop performance Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogonandO. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of theO. sativacv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance. 2023-03-21 2024-12-19T12:53:14Z 2024-12-19T12:53:14Z Journal Article https://hdl.handle.net/10568/163971 en Open Access Springer Zhou, Yong; Yu, Zhichao; Chebotarov, Dmytro; Chougule, Kapeel; Lu, Zhenyuan; Rivera, Luis F.; Kathiresan, Nagarajan; Al-Bader, Noor; Mohammed, Nahed; Alsantely, Aseel; Mussurova, Saule; Santos, João; Thimma, Manjula; Troukhan, Maxim; Fornasiero, Alice; Green, Carl D.; Copetti, Dario; Kudrna, David; Llaca, Victor; Lorieux, Mathias; Zuccolo, Andrea; Ware, Doreen; McNally, Kenneth; Zhang, Jianwei and Wing, Rod A. 2023. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nat Commun, Volume 14, no. 1 |
| spellingShingle | genetic diversity oryza sativa wild relatives plants gene expression linkage disequilibrium crop performance Zhou, Yong Yu, Zhichao Chebotarov, Dmytro Chougule, Kapeel Lu, Zhenyuan Rivera, Luis F. Kathiresan, Nagarajan Al-Bader, Noor Mohammed, Nahed Alsantely, Aseel Mussurova, Saule Santos, João Thimma, Manjula Troukhan, Maxim Fornasiero, Alice Green, Carl D. Copetti, Dario Kudrna, David Llaca, Victor Lorieux, Mathias Zuccolo, Andrea Ware, Doreen McNally, Kenneth Zhang, Jianwei Wing, Rod A. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice |
| title | Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice |
| title_full | Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice |
| title_fullStr | Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice |
| title_full_unstemmed | Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice |
| title_short | Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice |
| title_sort | pan genome inversion index reveals evolutionary insights into the subpopulation structure of asian rice |
| topic | genetic diversity oryza sativa wild relatives plants gene expression linkage disequilibrium crop performance |
| url | https://hdl.handle.net/10568/163971 |
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