Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat
Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessio...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2022
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/129915 |
| _version_ | 1855514796642795520 |
|---|---|
| author | Fei He Wei Wang Rutter, William B. Jordan, Katherine Jie Ren Taagen, Ellie DeWitt, Noah Sehgal, Deepmala Sukumaran, Sivakumar Dreisigacker, Susanne Reynolds, Matthew P. Halder, Jyotirmoy Sehgal, Sunish Kumar Shuyu Liu Jianli Chen Fritz, Allan K. Cook, Jason Brown-Guedira, Gina Pumphrey, Mike Carter, Arron Sorrells, Mark E. Dubcovsky, Jorge Hayden, Matthew Akhunova, Alina Morrell, Peter L. Szabo, Les J. Rouse, Matthew N. Akhunov, Eduard |
| author_browse | Akhunov, Eduard Akhunova, Alina Brown-Guedira, Gina Carter, Arron Cook, Jason DeWitt, Noah Dreisigacker, Susanne Dubcovsky, Jorge Fei He Fritz, Allan K. Halder, Jyotirmoy Hayden, Matthew Jianli Chen Jie Ren Jordan, Katherine Morrell, Peter L. Pumphrey, Mike Reynolds, Matthew P. Rouse, Matthew N. Rutter, William B. Sehgal, Deepmala Sehgal, Sunish Kumar Shuyu Liu Sorrells, Mark E. Sukumaran, Sivakumar Szabo, Les J. Taagen, Ellie Wei Wang |
| author_facet | Fei He Wei Wang Rutter, William B. Jordan, Katherine Jie Ren Taagen, Ellie DeWitt, Noah Sehgal, Deepmala Sukumaran, Sivakumar Dreisigacker, Susanne Reynolds, Matthew P. Halder, Jyotirmoy Sehgal, Sunish Kumar Shuyu Liu Jianli Chen Fritz, Allan K. Cook, Jason Brown-Guedira, Gina Pumphrey, Mike Carter, Arron Sorrells, Mark E. Dubcovsky, Jorge Hayden, Matthew Akhunova, Alina Morrell, Peter L. Szabo, Les J. Rouse, Matthew N. Akhunov, Eduard |
| author_sort | Fei He |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops. |
| format | Journal Article |
| id | CGSpace129915 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1299152025-11-06T13:02:55Z Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat Fei He Wei Wang Rutter, William B. Jordan, Katherine Jie Ren Taagen, Ellie DeWitt, Noah Sehgal, Deepmala Sukumaran, Sivakumar Dreisigacker, Susanne Reynolds, Matthew P. Halder, Jyotirmoy Sehgal, Sunish Kumar Shuyu Liu Jianli Chen Fritz, Allan K. Cook, Jason Brown-Guedira, Gina Pumphrey, Mike Carter, Arron Sorrells, Mark E. Dubcovsky, Jorge Hayden, Matthew Akhunova, Alina Morrell, Peter L. Szabo, Les J. Rouse, Matthew N. Akhunov, Eduard agronomic characters gene expression polyploidy wheat Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops. 2022-02-11 2023-04-06T14:08:45Z 2023-04-06T14:08:45Z Journal Article https://hdl.handle.net/10568/129915 en Open Access application/pdf Springer He, F., Wang, W., Rutter, W. B., Jordan, K. W., Ren, J., Taagen, E., DeWitt, N., Sehgal, D., Sukumaran, S., Dreisigacker, S., Reynolds, M., Halder, J., Sehgal, S. K., Liu, S., Chen, J., Fritz, A., Cook, J., Brown-Guedira, G., Pumphrey, M., … Akhunov, E. (2022). Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-28453-y |
| spellingShingle | agronomic characters gene expression polyploidy wheat Fei He Wei Wang Rutter, William B. Jordan, Katherine Jie Ren Taagen, Ellie DeWitt, Noah Sehgal, Deepmala Sukumaran, Sivakumar Dreisigacker, Susanne Reynolds, Matthew P. Halder, Jyotirmoy Sehgal, Sunish Kumar Shuyu Liu Jianli Chen Fritz, Allan K. Cook, Jason Brown-Guedira, Gina Pumphrey, Mike Carter, Arron Sorrells, Mark E. Dubcovsky, Jorge Hayden, Matthew Akhunova, Alina Morrell, Peter L. Szabo, Les J. Rouse, Matthew N. Akhunov, Eduard Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat |
| title | Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat |
| title_full | Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat |
| title_fullStr | Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat |
| title_full_unstemmed | Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat |
| title_short | Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat |
| title_sort | genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat |
| topic | agronomic characters gene expression polyploidy wheat |
| url | https://hdl.handle.net/10568/129915 |
| work_keys_str_mv | AT feihe genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT weiwang genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT rutterwilliamb genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT jordankatherine genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT jieren genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT taagenellie genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT dewittnoah genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT sehgaldeepmala genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT sukumaransivakumar genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT dreisigackersusanne genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT reynoldsmatthewp genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT halderjyotirmoy genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT sehgalsunishkumar genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT shuyuliu genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT jianlichen genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT fritzallank genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT cookjason genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT brownguediragina genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT pumphreymike genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT carterarron genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT sorrellsmarke genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT dubcovskyjorge genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT haydenmatthew genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT akhunovaalina genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT morrellpeterl genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT szabolesj genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT rousematthewn genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat AT akhunoveduard genomicvariantsaffectinghomoeologousgeneexpressiondosagecontributetoagronomictraitvariationinallopolyploidwheat |