Identification of growth regulators using cross-species network analysis in plants. Curci, P. L., Zhang, J., Mähler, N., Seyfferth, C., Mannapperuma, C., Diels, T., Van Hautegem, T., Jonsen, D., Street, N., Hvidsten, T. R, Hertzberg, M., Nilsson, O., Inzé, D., Nelissen, H., & Vandepoele, K. Plant Physiology, 190(4):2350–2365, December, 2022. ![Identification of growth regulators using cross-species network analysis in plants [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.
@article{curci_identification_2022,
title = {Identification of growth regulators using cross-species network analysis in plants},
volume = {190},
issn = {0032-0889},
url = {https://doi.org/10.1093/plphys/kiac374},
doi = {10.1093/plphys/kiac374},
abstract = {With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.},
number = {4},
urldate = {2022-12-02},
journal = {Plant Physiology},
author = {Curci, Pasquale Luca and Zhang, Jie and Mähler, Niklas and Seyfferth, Carolin and Mannapperuma, Chanaka and Diels, Tim and Van Hautegem, Tom and Jonsen, David and Street, Nathaniel and Hvidsten, Torgeir R and Hertzberg, Magnus and Nilsson, Ove and Inzé, Dirk and Nelissen, Hilde and Vandepoele, Klaas},
month = dec,
year = {2022},
pages = {2350--2365},
}
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Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). 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Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.},\n\tnumber = {4},\n\turldate = {2022-12-02},\n\tjournal = {Plant Physiology},\n\tauthor = {Curci, Pasquale Luca and Zhang, Jie and Mähler, Niklas and Seyfferth, Carolin and Mannapperuma, Chanaka and Diels, Tim and Van Hautegem, Tom and Jonsen, David and Street, Nathaniel and Hvidsten, Torgeir R and Hertzberg, Magnus and Nilsson, Ove and Inzé, Dirk and Nelissen, Hilde and Vandepoele, Klaas},\n\tmonth = dec,\n\tyear = {2022},\n\tpages = {2350--2365},\n}\n\n","author_short":["Curci, P. L.","Zhang, J.","Mähler, N.","Seyfferth, C.","Mannapperuma, C.","Diels, T.","Van Hautegem, T.","Jonsen, D.","Street, N.","Hvidsten, T. 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