Identification of gene modules associated with low temperatures response in Bambara groundnut by network-based analysis
Bambara groundnut (Vigna subterranea (L.) Verdc.) is an African legume and is a promising underutilized crop with good seed nutritional values. Low temperature stress in a number of African countries at night, such as Botswana, can effect the growth and development of bambara groundnut, leading to l...
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| Format: | Article |
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Public Library of Science
2016
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| Online Access: | https://eprints.nottingham.ac.uk/32811/ |
| _version_ | 1848801176842141696 |
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| author | Bonthala, Venkata Suresh Mayes, Sean Moreton, Joanna Blythe, Martin J. Wright, Victoria May, Sean Massawe, Festo Mayes, Sean Twycross, Jamie |
| author_facet | Bonthala, Venkata Suresh Mayes, Sean Moreton, Joanna Blythe, Martin J. Wright, Victoria May, Sean Massawe, Festo Mayes, Sean Twycross, Jamie |
| author_sort | Bonthala, Venkata Suresh |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | Bambara groundnut (Vigna subterranea (L.) Verdc.) is an African legume and is a promising underutilized crop with good seed nutritional values. Low temperature stress in a number of African countries at night, such as Botswana, can effect the growth and development of bambara groundnut, leading to losses in potential crop yield. Therefore, in this study we developed a computational pipeline to identify and analyze the genes and gene modules associated with low temperature stress responses in bambara groundnut using the cross-species microarray technique (as bambara groundnut has no microarray chip) coupled with network-based analysis. Analyses of the bambara groundnut transcriptome using cross-species gene expression data resulted in the identification of 375 and 659 differentially expressed genes (p<0.01) under the sub-optimal (23°C) and very sub-optimal (18°C) temperatures, respectively, of which 110 genes are commonly shared between the two stress conditions. The construction of a Highest Reciprocal Rank-based gene co-expression network, followed by its partition using a Heuristic Cluster Chiseling Algorithm resulted in 6 and 7 gene modules in sub-optimal and very sub-optimal temperature stresses being identified, respectively. Modules of sub-optimal temperature stress are principally enriched with carbohydrate and lipid metabolic processes, while most of the modules of very sub-optimal temperature stress are significantly enriched with responses to stimuli and various metabolic processes. Several transcription factors (from MYB, NAC, WRKY, WHIRLY & GATA classes) that may regulate the downstream genes involved in response to stimulus in order for the plant to withstand very sub-optimal temperature stress were highlighted. The identified gene modules could be useful in breeding for low-temperature stress tolerant bambara groundnut varieties. |
| first_indexed | 2025-11-14T19:17:05Z |
| format | Article |
| id | nottingham-32811 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T21:03:18Z |
| publishDate | 2016 |
| publisher | Public Library of Science |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-328112025-09-09T14:25:37Z https://eprints.nottingham.ac.uk/32811/ Identification of gene modules associated with low temperatures response in Bambara groundnut by network-based analysis Bonthala, Venkata Suresh Mayes, Sean Moreton, Joanna Blythe, Martin J. Wright, Victoria May, Sean Massawe, Festo Mayes, Sean Twycross, Jamie Bambara groundnut (Vigna subterranea (L.) Verdc.) is an African legume and is a promising underutilized crop with good seed nutritional values. Low temperature stress in a number of African countries at night, such as Botswana, can effect the growth and development of bambara groundnut, leading to losses in potential crop yield. Therefore, in this study we developed a computational pipeline to identify and analyze the genes and gene modules associated with low temperature stress responses in bambara groundnut using the cross-species microarray technique (as bambara groundnut has no microarray chip) coupled with network-based analysis. Analyses of the bambara groundnut transcriptome using cross-species gene expression data resulted in the identification of 375 and 659 differentially expressed genes (p<0.01) under the sub-optimal (23°C) and very sub-optimal (18°C) temperatures, respectively, of which 110 genes are commonly shared between the two stress conditions. The construction of a Highest Reciprocal Rank-based gene co-expression network, followed by its partition using a Heuristic Cluster Chiseling Algorithm resulted in 6 and 7 gene modules in sub-optimal and very sub-optimal temperature stresses being identified, respectively. Modules of sub-optimal temperature stress are principally enriched with carbohydrate and lipid metabolic processes, while most of the modules of very sub-optimal temperature stress are significantly enriched with responses to stimuli and various metabolic processes. Several transcription factors (from MYB, NAC, WRKY, WHIRLY & GATA classes) that may regulate the downstream genes involved in response to stimulus in order for the plant to withstand very sub-optimal temperature stress were highlighted. The identified gene modules could be useful in breeding for low-temperature stress tolerant bambara groundnut varieties. Public Library of Science 2016-02-09 Article PeerReviewed Bonthala, Venkata Suresh, Mayes, Sean, Moreton, Joanna, Blythe, Martin J., Wright, Victoria, May, Sean, Massawe, Festo, Mayes, Sean and Twycross, Jamie (2016) Identification of gene modules associated with low temperatures response in Bambara groundnut by network-based analysis. PLoS ONE, 11 (2). e0148771. ISSN 1932-6203 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148771 doi:10.1371/journal.pone.0148771 doi:10.1371/journal.pone.0148771 |
| spellingShingle | Bonthala, Venkata Suresh Mayes, Sean Moreton, Joanna Blythe, Martin J. Wright, Victoria May, Sean Massawe, Festo Mayes, Sean Twycross, Jamie Identification of gene modules associated with low temperatures response in Bambara groundnut by network-based analysis |
| title | Identification of gene modules associated with low temperatures response in Bambara groundnut by network-based analysis |
| title_full | Identification of gene modules associated with low temperatures response in Bambara groundnut by network-based analysis |
| title_fullStr | Identification of gene modules associated with low temperatures response in Bambara groundnut by network-based analysis |
| title_full_unstemmed | Identification of gene modules associated with low temperatures response in Bambara groundnut by network-based analysis |
| title_short | Identification of gene modules associated with low temperatures response in Bambara groundnut by network-based analysis |
| title_sort | identification of gene modules associated with low temperatures response in bambara groundnut by network-based analysis |
| url | https://eprints.nottingham.ac.uk/32811/ https://eprints.nottingham.ac.uk/32811/ https://eprints.nottingham.ac.uk/32811/ |