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 |
| Language: | English |
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Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0148771 |
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| author | Venkata Suresh Bonthala Katie Mayes Joanna Moreton Martin Blythe Victoria Wright Sean Tobias May Festo Massawe Sean Mayes Jamie Twycross |
| author_facet | Venkata Suresh Bonthala Katie Mayes Joanna Moreton Martin Blythe Victoria Wright Sean Tobias May Festo Massawe Sean Mayes Jamie Twycross |
| author_sort | Venkata Suresh Bonthala |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-07da74aa972340f9aac37512243b658e |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-07da74aa972340f9aac37512243b658e2025-08-20T03:46:12ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01112e014877110.1371/journal.pone.0148771Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis.Venkata Suresh BonthalaKatie MayesJoanna MoretonMartin BlytheVictoria WrightSean Tobias MayFesto MassaweSean MayesJamie TwycrossBambara 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.https://doi.org/10.1371/journal.pone.0148771 |
| spellingShingle | Venkata Suresh Bonthala Katie Mayes Joanna Moreton Martin Blythe Victoria Wright Sean Tobias May Festo Massawe Sean Mayes Jamie Twycross Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis. PLoS ONE |
| 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://doi.org/10.1371/journal.pone.0148771 |
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