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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| 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 |
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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0148771</identifier><identifier>PMID: 26859686</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abiotic stress ; Acetylcysteine ; Analysis ; Atmospheric temperature ; Bambara groundnut ; Biology and Life Sciences ; Breeding ; Carbohydrate Metabolism - genetics ; Carbohydrates ; Cold Temperature - adverse effects ; Computer and Information Sciences ; Computer applications ; Crop science ; Crop yield ; Crops ; Crops, Agricultural - genetics ; Crops, Agricultural - growth & development ; Crops, Agricultural - metabolism ; DNA microarrays ; Ecology and Environmental Sciences ; Fabaceae - genetics ; Fabaceae - growth & development ; Fabaceae - metabolism ; Gene Expression ; Gene Expression Profiling ; Gene Ontology ; Gene Regulatory Networks ; Genes ; Genes, Plant ; Genetic aspects ; Genomes ; Genomics ; Growth ; Identification ; Legumes ; Life sciences ; Lipid Metabolism - genetics ; Low temperature ; Modules ; Nutrient deficiency ; Peanuts ; Physical Sciences ; Physiological aspects ; Plant biology ; Plant Breeding ; Plant Proteins - genetics ; Research and Analysis Methods ; Seeds ; Stress ; Stress, Physiological ; Stresses ; Studies ; Temperature ; Temperature effects ; Temperature tolerance ; Transcription factors ; Transcription Factors - genetics ; Vigna subterranea</subject><ispartof>PloS one, 2016-02, Vol.11 (2), p.e0148771</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Bonthala et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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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.</description><subject>Abiotic stress</subject><subject>Acetylcysteine</subject><subject>Analysis</subject><subject>Atmospheric temperature</subject><subject>Bambara groundnut</subject><subject>Biology and Life Sciences</subject><subject>Breeding</subject><subject>Carbohydrate Metabolism - genetics</subject><subject>Carbohydrates</subject><subject>Cold Temperature - adverse effects</subject><subject>Computer and Information Sciences</subject><subject>Computer applications</subject><subject>Crop science</subject><subject>Crop yield</subject><subject>Crops</subject><subject>Crops, Agricultural - genetics</subject><subject>Crops, Agricultural - growth & development</subject><subject>Crops, Agricultural - metabolism</subject><subject>DNA microarrays</subject><subject>Ecology and Environmental Sciences</subject><subject>Fabaceae - genetics</subject><subject>Fabaceae - growth & development</subject><subject>Fabaceae - metabolism</subject><subject>Gene Expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Ontology</subject><subject>Gene Regulatory Networks</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Growth</subject><subject>Identification</subject><subject>Legumes</subject><subject>Life sciences</subject><subject>Lipid Metabolism - genetics</subject><subject>Low temperature</subject><subject>Modules</subject><subject>Nutrient deficiency</subject><subject>Peanuts</subject><subject>Physical Sciences</subject><subject>Physiological aspects</subject><subject>Plant biology</subject><subject>Plant Breeding</subject><subject>Plant Proteins - genetics</subject><subject>Research and Analysis Methods</subject><subject>Seeds</subject><subject>Stress</subject><subject>Stress, Physiological</subject><subject>Stresses</subject><subject>Studies</subject><subject>Temperature</subject><subject>Temperature effects</subject><subject>Temperature tolerance</subject><subject>Transcription factors</subject><subject>Transcription Factors - 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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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26859686</pmid><doi>10.1371/journal.pone.0148771</doi><oa>free_for_read</oa></addata></record> |
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| ispartof | PloS one, 2016-02, Vol.11 (2), p.e0148771 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1764135170 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Abiotic stress Acetylcysteine Analysis Atmospheric temperature Bambara groundnut Biology and Life Sciences Breeding Carbohydrate Metabolism - genetics Carbohydrates Cold Temperature - adverse effects Computer and Information Sciences Computer applications Crop science Crop yield Crops Crops, Agricultural - genetics Crops, Agricultural - growth & development Crops, Agricultural - metabolism DNA microarrays Ecology and Environmental Sciences Fabaceae - genetics Fabaceae - growth & development Fabaceae - metabolism Gene Expression Gene Expression Profiling Gene Ontology Gene Regulatory Networks Genes Genes, Plant Genetic aspects Genomes Genomics Growth Identification Legumes Life sciences Lipid Metabolism - genetics Low temperature Modules Nutrient deficiency Peanuts Physical Sciences Physiological aspects Plant biology Plant Breeding Plant Proteins - genetics Research and Analysis Methods Seeds Stress Stress, Physiological Stresses Studies Temperature Temperature effects Temperature tolerance Transcription factors Transcription Factors - genetics Vigna subterranea |
| title | Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-08T00%3A05%3A23IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Identification%20of%20Gene%20Modules%20Associated%20with%20Low%20Temperatures%20Response%20in%20Bambara%20Groundnut%20by%20Network-Based%20Analysis&rft.jtitle=PloS%20one&rft.au=Bonthala,%20Venkata%20Suresh&rft.date=2016-02-09&rft.volume=11&rft.issue=2&rft.spage=e0148771&rft.pages=e0148771-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0148771&rft_dat=%3Cgale_plos_%3EA442842103%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1764135170&rft_id=info:pmid/26859686&rft_galeid=A442842103&rft_doaj_id=oai_doaj_org_article_07da74aa972340f9aac37512243b658e&rfr_iscdi=true |