title: Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis.
abstract: 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.
authors: School of Computer Sciences, Jubilee Campus, University of Nottingham, Nottingham, United Kingdom.|School of Biosciences, University of Nottingham Malaysia Campus, Kuala Lumpur, Malaysia.|Crops For the Future, Jalan Broga, 43500 Semenyih, Malaysia.
authors: Venkata Suresh
authors: VS
authors: Bonthala
authors: Plant and Crop Sciences, Biosciences, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom.
authors: Katie
authors: K
authors: Mayes
authors: Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom.|School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom.|Deep Seq, School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom.
authors: Joanna
authors: J
authors: Moreton
authors: Deep Seq, School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom.
authors: Martin
authors: M
authors: Blythe
authors: Deep Seq, School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom.
authors: Victoria
authors: V
authors: Wright
authors: Plant and Crop Sciences, Biosciences, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom.
authors: Sean Tobias
authors: ST
authors: May
authors: School of Biosciences, University of Nottingham Malaysia Campus, Kuala Lumpur, Malaysia.
authors: Festo
authors: F
authors: Massawe
authors: Crops For the Future, Jalan Broga, 43500 Semenyih, Malaysia.|Plant and Crop Sciences, Biosciences, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom.
authors: Sean
authors: S
authors: Mayes
authors: School of Computer Sciences, Jubilee Campus, University of Nottingham, Nottingham, United Kingdom.
authors: Jamie
authors: J
authors: Twycross
mesh_terms: D050260:Carbohydrate Metabolism / Q000235:genetics; D003080:Cold Temperature / Q000009:adverse effects; D018556:Crops, Agricultural / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D007887:Fabaceae / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D015870:Gene Expression; D020869:Gene Expression Profiling; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D050356:Lipid Metabolism / Q000235:genetics; D000069600:Plant Breeding; D010940:Plant Proteins / Q000235:genetics; D013312:Stress, Physiological; D014157:Transcription Factors / Q000235:genetics
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors