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.
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Claims 9
Claim · model-written summary
At 23°C, 375 genes were differentially expressed.
- Taxon
- bambara groundnut
Vigna subterraneae1 - Treatment
- sub-optimal (23°C)e0
- Outcome
- differentially expressed genese0
- Value
- 375e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“375 and 659 differentially expressed genes (p<0.01) under the sub-optimal (23°C) and very sub-optimal (18°C) temperatures, respectively”
e1“bambara groundnut transcriptome”
Claim · model-written summary
At 18°C, 659 genes were differentially expressed.
- Taxon
- bambara groundnutVigna subterraneae1
- Treatment
- very sub-optimal (18°C)e0
- Outcome
- differentially expressed genese0
- Value
- 659e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“375 and 659 differentially expressed genes (p<0.01) under the sub-optimal (23°C) and very sub-optimal (18°C) temperatures, respectively”
e1“bambara groundnut transcriptome”
Claim · model-written summary
The two temperature conditions shared 110 genes.
- Taxon
- bambara groundnutVigna subterraneae1
- Outcome
- genes are commonly shared between the two stress conditionse0
- Value
- 110 genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“110 genes are commonly shared between the two stress conditions”
e1“bambara groundnut transcriptome”
Claim · model-written summary
Six gene modules were identified under sub-optimal temperature stress.
- Taxon
- bambara groundnutVigna subterraneae1
- Treatment
- sub-optimale0
- Outcome
- gene modulese0
- Value
- 6e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“6 and 7 gene modules in sub-optimal and very sub-optimal temperature stresses being identified, respectively”
e1“bambara groundnut transcriptome”
Claim · model-written summary
Seven gene modules were identified under very sub-optimal temperature stress.
- Taxon
- bambara groundnutVigna subterraneae1
- Treatment
- very sub-optimale0
- Outcome
- gene modulese0
- Value
- 7e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“6 and 7 gene modules in sub-optimal and very sub-optimal temperature stresses being identified, respectively”
e1“bambara groundnut transcriptome”
Claim · model-written summary
Sub-optimal temperature modules were principally enriched in carbohydrate and lipid metabolic processes.
- Taxon
- bambara groundnutVigna subterraneae1
- Treatment
- sub-optimal temperature stresse0
- Outcome
- enriched with carbohydrate and lipid metabolic processese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Modules of sub-optimal temperature stress are principally enriched with carbohydrate and lipid metabolic processes”
e1“bambara groundnut transcriptome”
Claim · model-written summary
Very sub-optimal temperature modules were enriched in stimulus responses and metabolic processes.
- Taxon
- bambara groundnutVigna subterraneae1
- Treatment
- very sub-optimal temperature stresse0
- Outcome
- enriched with responses to stimuli and various metabolic processese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“modules of very sub-optimal temperature stress are significantly enriched with responses to stimuli and various metabolic processes”
e1“bambara groundnut transcriptome”
Claim · model-written summary
Transcription factors in five named classes were highlighted as possible regulators of stress response genes.
- Taxon
- bambara groundnutVigna subterraneae1
- Gene
- MYB, NAC, WRKY, WHIRLY & GATAe0
- Outcome
- transcription factorse0
- Qualifier
- may regulate the downstream genes involved in response to stimuluse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e1“bambara groundnut transcriptome”
Claim · model-written summary
The identified gene modules could aid breeding for low-temperature tolerance.
- Taxon
- bambara groundnutVigna subterraneae0
- Outcome
- breeding for low-temperature stress tolerant bambara groundnut varietiese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“identified gene modules could be useful in breeding for low-temperature stress tolerant bambara groundnut varieties”