Dataset Information

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.

SUBMITTER: Bonthala VS

PROVIDER: S-EPMC4747569 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Publications

Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis.

Bonthala Venkata Suresh VS Mayes Katie K Moreton Joanna J Blythe Martin M Wright Victoria V May Sean Tobias ST Massawe Festo F Mayes Sean S Twycross Jamie J

PloS one 20160209 2

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 bam ...[more]

PMID: 26859686

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Project description:Bambara groundnut (BGN) is a drought-tolerant crop majorly cultivated in sub-Saharan Africa. Due to a lack of extensive research, marginalization, lack of awareness, and lack of available fund among others, this crop's improvement has been limited. The development of this crop depends on evaluation and selection of unique and stable breeding lines in different environments. This study aims to estimate genetic diversity using morphological traits at different locations in 95 accessions of BGN collected from the Genebank of the International Institute of Tropical Agriculture (IITA), Ibadan. The experiment was carried out in three replicates at IITA experimental sites in two agroecological zones in Ibadan (7°40'19.62″ N, 3°91'73.13″ E) and Ikenne (6°51'00.873″ N, 3°41'48.528″ E) using a randomized complete block design. Ten vegetative growth traits and eight yield traits were scored. The data was subjected to ANOVA, PCA, correlation, and cluster analysis. Estimations of genetic parameters and broad sense heritability were carried out on the traits. ANOVA revealed significant variation in each trait except for days to emergence. Significant variation was also observed for accession and location interactions (genotype x environment interactions) for plant height, leaf length, leaf width, chlorophyll content, number of petioles, germination count, number of pods, number of seeds, seed length, seed width, and yield. PC1 and PC2 show 42.3% of the total variations observed by the PC, with seed thickness contributing more to PC1 and the number of seeds contributing more to PC2. Cluster analysis categorized the accessions into four distinct groups. The number of pods had the highest genotypic coefficient of variation of 32.55% and the phenotypic coefficient of variation of 97.61%, while seed length (0.63), seed width (0.54), and seed thickness (0.58) have high heritability values. The genetic advance was highest in yield (76.15%) and lowest in days to 50% germination (0.21%). This study can be used to predict appropriate agroecological zones for the planting of BGN while the knowledge of the diversity of the accessions based on the traits could serve a guide in selecting the best trait for the improvement of the crop.

Dataset Information

Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis.

Publications

Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis.

Similar Datasets

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