Integrative meta-analysis of transcriptomic responses to abiotic stress in cotton

Ahmad Tahmasebi; Elham Ashrafi-Dehkordi; Amir Ghaffar Shahriari; Seyed Mohammad Mazloomi; Esmaeil Ebrahimie

doi:10.1016/j.pbiomolbio.2019.02.005

Integrative meta-analysis of transcriptomic responses to abiotic stress in cotton

Prog Biophys Mol Biol. 2019 Sep:146:112-122. doi: 10.1016/j.pbiomolbio.2019.02.005. Epub 2019 Feb 22.

Authors

Ahmad Tahmasebi¹, Elham Ashrafi-Dehkordi¹, Amir Ghaffar Shahriari², Seyed Mohammad Mazloomi³, Esmaeil Ebrahimie⁴

Affiliations

¹ Nutrition Research Center, Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran.
² Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, Iran. Electronic address: Shahriari.ag@eghlid.ac.ir.
³ Nutrition Research Center, Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.
⁴ School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, Australia; Genomics Research Platform, La Trobe University, Melbourne, Victoria 3086, Australia; Division of Information Technology, Engineering and the Environment, School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, SA, Australia; Faculty of Science and Engineering, School of Biological Sciences, Flinders University, Adelaide, SA, Australia.

PMID: 30802474
DOI: 10.1016/j.pbiomolbio.2019.02.005

Abstract

Abiotic environmental stresses are important factors that limit the growth, fiber yield, and quality of cotton. In this study, an integrative meta-analysis and a system-biology analysis were performed to explore the underlying transcriptomic mechanisms that are critical for response to stresses. From the meta-analysis, it was observed that a total of 1465 differentially expressed genes (DEGs) between normal and stress conditions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were significantly enriched in the ubiquitin-dependent process, biosynthesis of secondary metabolites, plant hormone, and signaled transduction. The results also indicated that some of DEGs were assigned to transcription factors (TFs). A total of 148 TFs belonged to 25 conserved families were identified that among them S1Fa-like, ERF, NAC, bZIP families, were the most abundant groups. Moreover, we searched in upstream regions of DEGs for over-represented DNA motifs and were able to identify 11 conserved sequence motifs. The functional analysis of these motifs revealed that they were involved in regulation of transcription, DNA replication, cytoskeleton organization, and translation. Weighted gene co-expression network analysis (WGCNA) uncovered 12 distinct co-expression modules. Four modules were significantly associated with genes involved in response to stress and cell wall organization. The network analysis also identified hub genes such as RTNLB5 and PRA1, which may be involved in regulating stress response. The findings could help to understand the mechanisms of response to abiotic stress and introduce candidate genes that may be beneficial to cotton plant breeding programs.

Keywords: Abiotic stress; Co-expression analysis; Gossypium ssp; Meta-analysis; Transcriptome data.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling*
Gene Ontology
Gene Regulatory Networks
Gossypium / genetics*
Gossypium / physiology*
Meta-Analysis as Topic*
Promoter Regions, Genetic / genetics
Stress, Physiological / genetics*