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.
Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, Iran.
Prog Biophys Mol Biol. 2019 Sep;146:112-122. doi: 10.1016/j.pbiomolbio.2019.02.005. Epub 2019 Feb 22.
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.
非生物环境胁迫是限制棉花生长、纤维产量和品质的重要因素。本研究通过整合的荟萃分析和系统生物学分析，探讨了对胁迫反应至关重要的潜在转录组机制。从荟萃分析中观察到，在正常和胁迫条件之间共有 1465 个差异表达基因（DEGs）。基因本体论（GO）和京都基因与基因组百科全书（KEGG）通路富集分析表明，DEGs 显著富集在泛素依赖过程、次生代谢物合成、植物激素和信号转导中。结果还表明，一些 DEGs 被分配到转录因子（TFs）。总共鉴定出 148 个属于 25 个保守家族的 TFs，其中 S1Fa-like、ERF、NAC、bZIP 家族是最丰富的家族。此外，我们在 DEGs 的上游区域搜索了过表达的 DNA 基序，并能够识别出 11 个保守的序列基序。这些基序的功能分析表明，它们参与了转录调控、DNA 复制、细胞骨架组织和翻译的调控。加权基因共表达网络分析（WGCNA）揭示了 12 个不同的共表达模块。四个模块与参与应激反应和细胞壁组织的基因显著相关。网络分析还鉴定了 RTNLB5 和 PRA1 等枢纽基因，它们可能参与调节应激反应。这些发现有助于理解对非生物胁迫的反应机制，并引入可能有益于棉花植物育种计划的候选基因。
