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. 2022 Apr 25:13:818472.
doi: 10.3389/fpls.2022.818472. eCollection 2022.

Transcriptome Meta-Analysis Associated Targeting Hub Genes and Pathways of Drought and Salt Stress Responses in Cotton (Gossypium hirsutum): A Network Biology Approach

Nasreen Bano  1   2 , Shafquat Fakhrah  1   3 , Chandra Sekhar Mohanty  1   2 , Sumit Kumar Bag  1   2
Affiliations

Transcriptome Meta-Analysis Associated Targeting Hub Genes and Pathways of Drought and Salt Stress Responses in Cotton (Gossypium hirsutum): A Network Biology Approach

Nasreen Bano et al. Front Plant Sci. .

Abstract

Abiotic stress tolerance is an intricate feature controlled through several genes and networks in the plant system. In abiotic stress, salt, and drought are well known to limit cotton productivity. Transcriptomics meta-analysis has arisen as a robust method to unravel the stress-responsive molecular network in crops. In order to understand drought and salt stress tolerance mechanisms, a meta-analysis of transcriptome studies is crucial. To confront these issues, here, we have given details of genes and networks associated with significant differential expression in response to salt and drought stress. The key regulatory hub genes of drought and salt stress conditions have notable associations with functional drought and salt stress-responsive (DSSR) genes. In the network study, nodulation signaling pathways 2 (NSP2), Dehydration-responsive element1 D (DRE1D), ethylene response factor (ERF61), cycling DOF factor 1 (CDF1), and tubby like protein 3 (TLP3) genes in drought and tubby like protein 1 (TLP1), thaumatin-like proteins (TLP), ethylene-responsive transcription factor ERF109 (EF109), ETS-Related transcription Factor (ELF4), and Arabidopsis thaliana homeodomain leucine-zipper gene (ATHB7) genes in salt showed the significant putative functions and pathways related to providing tolerance against drought and salt stress conditions along with the significant expression values. These outcomes provide potential candidate genes for further in-depth functional studies in cotton, which could be useful for the selection of an improved genotype of Gossypium hirsutum against drought and salt stress conditions.

Keywords: cotton; hub genes; meta-analysis; network; stress.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Venn diagram showing the number of shared and unique genes in differentially expressed genes (DEGs) of drought and salt stress data. In order to make drought and salt stress-responsive (DSSR) genes set compendium, we focused on 3,841 and 1,508 DSSR uniquely differentially expressed genes in drought and salt.
FIGURE 2
FIGURE 2
The drought-responsive gene network analysis of the top 100 upregulated (A,C) genes with their biological processes (B,D) in leaf and root tissues. Scales are showing from lower to higher degree connectivity.
FIGURE 3
FIGURE 3
The salt responsive genes network analysis of the top 100 upregulated (A,C,E) genes with their biological processes (B,D,F) in leaf, root, and seed tissues. Scales are showing from lower to higher degree connectivity.
FIGURE 4
FIGURE 4
Common enriched pathways in drought and salt dataset. Node color shows the normalized enrichment score (NES) from the core enrichment genes. A positive score (red) shows gene set enrichment at the top of the ranked list, and a negative score (blue) indicates gene set enrichment at the bottom of the ranked list. The color of the border represents the p-value of the enriched pathway.
FIGURE 5
FIGURE 5
Gene network of hub genes derived from GeneMANIA along with functional enrichment in (A) drought and (B) salt stress conditions.
FIGURE 6
FIGURE 6
Gene ontology (GO) classification of hub genes in (A) drought (B) salt stress condition. The x-axis represents significant P-values. The y-axis denotes the enriched functions. Bubble size denotes the number of DEGs enriched in the putative functions.
FIGURE 7
FIGURE 7
Advanced bubble chart shows putative KEGG pathways in (A) drought (B) salt stress conditions. The x-axis represents GeneRatio, which is the ratio of the number of DEGs and all annotated genes. The y-axis denotes the enriched pathways. Enrichment significance is shown with color and bubble size denotes the number of DEGs enriched in the pathway.
FIGURE 8
FIGURE 8
Expression profiles of putative hub genes under (A) drought and (B) salt stress conditions. These expressions have been shown with the pheatmap package in R using Log2FC values.
FIGURE 9
FIGURE 9
The expression pattern of key hub genes in G. hirsutum. qRT-PCR expression pattern of four putative genes in normal (0 h), 12, 24, 48, and 72 h of salt (300 MM) (A–D) and drought (20% PEG solutions PEG8000) stress (E–H) in cotton. Ubiquitin was used as the loading control. Three biological replicates were used for each experiment. The statistical analysis was performed, using two-tailed Student’s t-test. The data are plotted as means ± SD. The error bars represent standard deviations. (I,J) Correlation analysis against the expression values of qRT-PCR and RNA-Seq data in drought and salt stress conditions. The R represents the Pearson correlation coefficient, respectively. Graph showing a significant positive correlation between qRT-PCR and RNA-Seq data values.
FIGURE 10
FIGURE 10
Illustration of cis-regulatory elements of putative hub genes in (A) drought and (B) salt conditions. The micro-parts in diverse colors are the sequence of the putative elements.
FIGURE 11
FIGURE 11
The overall flow chart and strategy for designing and analyzing drought and salt stress-responsive genes.
See this image and copyright information in PMC

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