Revealing critical mechanisms in determining sorghum resistance to drought and salt using mRNA, small RNA and degradome sequencing

Abstract

Background: Plant growth and development are severely threatened by drought and salt stresses. Compared with structural genes, transcription factors (TFs) play more pivotal roles in plant growth and stress adaptation. However, the underlying mechanisms of sorghum adapting to drought and salt are insufficient, and systematic analysis of TFs in response to the above stresses is lacking.

Results: In this study, TFs were identified in sorghum and model plants (Arabidopsis thaliana and rice), and gene number and conserved domain were compared between sorghum and model plants. According to syntenic analysis, the expansion of sorghum and rice TFs may be due to whole-genome duplications. Between sorghum and model plants TFs, specific conserved domains were identified and they may be related to functional diversification of TFs. Forty-five key genes in sorghum, including four TFs, were likely responsible for drought adaption based on differently expression analysis. MiR5072 and its target gene (Sobic.001G449600) may refer to the determination of sorghum drought resistance according to small RNA and degradome analysis. Six genes were associated with drought adaptation of sorghum based on weighted gene co-expression network analysis (WGCNA). Similarly, the core genes in response to salt were also characterized using the above methods. Finally, 15 candidate genes, particularly two TFs (Sobic.004G300300, HD-ZIP; Sobic.003G244100, bZIP), involved in combined drought and salt resistance of sorghum were identified.

Conclusions: In summary, the findings in this study help clarify the molecular mechanisms of sorghum responding to drought and salt. We identified candidate genes and provide important genetic resource for potential development of drought-tolerant and salt-tolerant sorghum plants.

Keywords: Drought; Multiomics; Salt; Sorghum; Transcription factor.

Fig. 1

The DEGs between control and drought-treated sorghum seedlings from different genotypes (a) Venn diagram showing the common DEGs of the eight pairwise comparisons. (b) Expression profile of the common DEGs in the eight pairwise comparisons. Genes with high expression which induced by drought were labeled with red asterisk. (c) GO analysis of the common DEGs. (d) KEGG analysis of the common DEGs

Fig. 2

The analysis of miRNA and its target responding to drought. (a) The number of miRNAs identified in control and drought-treated sorghum. (b) Venn diagram showing the common genes between the targets of miRNAs identified by degradome sequencing and DEGs in response to drought stress. (c) Target plot (t-plot) for miR5072 targets confirmed by degradome sequencing. (d) Expression analysis of miR5072 in response to drought. (e) Expression analysis of miR5072’ target (Sobic.001G449600) in response to drought

Fig. 3

Regulatory network of TFs-mediated drought response in sorghum

Fig. 4

WGCNA of gene expression and root as well seedlings length in sorghum under drought stress. (a) Hierarchical clustering tree showing 24 modules of co-expressed genes by WGCNA. (b) The correlations between modules and sorghum growth. The number in each cell indicates the correlation coefficient (r), and the P-value (in parentheses) represents correlation significance (P < 0.05 indicated the significant correlation). (c) GO analysis of the genes in ‘brown4’, ‘coral1’ and ‘navajowhite2’ modules. (d) KEGG analysis of the genes in ‘brown4’, ‘coral1’ and ‘navajowhite2’ modules

Fig. 5

Cytoscape representation of relationship of genes in ‘brown4’, ‘coral1’ and ‘navajowhite2’ modules. (a) Cytoscape representation of relationship of genes in ‘brown4’ module. (b) Cytoscape representation of relationship of genes in ‘coral1’ module. (c) Cytoscape representation of relationship of genes in ‘navajowhite2’ module. (d) Cytoscape representation of relationship of TFs in ‘brown4’, ‘coral1’ and ‘navajowhite2’ modules

Fig. 6

The DEGs between control and salt-treated sorghum seedlings at different tissues. (a) Venn diagram showing the common DEGs of the six pairwise comparisons. (b) Expression profile of the common DEGs in the six pairwise comparisons. Genes with high expression which repressed or induced by drought were labeled with green or red asterisk. (c) GO analysis of the common DEGs. (d) KEGG analysis of the common DEGs

Fig. 7

The analysis of miRNA and its target responding to salt. (a) The number of miRNAs identified in control and salt-treated sorghum. (b) Venn diagram showing the common genes between the targets of miRNAs identified by degradome sequencing and DEGs in response to salt stress. (c) Target plot (t-plot) for miR156b targets confirmed by degradome sequencing. (d) Target plot (t-plot) for miR156g targets confirmed by degradome sequencing. (e) Target plot (t-plot) for miR408 targets confirmed by degradome sequencing. (f) Target plot (t-plot) for miR398 targets confirmed by degradome sequencing. (g) Target plot (t-plot) for miR164c targets confirmed by degradome sequencing. (h) Expression analysis of miR5072 in response to drought. i Expression analysis of miR5072’ target (Sobic.001G449600) in response to drought

Fig. 8

Regulatory network of TFs-mediated salt response in sorghum

Fig. 9

WGCNA of gene expression and Na⁺, K⁺ as well as Cl⁻ in sorghum uder salt stress. (a) Hierarchical clustering tree showing 12 modules of co-expressed genes by WGCNA. (b) The correlations between modules and sorghum growth. The number in each cell indicates the correlation coefficient (r), and the P-value (in parentheses) represents correlation significance (P < 0.05 indicated the significant correlation). (c) GO analysis of the genes in ‘darkolivegreen’, ‘lightpink4’ and ‘plum1’ modules. (d) KEGG analysis of the genes in ‘darkolivegreen’, ‘lightpink4’ and ‘plum1’ modules

Fig. 10

Cytoscape representation of relationship of genes in ‘darkolivegreen’, ‘lightpink4’ and ‘plum1’ modules. (a) Cytoscape representation of relationship of genes in ‘darkolivegreen’ module. (b) Cytoscape representation of relationship of genes in ‘lightpink4’ module. (c) Cytoscape representation of relationship of genes in ‘plum1’ module. (d) Cytoscape representation of relationship of TFs in ‘darkolivegreen’, ‘lightpink4’ and ‘plum1’ modules

Fig. 11

Venn diagram showing common candidate genes in response to drought and salt stresses