Identifying Signal-Crosstalk Mechanism in Maize Plants during Combined Salinity and Boron Stress Using Integrative Systems Biology Approaches

Abstract

Combined stress has been seen as a major threat to world agriculture production. Maize is one of the leading cereal crops of the world due to its wide spectrum of growth conditions and is moderately sensitive to salt stress. A saline soil environment is a major factor that hinders its growth and overall yield and causes an increase in the concentration of micronutrients like boron, leading to excess over the requirement of the plant. Boron toxicity combined with salinity has been reported to be a serious threat to the yield and quality of maize. The response signatures of the maize plants to the combined effect of salinity and boron stress have not been studied well. We carried out an integrative systems-level analysis of the publicly available transcriptomic data generated on tolerant maize (Lluteño maize from the Atacama Desert, Chile) landrace under combined salt and boron stress. We identified significant biological processes that are differentially regulated in combined salt and boron stress in the leaves and roots of maize, respectively. Protein-protein interaction network analysis identified important roles of aldehyde dehydrogenase (ALDH), galactinol synthase 2 (GOLS2) proteins of leaf and proteolipid membrane potential regulator (pmpm4), metallothionein lea protein group 3 (mlg3), and cold regulated 410 (COR410) proteins of root in salt tolerance and regulating boron toxicity in maize. Identification of transcription factors coupled with regulatory network analysis using machine learning approach identified a few heat shock factors (HSFs) and NAC (NAM (no apical meristem, Petunia), ATAF1-2 (Arabidopsis thaliana activating factor), and CUC2 (cup-shaped cotyledon, Arabidopsis)) family transcription factors (TFs) to play crucial roles in salt tolerance, maintaining reactive oxygen species (ROS) levels and minimizing oxidative damage to the cells. These findings will provide new ways to design targeted functional validation experiments for developing multistress-resistant maize crops.

Figure 1

Sequential steps of the RNA-Seq data analysis pipeline, beginning with data retrieval, preprocessing, alignment, assembly, and normalization followed by downstream analysis.

Figure 2

Bar plot showing the number of upregulated, downregulated, and total DEGs in leaf and root, respectively.

Figure 3

Representation of individual and commonly expressed DEGs in leaf and root. (a) Venn diagram showing overlap of the upregulated DEGs of leaf and root. (b) Heatmap showing expression patterns of the 94 overlapping DEGs in leaf and root of maize. The heat map has been constructed taking the highest and lowest value of expression of a DEG (in terms of log2fold change) in leaf and root, respectively. Blue color represents the lowest, and yellow color represents the highest fold change value.

Figure 4

Scatter plot showing gene set enrichment analysis of biological processes in (a) leaf and (b) root.

Figure 5

Protein-protein interaction network showing the hub genes with the highest degree centrality in (a) leaf and (b) root.

Figure 6

Transcriptional regulatory network showing hub TFs with the highest degree centrality in (a) leaf and (b) root.

Figure 7

Overview of the transcriptional regulatory mechanism in maize in response to combined salinity and boron stress. (SOS: salt sensitive overlay; CaM: calmodulin; HSP: heat shock protein; MAPK: mitogen associated protein kinase; HB41: homeobox 41; bHLH: basic helix loop helix; SOD: superoxide dismutase; POD: peroxidase; AtNHX1/6: Arabidopsis thaliana sodium hydrogen antiporter; AP2/ERF: apetala2/ethylene responsive factor; dbf1: DRE binding factor; DRE/CRT: drought response element/C-repeat; GA20oxs: gibberelin-20 oxidase; ABA: abscisic acid; GA: gibberelic acid; GRAS: (Gibberellic-Acid Insensitive (GAI), Repressor of GAI (Rga), and Scarecrow (SCR)); SOM: SOMNUS; SCL3: scarecrow-like 3; PKL: PICKLE; BZR: brassinosteroid-resistant; JA: jasmonic acid; JAZ: jasmonate zim domain; COL1: CONSTANS-like 1; JA-Ile: jasmonic acid induced isoleucine; HSF: heat shock factor; hsa32: heat stress-associated 32; ROF1: rotamase FKBP 1; APX2: ascorbate peroxidase 2; Gols1: Galactinol synthase 1; NAC: (NAM (no apical meristem, Petunia), ATAF1–2 (Arabidopsis thaliana activating factor), and CUC2 (cup-shaped cotyledon, Arabidopsis)); OsLEA3-1: Oryza sativa late embryogenesis abundant 3-1; GST: glutathione S-transferase).