Deciphering Molecular Mechanisms Involved in Salinity Tolerance in Guar (Cyamopsis tetragonoloba (L.) Taub.) Using Transcriptome Analyses

Abstract

Guar is a commercially important legume crop known for guar gum. Guar is tolerant to various abiotic stresses, but the mechanisms involved in its salinity tolerance are not well established. This study aimed to understand molecular mechanisms of salinity tolerance in guar. RNA sequencing (RNA-Seq) was employed to study the leaf and root transcriptomes of salt-tolerant (Matador) and salt-sensitive (PI 340261) guar genotypes under control and salinity. Our analyses identified a total of 296,114 unigenes assembled from 527 million clean reads. Transcriptome analysis revealed that the gene expression differences were more pronounced between salinity treatments than between genotypes. Differentially expressed genes associated with stress-signaling pathways, transporters, chromatin remodeling, microRNA biogenesis, and translational machinery play critical roles in guar salinity tolerance. Genes associated with several transporter families that were differentially expressed during salinity included ABC, MFS, GPH, and P-ATPase. Furthermore, genes encoding transcription factors/regulators belonging to several families, including SNF2, C₂H₂, bHLH, C3H, and MYB were differentially expressed in response to salinity. This study revealed the importance of various biological pathways during salinity stress and identified several candidate genes that may be used to develop salt-tolerant guar genotypes that might be suitable for cultivation in marginal soils with moderate to high salinity or using degraded water.

Keywords: RNA-Seq; gene expression; guar; qRT-PCR; salinity; salt stress; salt tolerance; stress; transcriptome.

Figure 1

Heatmap-based clustering of differentially expressed genes (DEGs). The heatmap and hierarchical clustering show the status of gene expression and clustering of DEGs (those that were differentially expressed at least in one comparison) across all eight indicated samples in a specific column.

Figure 2

qRT-PCR validation of gene expression observed through RNA-Seq analysis. The y-axis indicates relative normalized expression, and the x-axis indicates cluster number (gene IDs). Graphs for upregulated (U) and downregulated (D) genes are shown separately. An asterisk (*) indicates a significant difference (t-test at p ≤ 0.05). T03L, Treatment ‘03’ Leaf; C03L, Control ‘03’ Leaf; T22L, Treatment ‘22’ Leaf; C22L, Control ‘22’ Leaf; T22R, Treatment ‘22’ Root; C22R, Control ‘22’ Root, T03R, treatment ‘03’ Root, and C03R, Control ‘03’ Root.

Figure 3

DEGs associated with phytohormone, calcium signaling, and redox pathways. (a) DEGs associated with phytohormone pathways (are indicated at the top). (b) DEGs associated with calcium signaling (Ca). (c) DEGs associated with redox signaling pathways (indicated at the top). The red color indicates downregulated DEGs, and the blue indicates upregulated DEGs. Left-side texts show pairwise comparisons. The top four compared samples indicate treatment vs. control, and the bottom four compared samples indicate salt-sensitive vs. salt-tolerant comparisons. IAA, indole acetic acid (auxin); ABA, abscisic acid; GA, gibberellins; SA, salicylic acid; Ca, calcium; GSH, glutathione; PRDX, peroxiredoxin; GRX, glutaredoxin.

Figure 4

Transporter analysis of DEGs. The y-axis indicates transporter superfamilies. The x-axis shows gene counts. Salt treatment vs. control comparisons are shown in the top four panels (a–d). Salt-tolerant vs. salt-sensitive comparisons are shown in the bottom panels (e–h). The red color indicates downregulated DEGs, and the blue indicates upregulated DEGs. Compared samples are indicated at the top of each panel.

Figure 5

Transcription factor analysis of DEGs. The y-axis indicates transcription factor families. The x-axis shows gene counts. Salt treatment vs. control comparisons are shown in the top four panels (a–d). Salt-tolerant vs. salt-sensitive comparisons are shown in the bottom panels (e–h). The red color indicates downregulated DEGs, and the blue indicates upregulated DEGs. Compared samples are indicated at the top of each panel.