Root transcriptome profiling of contrasting wheat genotypes provides an insight to their adaptive strategies to water deficit

Abstract

Water deficit limits plant growth and productivity in wheat. The effect of water deficit varies considerably in the contrasting genotypes. This study attempted comparative transcriptome profiling of the tolerant (Abura) and susceptible (AUS12671) genotypes under PEG-simulated water stress via genome-wide RNA-seq technology to understand the dynamics of tolerance mechanism. Morphological and physiological analyses indicated that the tolerant genotype Abura had a higher root growth and net photosynthesis, which accounted for its higher root biomass than AUS12671 under stress. Transcriptomic analysis revealed a total of 924 differentially expressed genes (DEGs) that were unique in the contrasting genotypes under stress across time points. The susceptible genotype AUS12671 had slightly more abundant DEGs (505) than the tolerant genotype Abura (419). Gene ontology enrichment and pathway analyses of these DEGs suggested that the two genotypes differed significantly in terms of adaptive mechanism. Predominant upregulation of genes involved in various metabolic pathways was the key adaptive feature of the susceptive genotype AUS12671 indicating its energy-consuming approach in adaptation to water deficit. In contrast, downregulation the expression of genes of key pathways, such as global and overview maps, carbohydrate metabolism, and genetic information processing was the main strategy for the tolerant genotype Abura. Besides, significantly higher number of genes encoding transcription factors (TF) families like MYB and NAC, which were reported to be associated with stress defense, were differentially expressed in the tolerant genotype Abura. Gene encoding transcription factors TIFY were only differentially expressed between stressed and non-stressed conditions in the sensitive genotype. The identified DEGs and the suggested differential adaptive strategies of the contrasting genotypes provided an insight for improving water deficit tolerance in wheat.

Figure 1

Effect of water stress on root morphology. (A) Root length of the contrasting tolerant genotype, Abura (ABU) and susceptible genotype, AUS12671 (AUS) under control (WW) and stressed (DD) conditions; (B) Root biomass of the contrasting genotypes under control (WW) and stressed conditions (DD). Values in white boxes show % reduction due to stress.

Figure 2

Effect of water stress on gas exchange parameters. (A) Net photosynthetic rate (A,B) Stomatal conductance (Gs) and (C) Transpiration rate (Tr) of the tolerant genotype, Abura (ABU) and susceptible genotype, AUS12671 (AUS) under control (WW) and stressed (DD) conditions.

Figure 3

Differential gene expressions (control vs stressed) in the two genotypes, Abura (ABU) and AUS12671 (AUS) in two time-points of stress period (6 & 48 hours). (A) Scatter plots of gene expression in the tolerant genotype (ABU) at 6 h (left) and 48 h (right), showing that DEGs were greater in number at 48 h; (B) Scatter plots of gene expression in the susceptible genotype (AUS) at 6 h (left) and 48 h (right), showing that DEGs were greater in number at 48 h; and (C) Venn diagram showing the number of upregulated (left) and downregulated genes (right) in different combination of treatment-time points.

Figure 4

Number of differentially expressed genes (DEGs) enriched with different Gene Ontology (GO) terms in the tolerant genotype Abura (ABU, in blue) and susceptible genotype Aus12671 (AUS, in orange). The GO terms were grouped into three categories: (i) biological process, (ii) cellular component, and (iii) molecular function.

Figure 5

Number of differentially expressed genes (DEGs) enriched with different KEGG pathways in the tolerant genotype Abura (ABU, in blue) and susceptible genotype Aus12671 (AUS, in orange). Pathways were grouped into six categories (i) cellular process, (ii) environmental information processing, (iii) genetic information processing, (iv) disease-related processes, (v) metabolism, and (vi) organismal systems.

Figure 6

Distribution of DEGs in different Transcript factors (TF) families considering the whole transcriptome.

Figure 7

Transcription factors encoding DEGs (genotype-specific and consistently expressed) and their distributions. (A) Distribution of the consistently expressed and tolerant genotype-specific DEGs encoding different TFs; (B) Distribution of the consistently expressed and susceptible genotype-specific DEGs encoding different TFs.