Unravelling the molecular mechanism underlying drought stress response in chickpea via integrated multi-omics analysis

Drought stress affects growth and productivity significantly in chickpea. An integrated multi-omics analysis can provide a better molecular-level understanding of drought stress tolerance. In the present study, comparative transcriptome, proteome and metabolome analyses of two chickpea genotypes with contrasting responses to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS), was performed to gain insights into the molecular mechanisms underlying drought stress response/tolerance. Pathway enrichment analysis of differentially abundant transcripts and proteins suggested the involvement of glycolysis/gluconeogenesis, galactose metabolism, and starch and sucrose metabolism in the DT genotype. An integrated multi-omics analysis of transcriptome, proteome and metabolome data revealed co-expressed genes, proteins and metabolites involved in phosphatidylinositol signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways, specifically in the DT genotype under drought. These stress-responsive pathways were coordinately regulated by the differentially abundant transcripts, proteins and metabolites to circumvent the drought stress response/tolerance in the DT genotype. The QTL-hotspot associated genes, proteins and transcription factors may further contribute to improved drought tolerance in the DT genotype. Altogether, the multi-omics approach provided an in-depth understanding of stress-responsive pathways and candidate genes involved in drought tolerance in chickpea.

1 Introduction

Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated worldwide, especially in developing countries. India ranks first in chickpea production accounting for approximately 75% of the total production (FAO, 2016). Chickpea has high nutritional value containing proteins (20–25%), carbohydrates (61.5%) and fatty acids (4.5%), along with a significant amount of essential amino acids and vitamin content (Jukanti et al., 2012). Chickpea is cultivated mainly in arid and semi-arid regions with limited water availability. Therefore, drought stress is a major constraint that causes significant loss in growth and productivity of chickpea. Chickpea employs an adaptive strategy to tolerate limited drought stress due to its well-established root system architecture. Significant phenotypic variations in root characteristics have been reported among various chickpea genotypes. Higher biomass, root length density and better root system architecture are the characteristics of drought-tolerant (DT) genotypes, whereas drought-sensitive (DS) genotypes exhibit reduced root characteristics (Gaur et al., 2008; Kashiwagi et al., 2015).

The implementation of different high-throughput “omics” techniques in silos, including transcriptomics, proteomics and metabolomics have enabled the understanding of drought stress responses in chickpea to some extent (Garg et al., 2016; Khan et al., 2019; Bhaskarla et al., 2020; Gupta et al., 2020). A few studies have been performed to elucidate the global transcriptional dynamics to identify the genes and regulatory networks under various abiotic stress conditions (Garg et al., 2015; Garg et al., 2016; Kudapa et al., 2018; Mashaki et al., 2018; Kumar et al., 2019). The transcriptome analysis of chickpea roots under drought stress for different DT and DS genotypes revealed the involvement of various transcription factors (TFs), metabolic pathways and biological processes in the drought stress responses (Garg et al., 2016; Bhaskarla et al., 2020). The proteomics approaches have also been employed to examine the complexity of drought stress response. The proteins localized in different cellular compartments and those involved in different metabolic processes were found to contribute to drought tolerance in chickpea (Barua et al., 2019; Cevik et al., 2019; Gupta et al., 2020; Vessal et al., 2020). However, limited progress has been made towards metabolome analysis in chickpea under stress conditions. The metabolite profiling of leaves of two chickpea genotypes, Noor‐2009 (drought-sensitive) and 93127 (drought-tolerant) revealed the changes in amino acids composition under drought stress (Khan et al., 2019).However, these studies employed a stand-alone omics approach to investigate the drought stress response in chickpea. The integration of transcriptome, proteome and/or metabolome data have provided an impressive understanding of biotic, abiotic and oxidative stress response, nitrogen metabolism, tiller production, alkaloids biosynthesis, iron homeostasis and fruit ripening in different plants (Amiour et al., 2012; Srivastava et al., 2013; Sudre et al., 2013; Zeng et al., 2013; Remmers et al., 2018; Li et al., 2019a; Wang et al., 2019; Yun et al., 2019; Chin et al., 2020; Moreno et al., 2021; Bittencourt et al., 2022; Leão et al., 2022; Shu et al., 2022). An integrated analysis of transcriptome, proteome and metabolome in different chickpea genotypes can provide a better understanding of molecular mechanisms and pathways underlying drought stress response/tolerance.

In this study, we used two chickpea genotypes with contrasting responses to drought stress, namely ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS). These chickpea genotypes have been characterized extensively for their contrasting responses to drought stress and used for the generation of bi-parental populations for the QTL mapping (Jaganathan et al., 2015). These genotypes showed different root traits, phenotypic responses and yield under drought stress (Kashiwagi et al., 2005; Krishnamurthy et al., 2010; Kashiwagi et al., 2013; Garg et al., 2016; Purushothaman et al., 2017). ICC 4958 showed higher root and shoot dry weight, and larger roots in comparison to ICC 1882 (Garg et al., 2016). Moreover, higher shoot biomass, grain yield and harvest index were also observed for ICC 4958 under drought stress (Purushothaman et al., 2016). Here, we analyzed the transcriptome, proteome and metabolome of the roots of ICC 4958 and ICC 1882 genotypes under control and drought stress conditions to gain mechanistic insights into the drought stress tolerance in chickpea. The differential expression analyses identified the differentially abundant transcripts, proteins and metabolites under control and/or drought stress conditions in/between the chickpea genotypes. Weighted gene co-expression network analysis (WGCNA) was performed to explore the co-expressed genes, proteins and metabolites. The co-expressed genes/modules were further investigated for the identification of TF encoding genes, and those located within the known QTL-hotspot region for drought tolerance in chickpea. The integrated analysis of transcriptome, proteome and metabolome data revealed a crucial role of phosphatidylinositol (PI) signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways in drought tolerance. These results provide new insights into the drought tolerance mechanism in chickpea and prioritization of candidate genes for functional analysis.

2 Materials and methods

2.1 Plant materials and drought stress treatment

The seeds of two chickpea genotypes with contrasting response to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS) were procured from International Crops Research Institute for the Semi-arid Crops (ICRISAT), Hyderabad, India. The seeds of both genotypes were grown in pots containing soilrite saturated with reverse osmosis water. The pots were kept in a plant growth chamber with day (28°C in 400 µmol photons/m²/s of light intensity) and night (23°C in dark) cycle of 14 h and 10 h, respectively. Drought stress was imposed on 11 d old plants by withholding water for 15 d, while control seedlings were watered on alternate days until the end of the experiment. Water withholding for different days has been used for imposing drought stress in previous studies (Garg et al., 2016; Sinha et al., 2019). We observed significant difference in the root growth of DT and DS genotypes under drought stress after 15 d and collected the root samples from the control and drought-stressed plants of both genotypes to investigate the molecular changes. The samples were harvested in multiple technical replicates, snap frozen in liquid nitrogen and stored at -80 °C until further analysis. The root tissues were harvested in three independent biological replicates. The root tissues harvested from the same experiments were used for transcriptome, proteome and metabolome analyses.

2.2 RNA sequencing and data pre-processing

Total RNA from each sample was extracted using TRI reagent according to the manufacturer’s instructions (Sigma Life Sciences). RNA quality and quantity were assessed using Nanodrop Spectrophotometer and Agilent Bioanalyzer (Agilent technologies, Singapore) as described previously (Garg et al., 2010). Further, libraries from two biological replicates of each sample were prepared and sequencing was performed on the Illumina platform to generate 49-nt single-end reads. Quality control of raw reads was performed using NGS QC Toolkit (v2.3.3) (Patel and Jain, 2012) for removal of reads harboring adapter sequence and/or bases with poor quality. The filtered high-quality reads were used for downstream analysis.

2.2.1 Read mapping and differential gene expression analysis

The filtered high-quality reads were mapped on the kabuli chickpea genome (v1.0; Varshney et al., 2013b) using Tophat (v2.1.1) (Trapnell et al., 2009) software. To analyze gene expression, a reference-guided assembly of the transcriptome data from all samples was generated using Cufflinks (v2.2.1) (Trapnell et al., 2012). Cuffmerge was used to create consensus assembly from the reference-guided assemblies generated for each sample. Differential expression analysis was performed for DT and DS genotypes under drought (D) relative to control (C), [DT(D/C)] and [DS(D/C)], respectively, and for DT genotype relative to DS genotype under control (C) conditions, [DT(C)/DS(C)]. The differential expression analysis between different samples was performed using Cuffdiff. The transcripts with P-value ≤ 0.05 and log₂ fold change of ≥ 1 (up-regulated) and ≤ -1 (down-regulated) were considered to be differentially abundant.

2.3 Total protein extraction

Grounded root tissue (~1 g) for each sample (in three biological replicates) was suspended into 3 ml of extraction buffer (pH, 8.0) [Tris-HCl (500 mM), EDTA (50 mM), sucrose (700 mM), KCl (100 mM), β-mercaptoethanol (2%) and phenylmethylsulfonyl fluoride (1 mM)], vortexed briefly and incubated in ice for 10 min. An equal volume of Tris-HCl saturated phenol (pH, 6.6–7.9) was added to the sample and kept at room temperature for 10 min. Samples were centrifuged at 12,000 g for 10 min at 4°C and upper phenolic phase was recovered carefully into a new tube. The phenolic phase was once again extracted with 3 ml of extraction buffer as described above. Following centrifugation, the upper phase was carefully recovered and transferred into a new tube. Afterwards, 4 volumes of precipitation solution (0.1 M ammonium acetate in cold methanol) was added. The properly mixed solution was incubated overnight at -20°C. Finally, total proteins were pelleted down by centrifugation at 5500 g for 10 min at 4°C. The protein pellet was dissolved in solubilization buffer [Tris-HCl (1.5 M, pH 8.0) and urea (8 M)] and the solubilized protein sample was used for nanoLC-MS/MS analysis.

2.3.1 Nano-LC-MS/MS and data processing

Each protein sample (25 µl) was reduced using 5 mM tris (2-carboxyethyl)phosphine (TCEP) followed by alkylation with iodoacetamide (50 mM) and digestion with trypsin (1:50 of trypsin/lysate ratio) for 16 h at 37°C. Digested samples were cleaned using C18 silica cartridge to remove the salts and dried using speed vacuum. Dried protein pellet was resuspended in solubilization buffer A [acetonitrile (5%) and formic acid (0.1%)]. NanoLC-MS/MS analysis of the solubilized protein sample was performed using EASY-nLC 1000 system (Thermo Fisher Scientific) coupled to Thermo Q-Exactive equipped with nanoelectrospray ion source by the commercial service provider (Valerian Chem Pvt. Ltd., New Delhi). About 1.0 µg of the digested protein (peptides) was resolved using 60 cm Viper column (360 µm outer diameter, 75 µm inner diameter, 10 µm tip) filled with 3.0 µm of C18-resin. Further, peptides were loaded with buffer A (5% acetonitrile and 0.1% formic acid) and eluted with 0 – 40% gradient of buffer B [acetonitrile (95%) and formic acid (0.1%)] at a flow rate of 300 nl/min for 100 min.

The raw data was analyzed for qualitative and quantitative proteome using MaxQuant (MQ) (version 1.6.14.0) (Tyanova et al., 2016). The collected spectra of all peptides were searched against all the annotated protein sequences (28,269) in the reference chickpea genome (Varshney et al., 2013a) to identify its corresponding proteins using Andromeda, a peptide search engine (Cox et al., 2011). The protease used to generate peptides was set as enzyme specificity for trypsin/P. The estimated false discovery rate (FDR) of all peptide and protein identifications was set to 1%. The mass tolerance was kept to 7 ppm for precursor and fragment ions. Two missed cleavage values were allowed, and the minimum peptide length was set to 7 amino acids. The label-free method was used for protein quantification with classic type normalization and minimum ratio count of two. MQ provided the MS/MS spectrum details of all the identified peptides. Both unique and razor peptides were used for the identification of proteins, and protein quantification (abundance) was referred to their intensities. Differential expression analysis of proteins was performed using edgeR for DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons. Proteins with log₂ fold change of ≥ 1 (up-regulated) and ≤ -1 (down-regulated) and P-value ≤ 0.05 were considered as differentially abundant.

2.4 Sample preparation and gas chromatography-mass spectrometry for metabolome analysis

Frozen root samples (three biological replicates of each sample) were grounded into fine powder using liquid nitrogen. About 200 mg of each grounded sample was homogenized with 5 ml of pre-chilled methanol:acetonitrile (2:1) solvent in pestle and mortar. The solution was centrifuged at 9,500 rpm for 15 min at 25°C and supernatant was divided into two aliquots representing the technical replicates. Thereafter, 50 μl of ribitol (2 mg/ml in ddw) was added to each sample to serve as internal standard. The supernatant was dried in a speed vacuum concentrator at 25°C until the sample dryness reached to ~95%. Further, derivatization of samples was done by adding 50 μl of methoxyamine hydrochloride solution (30 mg methoxyamine hydrochloride in 1 ml of pyridine) followed by incubation at 30°C for 90 min. Subsequently, 100 μl of N-methyl-N-trimethyl silyl tri-flouro acetamide (MSTFA) was added to each sample and incubated at 37°C for 60 min for tri-methyl-sialylation (TMS).

Two technical replicates of each derivatized sample (biological replicate) were analyzed by GC-MS (QP2010 ULTRA, Shimadzu, Japan). The derivatized sample (1 μl) was injected into a Rtx-5Sil-MS (30 m × 0.25 mm × 0.25 μm) column using a split injection mode with the sampling time of 1 min, injection temperature 260°C and column oven temperature of 70°C using the flow control mode as linear velocity. Helium was used as a carrier gas with a flow rate of 1 ml min^-1. The initial oven temperature was set as 70°C for 3 min and then increased to 280°C until full run. The following parameters was adjusted for MS analysis, ion source temperature at 230°C, interference temperature at 270°C, run time of 50 min, scan speed of 3333 and mass by charge ratio (m/z) of 40 – 650. Acquisition of total ion chromatogram (TIC) was done for metabolite identification and quantification via GCMS solution 4.20 software (Shimadzu, Japan). Peak integration was performed to calculate the peak area, height and retention time (RT), and identification of metabolites was done by the similarity search of obtained mass spectra with the mass spectra available in NIST14, NIST14s and Wiley08 libraries. The manual curation of all the identified metabolites was performed to retain a unique set of metabolites for each sample analyzed. The metabolites identified in at least three replicates of each sample were used for further analysis and metabolite levels were normalized using ribitol as an internal standard. Differential expression analysis of metabolites was done by edgeR for DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons, and metabolites with log₂ fold change of ≥1 (up-regulated) and ≤-1 (down-regulated) and P-value ≤0.05 were considered as differentially abundant.

2.5 Co-expression network analysis

We used WGCNA (v 1.70-3; Langfelder and Horvath, 2008) to perform co-expression analysis for transcriptome, proteome and metabolome data sets for all the four samples, DT(C), DT(D), DS(C) and DS(D). Co-expression analysis was performed by using log₂ normalized values of FPKM (for 9847 genes showing ≥ 0.1 variance), intensity (for 2430 proteins) and relative amount (for 133 metabolites) of transcriptome, proteome and metabolome data, respectively. The matrix of co-expression data was generated using an optimized beta power (β) of three for transcriptome, seven for proteome and four for metabolome, and transformed into topological overlap matrix (TOM). The hierarchical clustering was performed using an average method to generate dendrogram. Module identification was done by dynamicTreeCut function to generate clusters with minimum size of 30 for transcriptome and proteome, and 15 for metabolome, and deepSplit value of 2. Highly correlated modules were merged at cutHeight of 0.2 to obtain the final set of modules.

2.6 Integrated analysis of transcriptome, proteome and metabolome

The integrated analysis of transcriptome, proteome and metabolome data was done using WGCNA as described earlier (Kelly et al., 2018; Liu et al., 2020). Integration of transcriptome, proteome and metabolome data was done by using their module eigenvectors. Two-way integration approach was adopted for the data integration, where transcriptome and proteome data were integrated using eigenvector for co-expressed gene modules (eigengenes) and co-expressed protein modules (eigenproteins) to identify the correlation between eigengenes and eigenproteins. Similarly, integration of transcriptome and metabolome data using eigenvectors for co-expressed gene modules (eigengenes) and co-expressed metabolite modules (eigenmetabolites) was performed to reveal correlation between eigengenes and eigenmetabolites.

2.7 GO and pathway enrichment analysis

GO enrichment analysis for differentially abundant transcripts (DATs) and differentially abundant proteins (DAPs) were performed using BiNGO tool in Cytoscape (v3.7). The GO terms with P-value ≤ 0.05 were considered as significantly enriched. The pathway enrichment analysis for DATs and DAPs was performed using KOBAS 3.0 (http://kobas.cbi.pku.edu.cn/) considering KEGG, BioCys and PANTHER databases at the P-value cut-off of ≤ 0.05. Pathway enrichment analysis for differentially abundant metabolites (DAMs) was performed using MetaboAnalyst (v.3.0) at P-value cut-off of ≤ 0.05.

2.8 Reverse transcriptase- quantitative polymerase chain reaction analysis

The RT-qPCR analysis was performed to validate the expression levels of selected candidate genes. A total of 17 genes exhibiting differential expression in DS(D/C), DT(D/C) and/or DT(C)/DS(C) comparisons were selected for the analysis. The primers were designed using Primer Express (3.0) software (Thermo Fischer; USA) and are listed in Table S11. The differential abundance levels of the selected genes were determined and compared with the RNA-seq data.

3 Results

Drought response/tolerance in different chickpea genotypes has been attributed mainly due to the root system architecture and related traits (Gaur et al., 2008; Garg et al., 2016; Purushothaman et al., 2016). The chickpea genotypes used in this study, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS), showed different root traits and have been characterized extensively for their contrasting responses to drought stress (Kashiwagi et al., 2005; Krishnamurthy et al., 2010; Kashiwagi et al., 2013; Jaganathan et al., 2015; Garg et al., 2016; Purushothaman et al., 2017). To gain deeper mechanistic insights into the drought stress tolerance in chickpea, we implemented a multi-omics (transcriptomics, proteomics and metabolomics) approach to analyze the roots of ICC 4958 and ICC 1882 genotypes under control and drought stress conditions.

3.1 Differential gene expression profiling and pathway/GO enrichment analysis

RNA-sequencing of root samples from the two chickpea genotypes, ICC 4958 (DT) and ICC 1882 (DS) was performed under control (C) and drought stress (D) conditions. The high-quality filtered reads for each sample were mapped to the chickpea genome (Table S1). The reference-guided assembly resulted in a total of 30978 gene loci, including 27881 known and 3097 novel loci (Table S2). Differential expression analysis revealed a total of 1718 (478 up- and 1240 down-regulated) and 1702 (680 up- and 1022 down-regulated) Differentially Abundant Transcripts (DATs) in DT [DT(D/C)] and DS [DS(D/C)] genotypes, respectively, under drought stress. Further, at least 1222 (864 up- and 358 down-regulated) DATs were identified between DT and DS genotypes under control conditions [DT(C)/DS(C)] (Figures 1, S1A) (Table S3). A comparative analysis of DT(D/C), DS(D/C) and DT(C)/DS(C) identified common and specific DATs among different comparisons. A total of 1128 (409 up- and 719 down-regulated), 841 (406 up- and 435 down-regulated), and 900 (644 up- and 256 down-regulated) DATs were specific for DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons, respectively. However, 580 (62 up- and 518 down-regulated) DATs were common between DT(D/C) and DS(D/C), and only 31 (1 up- and 30 down-regulated) DATs were common among all the comparisons (Figure 1A).

FIGURE 1

Figure 1 Differentially abundant transcripts (DATs) in drought-tolerant (DT) and drought-sensitive (DS) chickpea genotypes under control (C) and drought stress (D) conditions. DATs in the DT and DS genotypes were identified under drought stress as compared to control, DT(D/C) and DS(D/C), respectively, and between DT and DS genotypes under control condition, [DT(C)/DS(C)]. (A) Venn diagram showing common and specific DATs in DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons, where total number of transcripts are shown by black color font, and up- and down-regulated transcripts are presented by red and blue color fonts, respectively. (B, C) Bubble plots showing significantly enriched pathways among up- (B) and down-regulated (C) transcripts in DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons. Top 20 pathways with P-value ≤ 0.05 were selected. The bubble size defines the number of transcripts assigned to the pathway and bubble color represents P-value as per the given scale.

To investigate the metabolic pathways associated with DATs, pathway enrichment analysis was performed for the up- or down-regulated sets of genes for DT(D/C), DS(D/C) and DT(C)/DS(C). A total of 136, 108 and 174 significantly enriched pathways were identified among the up-regulated genes in DT(D/C), DS(D/C) and DT(C)/DS(C), respectively (Figure 1B). The most enriched pathways for DT(D/C) included plant hormone signaling, phenylpropanoid biosynthesis, carbon metabolism, anthocyanin modification, sucrose biosynthesis, glycolysis, gluconeogenesis, galactose metabolism, pentose phosphate pathway, and fructose and mannose metabolism. Among the up-regulated genes in DS(D/C), those encoding ABC transporters, and involved in callose biosynthesis, and circadian rhythm were enriched. However, DT(C)/DS(C) showed enrichment of plant-pathogen interaction, cellulose biosynthesis, starch and sucrose metabolism, phospholipases, phospholipid remodeling, wnt signaling pathway, triacylglycerol biosynthesis/degradation, glycerolipid metabolism, phosphatidylcholine acyl editing and MAPK signaling pathways among the up-regulated genes. The nitrogen metabolism pathway was enriched in both DT(D/C) and DS(D/C), while the diterpenoid biosynthesis pathway was enriched among the up-regulated genes in all the comparisons. Similarly, down-regulated genes in DT(D/C), DS(D/C) and DT(C)/DS(C) were found to be involved in 224, 209 and 91 pathways, respectively (Figure 1C). Most enriched pathways among down-regulated genes in DT(D/C) were, triacylglycerol biosynthesis and degradation, phospholipases, and cysteine and methionine metabolism, whereas terpenoid biosynthesis, flavonoid biosynthesis, glycolysis/gluconeogenesis, coumarins biosynthesis, amino sugar and nucleotide sugar metabolism, and fatty acid degradation pathways were enriched in DS(D/C). The pathways related to plant-pathogen interaction, MAPK signaling pathway, phenylpropanoid biosynthesis, pyridine nucleotide cycling, phosphatidylcholine acyl editing, and cellulose biosynthesis were enriched in both DT(D/C) and DS(D/C), whereas plant hormone signal transduction pathway was enriched in DT(D/C), DS(D/C) and DT(C)/DS(C).

To further investigate the biological functions of DATs, comparative GO enrichment analysis of the up- (Figure S1B) or down-regulated (Figure S1C) genes in DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons were performed. The up-regulated genes in DT(D/C) were involved mainly in amino acid metabolism and transport, ion transport, response to ions, and cell wall modification. However, negative regulation of biosynthesis and development, pigment metabolism, terpene metabolism, DNA modifications, regulation of transport, DNA maintenance and recombination, and hormone stimulus biological process terms were enriched in DS(D/C). GO terms related to signaling, root morphogenesis, hormone signaling, phenylpropanoid metabolism, and carbohydrate metabolism were enriched in DT(C)/DS(C). GO terms, including gene silencing, cell division, DNA replication and repair, and root development were represented in both DS(D/C) and DT(C)/DS(C). The down-regulated genes were involved in the signaling pathway, response to abiotic stress, immune response, hormone signaling, carbohydrate biosynthesis and protein modification in DT(D/C). Lipid biosynthesis and cellular respiration terms were enriched in DS(D/C) and DT(C)/DS(C), respectively. However, hormone stimulus, response to biotic and abiotic stimulus, and cell wall modification were commonly represented in both DS(D/C) and DT(C)/DS(C).

3.2 Differentially abundant proteins and pathway/GO enrichment analysis

Overall proteome analysis identified a total of 25742 peptides representing 2430 unique proteins in all the samples. Among these, 2180, 2205, 2171 and 2138 proteins were identified in DT(C), DT(D), DS(C) and DS(D) samples, respectively (Table S4). The differential expression analysis revealed a total of 306 (162 up- and 144 down-regulated), 336 (143 up- and 193 down-regulated) and 360 (176 up- and 184 down-regulated) DAPs in the DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons, respectively (Figures 2A, S2A) (Table S5). A comparative analysis of DT(D/C), DS(D/C) and DT(C)/DS(C) identified 231 (128 up- and 103 down-regulated), 109 (49 up- and 60 down-regulated) and 190 (106 up- and 84 down-regulated) DAPs specific to DT(D/C), DS(D/C), DT(C)/DS(C), respectively. However, 70 (31 up- and 39 down-regulated) DAPs were common between DT(D/C) and DS(D/C), and 8 (4 up- and 4 down-regulated) DAPs were common among all the comparisons (Figure 2A).

FIGURE 2

Figure 2 Differentially abundant proteins (DAPs) in drought-tolerant (DT) and drought-sensitive (DS) chickpea genotypes under control (C) and drought stress (D) conditions. DAPs in the DT and DS genotypes were identified under drought stress as compared to control, DT(D/C) and DS(D/C), respectively, and between DT and DS genotypes under control condition, [DT(C)/DS(C)]. (A) Venn diagram showing common and specific DAPs in DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons, where total number of proteins are shown by black color font, and up- and down-regulated proteins are presented by red and blue color fonts, respectively. (B, C) Bubble plots showing significantly enriched pathways among up- (B) and down-regulated (C) proteins in DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons. Top 20 pathways with P-value ≤ 0.05 were selected. The bubble size defines the number of proteins assigned to the pathway and bubble color represents P-value as per the given scale.

The pathway enrichment analysis was performed for the up- or down-regulated proteins in DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons. The up-regulated proteins contributed to 116, 128 and 14 metabolic pathways, whereas down-regulated proteins were involved in 115, 56 and 83 metabolic pathways in DT(D/C), DS(D/C) and DT(C)/DS(C), respectively. The up-regulated proteins were involved mainly in pyruvate metabolism and protein processing in DT(D/C), amino acid biosynthesis, sucrose biosynthesis and glutathione metabolism in DS(D/C), and starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, ribosome, spliceosome and protein processing in DT(C)/DS(C) (Figure 2B). The galactose metabolism, glycolysis/gluconeogenesis, and ascorbate and aldarate metabolism pathways were commonly enriched in DT(D/C) and DS(D/C), whereas phenylpropanoid biosynthesis, endocytosis and cyanoamino acid metabolism were detected in all the three comparisons, DT(D/C), DS(D/C) and DT(C)/DS(C) (Figure 2B). Similarly, enriched pathways among the down-regulated proteins were, purine metabolism, amino sugar and nucleotide sugar metabolism, MAPK signaling pathway and phenylpropanoid biosynthesis in DT(D/C); RNA transport, phagosome and pyruvate metabolism in DS(D/C); and glutathione-mediated detoxification and RNA transport in DT(C)/DS(C) (Figure 2C). Glycolysis/gluconeogenesis, ribosome, proteasome, fatty acid degradation, and starch and sucrose metabolism were enriched in both DT(D/C) and DS(D/C), whereas sucrose biosynthesis, colanic acid building blocks biosynthesis, and ascorbate and aldarate metabolism were common in DT(D/C) and DT(C)/DS(C) (Figure 2C).

Next, GO enrichment analyses of up- or down-regulated proteins in DT(D/C), DS(D/C) and DT(C)/DS(C) were performed to gain more insights into their biological functions (Figures S2B, C). The up-regulated proteins in DT(D/C) were enriched in fatty acid metabolism, auxin homeostasis and cell growth related GO terms. However, in DS(D/C) transport and, purine and pyrimidine metabolism; and in DT(C)/DS(C), hormone signaling, amino acid metabolic process, cell wall modification, chromosome organization and phenylpropanoid pathway were enriched. The amino acid metabolism and MAPK signaling were common in DS(D/C) and DT(C)/DS(C). The GO enrichment analysis of down-regulated proteins suggested the involvement of phenylpropanoid metabolism, jasmonic acid and ethylene dependent signaling, abiotic stress, immune response and nucleotide metabolism in DT(D/C). However, hormone signaling, RNA splicing, fatty acid oxidation, protein targeting, transport and localization terms were specific to DT(C)/DS(C).

3.3 Differential metabolite profiling and pathway enrichment analysis

After processing the raw data obtained via GC-MS analysis, we identified high-confidence metabolites in all the samples. Overall, a total of 133 high-confidence metabolites were obtained in all the samples, of which 87, 98, 94 and 88 metabolites were represented in DT(C), DT(D), DS(C) and DS(D), respectively (Figure S3A; Table S6). The analysis identified a total of 32 (17 up- and 15 down-regulated), 74 (34 up- and 40 down-regulated) and 36 (13 up- and 23 down-regulated) DAMs in DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons, respectively (Figure 3A; Table S7). A comparative analysis of DT(D/C), DS(D/C) and DT(C)/DS(C) identified 21 (12 up- and 9 down-regulated), 50 (27 up- and 23 down-regulated) and 19 (9 up- and 10 down-regulated) DAMs specific to DT(D/C), DS(D/C) and DT(C)/DS(C), respectively. However, 9 DAMs (4 up- and 5 down-regulated) were common between DT(D/C) and DS(D/C) (Figure 3A). The DAMs identified in all three comparisons, DT(D/C), DS(D/C) and DT(C)/DS(C), were comprised of different metabolite classes (Figure 3B). Among these, the metabolites representing carbohydrates, lipids and amino acids were most abundant in all the three comparisons. However, metabolites representing acids, alcohols, polyamines, organic compounds and other classes were comparatively less prominent (Figures S3B, C).

FIGURE 3

Figure 3 Differentially abundant metabolites (DAMs) in drought-tolerant (DT) and drought-sensitive (DS) chickpea genotypes under control (C) and drought stress (D) conditions. DAMs in the DT and DS genotypes were identified under drought stress as compared to control, DT(D/C) and DS(D/C) respectively, and between DT and DS genotypes under control condition, [DT(C)/DS(C)]. (A) Venn diagram showing common and specific DAMs in DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons, where total number of metabolites are shown by black color font, and up- and down-regulated metabolites are presented by red and blue color fonts, respectively. (B) Heatmap of DAMs identified in DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons. DAMs with log₂ fold change (FC) of ≥1 (up-regulated) or ≤-1 (down-regulated) at P-value ≤ 0.05 are shown. Various classes of metabolites represented among the DAMs are given. The name of each metabolite along with fold change value is given in Figure S3C. Scale at the bottom represents log₂ FC. (C) Enrichment ratio of the significantly enriched metabolic pathways represented among up- and down-regulated metabolites for DT(D/C), DS(D/C) and DT(C)/DS(C) comparisons are shown.

The pathway enrichment analysis of DAMs revealed that up-regulated metabolites in DT(D/C) were majorly involved in the arginine biosynthesis pathway (Figure S4). DAMs in DS(D/C) represented galactose metabolism, starch and sucrose metabolism, fructose and mannose metabolism as the most enriched pathways. However, glycine, serine and threonine metabolism, and aminoacyl-tRNA biosynthesis pathways were common in DT(D/C) and DS(D/C). The down-regulated metabolites were involved in glyoxylate and dicarboxylate metabolism, butanoate metabolism, alanine, aspartate and glutamate metabolism in DT(D/C), fructose and mannose metabolism in DS(D/C), and biosynthesis of unsaturated fatty acids, cyanoamino acid metabolism and linoleic acid metabolism in DT(C)/DS(C). Furthermore, galactose metabolism pathway was common between DT(D/C) and DS(D/C), glutathione metabolism between DT(D/C) and DT(C)/DS(C), and aminoacyl-tRNA biosynthesis between DS(D/C) and DT(C)/DS(C) (Figure S4). Among the identified pathways, galactose metabolism, and starch and sucrose metabolism were most enriched among the up-regulated metabolites in DS(D/C). However, down-regulated metabolites showed enrichment of galactose metabolism in DT(D/C) and DS(D/C), and unsaturated fatty acid biosynthesis, glutathione metabolism and linoleic acid metabolism in DT(C)/DS(C) (Figure 3C).

3.4 Co-expression network analysis of genes, proteins and metabolites

Co-expression analysis was performed via WGCNA to investigate the co-expressed transcripts, proteins and metabolites among DT(C), DT(D), DS(C) and DS(D) samples. The WGCNA is a co-expression network analysis utilized for the analyses of gene expression data providing the correlation of coexpressed genes with the samples (Langfelder and Horvath, 2008). For the transcriptome data, hierarchical clustering of 9847 genes (with variance > 0.1) via WGCNA generated 30 co-expressed modules. These modules were further clustered according to dissimilarity measure (1-TOM) and 11 highly co-expressed modules were obtained (Figure S5A). The module size varied from 60 (steelblue) to 2252 (black) genes. Further, the co-expressed modules were correlated with the samples (Figure S6A), and the modules with correlation coefficient (r) of ≥ 0.50 were assigned to the respective tissue sample. In total, five [brown (r = 0.98), grey60 (r = 0.83), midnightblue (r = 0.75), darkorange (r = 0.64) and blue (r = 0.54)] modules were found correlated with DT(C) and four [cyan (r = 0.78), black (r = 0.54), white (r = 0.95) and orange (r = 0.64)] modules with DT(D). One module, blue (r = 0.68) and steelblue (r = 0.53) was correlated with each of DS(C) and DS(D), respectively.

Similarly, WGCNA analysis for 2430 proteins generated 9 co-expressed modules (Figure S5B). The number of proteins identified in the modules ranged from 34 (darkgrey) to 551 (blue). The co-expressed modules showing correlation coefficient (r) of ≥ 0.35 with their respective samples were selected. The darkturquoise (r = 0.36) module showing correlation with DT(C); blue (r = 0.99), grey60 (r = 0.65) and darkturquoise (r = 0.37) with DT(D); darkgreen (r = 0.52), royalblue (r = 0.92), green (r = 0.49) and brown (r = 0.82) with DS(C); and darkgrey (r = 0.53) and royalblue (r = 0.85) with DS(D) were selected for further analysis (Figure S6B). The WGCNA analysis for 133 metabolites generated 5 modules comprised of 15 (green) to 48 (darkturquoise) metabolites. The co-expressed modules, highly correlated (r ≥ 0.50) with the samples, including darkturquoise (r = 0.74) module for DT(C); brown (r = 0.67) and darkturquoise (r = 0.82) for DT(D); yellow (r = 0.75) and darkturquoise (r = 0.97) for DS(C); and blue (r = 0.53) and green (r = 0.88) for DS(D), were identified (Figure S6C).

3.5 Integrated transcriptome, proteome and metabolome analysis

Integration of transcriptome, proteome and metabolome data was performed using module eigenvalues obtained for each data individually via WGCNA analysis. The module eigenvalue represents the first principal component and reflects the expression profiles of the given module. The integration of 11 co-expressed gene modules (eigengenes) and 9 co-expressed protein modules (eigenproteins) revealed five highly correlated eigengene-eigenprotein modules (Figure 4A). Similarly, 11 co-expressed gene modules (eigengenes) and 5 co-expressed metabolite modules (eigenmetabolites) identified highly correlated eigengene-eigenmetabolite modules (Figure 4B). The transcriptome modules correlated with both proteome and metabolome modules were selected for further analysis. Therefore, three transcriptome (mignightblue, brown and blue), one proteome (darkturquoise) and one metabolome (darkturquoise) modules were found correlated with DT(C), whereas four transcriptome (cyan, black, white and orange), three proteome (blue, darkturquoise and grey60) and two metabolome (brown and darkturquoise) modules were associated with DT(D). Similarly, one transcriptome (blue), two proteome (brown and darkgreen), and two metabolome (yellow and darkturquoise) modules were selected for DS(C). However, one module each of transcriptome (steelblue), proteome (darkgrey) and metabolome (green) was correlated with DS(D). These selected modules comprising of co-expressed genes, proteins and metabolites were analyzed together to identify the represented metabolic pathways and transcription factors among them. The stress-responsive pathways, including phosphatidylinositol (PI) signaling, glutathione metabolism and glycolysis/gluconeogenesis were found to be enriched and investigated further in more detail along with transcription factors to reveal the regulation of genes, proteins and metabolites involved.

FIGURE 4

Figure 4 Integrated analysis for transcriptome, proteome and metabolome using weighted gene co-expression network analysis (WGCNA). (A) Integration of transcriptome and proteome data using eigenvector for co-expressed gene modules (eigengenes) and co-expressed protein modules (eigenproteins). A total of 11 eigengenes and 9 eigenproteins generated a matrix showing correlated eigengenes-eigenproteins. Highly correlated modules were selected at correlation coefficients (r) ≥ 0.5. (B) Integration of transcriptome and metabolome data using eigenvector for co-expressed gene modules (eigengenes) and co-expressed metabolite modules (eigenmetabolites). A total of 11 eigengene and 5 eigenmetabolite generated a matrix showing correlated eigengenes-eigenmetabolites. Highly correlated modules were selected at correlation coefficients (r) ≥ 0.35. Correlation coefficient (r) for each module pair is shown as per scales shown on the right side. The total number of genes, proteins and metabolites included in each module are shown in parenthesis.

3.5.1 Phosphatidylinositol signaling pathway

PI signaling related membrane lipids, phosphatidylinositols (PIs), phosphatidylinositol phosphates (PIPs) and inositol phosphates (IPs) play a significant role in plant adaptation to abiotic stress (Heilmann, 2016). We found genes and proteins related to the PI signaling pathway to be co-expressed in one or more of the conditions analyzed (Figure 5; Table S8). Notably, the genes encoding inositol monophosphatase (IMPase; Ca_00700), diacylglycerol kinase 3 (DGK3; Ca_03279), phosphoinositide phosphatase (PIPase; Ca_10733), phosphatidylinositol-4-phosphate 5-kinase (PI4P5K; Ca_03113, PI4P5K1; Ca_04252), inositol-4-phosphate 5-kinase2 (I4P5K2; Ca_23825), vacuolar protein sorting 34 (Vps34)/phosphatidylinositol-3-kinase (PI3K; Ca_21468), phosphatidylinositol 3- and 4-kinase (PI3K, PI4K; Ca_04796), phosphatidylinositol 3-phosphate 5-kinase (PI3P5K; Ca_04329), and phosphatase and TENsin homolog 2 (PTEN 2; Ca_02178) were co-expressed specifically in DT(D). Furthermore, IMPase (Ca_00700 and Ca_05134), DGK3 (Ca_03279) and PIPase (Ca_10733) proteins were also found to be co-expressed in DT(D). The IMPase protein (Ca_05134) was up-regulated in DT(D/C). Moreover, an enhanced level of myo-inositol (an osmoprotectant) was detected in DT(C), DT(D) and DS(C). These co-expressed/stress-responsive genes, proteins and metabolites might contribute to coordinated regulation of PI signaling to impart better drought adaptation in the DT genotype.

FIGURE 5

Figure 5 Phosphatidylinositol (PI) signaling pathway showing co-expressed genes, proteins and metabolites in drought-tolerant (DT) and drought-sensitive (DS) chickpea genotypes under control (C) and drought (D) conditions. Co-expressed genes, proteins and metabolites are shown by orange, green and blue colored boxes, respectively. The up-regulated genes, proteins and metabolites are marked (*). PP-IPs- Diphosphoinositol phosphates; PI- Phosphatidylinositol; PIP, Phosphatidylinositol phosphate; IP, Inositol phosphate. Down-regulated genes, proteins and metabolites were not reported in this pathway.

3.5.2 Glutathione metabolism pathway

Glutathione metabolism is an antioxidant defense system that prevents cellular damage during abiotic stress (Banerjee and Roychoudhury, 2019). We identified genes, proteins and metabolites related to glutathione metabolism co-expressed in DT(C), DT(D), DS(C) and DS(D) samples (Figure 6; Table S9). The genes of glutathione S-transferase classes, namely, lambda (GST; Ca_12001) and TAU (GSTU25; Ca_03087, GSTU7; Ca_05354), and ascorbate peroxidase 3 (APX3; Ca_01955), and protein, GSTU8 (Ca_08326) were found to be co-expressed in DT(C), DT(D) and DS(C). The co-expression of these genes and proteins in both DT and DS genotypes may represent their fundamental role in the glutathione metabolism (Moons, 2005). However, genotype-specific co-expression was observed for GSTU19 (Ca_14389) gene, and GST7 (Ca_03442), glutathione peroxidase 3 (GPX3; Ca_10409) and glucose-6-phosphate dehydrogenase 6 (G6PDH; Ca_14672) proteins in DT(C) and DT(D). Importantly, correlation of genes including, GPX4 (Ca_07849), APX6 (Ca_01758), cysteine peroxiredoxin 1 (CysPrx1; Ca_05125), GSTU20 (Ca_23113), and proteins, 6-phosphogluconate dehydrogenase (6PGDH; Ca_05800, Ca_16508), cytosol aminopeptidase (AP; Ca_03329), peptidase M1 (PepM1; Ca_05761), isocitrate/isopropyl malate dehydrogenase (IDH; Ca_12583), thylakoidal ascorbate peroxidase (tAPX; Ca_12653), glutamate-cysteine ligase (GCL; Ca_05741) and G6PDH1 (Ca_10123) specifically in DT(D) indicated their important role in drought stress. Furthermore, genes of glutathione S-transferase classes, GSTU7 (Ca_05354) and GST (Ca_12001), and G6PDH1 (Ca_10123) protein were differentially abundant in DT(D/C). L-threonine was co-expressed mainly in DT(D), whereas cadaverine, leucine and asparagine were co-expressed in DT(C), DT(D) and DS(C). The co-expressed/stress-responsive genes, proteins and metabolites may confer an improved glutathione metabolism in the DT genotype.

FIGURE 6

Figure 6 Glutathione metabolism pathway showing co-expressed genes, proteins and metabolites in drought-tolerant (DT) and drought-sensitive (DS) chickpea genotypes under control (C) and drought (D) conditions. Co-expressed genes, proteins and metabolites are shown by orange, green and blue colored boxes, respectively. Up- (*) and down-regulated (**) genes, proteins and metabolites are marked. GSH- Glutathione reduced; GSSG- Glutathione oxidized.

3.5.3 Glycolysis/gluconeogenesis pathway

Glycolysis/gluconeogenesis is a fundamental carbohydrate metabolism pathway regulating cellular carbon metabolism and energy requirement. We found several glycolysis/gluconeogenesis associated genes, proteins and metabolites to be co-expressed in DT(C), DT(D), DS(C) and DS(D) (Figure 7; Table S10). The genes, namely aldolase (Ca_27205), glyceraldehyde-3-phosphate dehydrogenase C2 (GAPDHC2; Ca_11318), pyruvate decarboxylase-2 (PDC2; Ca_00374), pyruvate dehydrogenase (PDH) complex E1 alpha subunit (Ca_25091), phosphofructokinase (PFK; Ca_00673), aldehyde dehydrogenase 11A3 (ALDH11A3; Ca_03341), pyruvate orthophosphate dikinase (PPDK) (Ca_06801), and proteins encoding GAPDHC2 (Ca_11318), PDC2 (Ca_00374), PFK (Ca_00673), ALDH11A3 (Ca_03341), triosephosphate isomerase (TPI; Ca_00722) and pyruvate kinase (PK) (Ca_00753) were co-expressed in both DT(C) and DS(C). These co-expressed genes and proteins were considered key regulators of glycolysis/gluconeogenesis. However, PK (Ca_12631, Ca_06556), galactose mutarotase-like (GALM-like; Ca_02027, Ca_15348), PFK (Ca_14808), PFK4 (Ca_08339), phosphoglycerate kinase (PGK; Ca_22673), phosphoenolpyruvate carboxykinase 1 (PEPCK1; Ca_11524), lipoamide dehydrogenase 2 (LPD2; Ca_03055), ALDH7B4 (Ca_22351), phosphoglycerate mutase (PGAM; Ca_09253) and fructose 1,6-biphosphatase (FBPase; Ca_00102) genes, and GALM-like (Ca_15348); ALDH7B4 (Ca_22351); PGAM (Ca_09253), TPI (Ca_02616), enolase (ENO; Ca_00761), ENO1 (Ca_25827), glucose-6-phosphate isomerase (GPI; Ca_10559), dihydrolipoamide acetyltransferase (Dlat; Ca_08401) and acyl-activating enzyme 7 (AAE7; Ca_02996) proteins were correlated mainly with DT(D). Notably, FBPase (Ca_00102), PEPCK1 (Ca_11524), GALM-like (Ca_15348) and PGAM (Ca_09253) were differentially abundant in DT(D/C). The metabolites, including D-glucose, D-mannose and glycerol were co-expressed in DT(C), DT(D) and DS(C). However, D-mannitol was co-expressed mainly in DT(D) and DS(C); sorbitol in DT(C) and DS(C), and D-allose in DT(D). The up-regulation of D-glucose and D-mannitol was observed in DT(C)/DS(C) and DT(D/C), respectively. These co-expressed/stress-responsive genes, proteins and metabolites in the glycolysis/gluconeogenesis pathway possibly contribute to drought stress adaptation in the DT genotype.

FIGURE 7

Figure 7 Glycolysis/gluconeogenesis pathway showing co-expressed genes, proteins and metabolites in drought-tolerant (DT) and drought-sensitive (DS) chickpea genotypes under control (C) and drought (D) conditions. Co-expressed genes, proteins and metabolites are shown by orange, green and blue colored boxes, respectively. Up- (*) and down-regulated (**) genes, proteins and metabolites are marked.

3.6 Transcription factor encoding genes

TF encoding genes represented among the co-expressed genes of DT(C), DT(D), DS(C) and DS(D) were investigated. In total, 735 TFs (belonging to 79 families), including 319, 267, 143 and 6 were identified in DT(C), DT(D), DS(C) and DS(D), respectively (Figure S7A). The members of TF families, including MYB (55, 7.51%), bHLH (55, 7.51%), AP2-EREBP (45, 6.14%), HB (38, 5.2%), C3H (28, 3.8%), MADS, (26, 3.55%), bZIP (26, 3.55%), WRKY (26, 3.55%) and NAC (24, 3.27%) were most represented (Figure S7B). MYB, bHLH, HB and AP2-EREBP were the most abundant TF families identified in DT(C) and DT(D). A total of 39 TFs (14 up- and 25 down-regulated) were identified in black, cyan, orange and white modules correlated with DT(D). The DT(C) correlated modules (blue, brown, midnight blue and grey60) harbored 28 differentially abundant TFs (18 up- and 10 down-regulated). These modules represented the members of several TF-families (GNAT, GRAS, C3H, HB, G2-like, bZIP, PLATZ, sigma70-like, CCAAT, WRKY, Aux/IAA and C2C2-Dof) that are well known to be involved in the regulation of drought stress response (Figure S7C).

3.7 Identification of QTL-hotspot associated candidate genes/proteins involved in drought stress

A QTL-hotspot region spanning 3 Mb (Ca4_11,276,225 to Ca4_14,146,315 bp) harboring several QTLs for drought tolerance related traits has been identified in linkage group 4 (CaLG04) in chickpea (Varshney et al., 2014). We identified a total of 286 annotated protein-coding genes located within the QTL-hotspot region (Figure 8A). The QTL-hotspot region (11,284,553 bp to 14,082,277 bp) comprised of co-expressed genes was considered as co-expression QTL-hotspot (Figure 8A). The co-expression QTL-hotspot contained a total of 121 co-expressed genes. Among these, 57 genes (blue, brown, midnightblue, grey60 and darkorange modules) in DT(C), 42 genes (black, cyan, orange and white modules) in DT(D) and 22 genes (blue module) in DS(C) were co-expressed (Figure S8A). Twenty genes in blue module were found to be common between DT(C) and DS(C), however no genes were co-expressed in DS(D) and DT(D). Notably, at least 12 co-expressed genes encoded TFs, such as MADS-box (Ca_04518), OFP (Ca_04584), RWP-RK (Ca_04456), and AP2-EREBP (Ca_04503, Ca_04504) were specific to DT(C), Alfin-like (Ca_04596), SNF2 (Ca_04622), HSF (Ca_04488) and MYB (Ca_04621) were present in DT(D), whereas Trihelix (Ca_04385, Ca_04387) and AP2-EREBP (Ca_04370) were co-expressed in both DT(C) and DS(C) (Figure S8B). Further, QTL-hotspot region (11,396,081 to 14,093,770 bp) comprised of 38 co-expressed proteins was considered as protein QTL-hotspot (pQTL-hotspot) (Figure 8A). The pQTL-hotspot region associated proteins were present in darkturquoise module of DT(C); darkturquoise, grey60 and blue of DT(D); royalblue, green, darkgreen and brown of DS(C) and, royalblue and darkgrey modules of DS(D) (Figure S8C).

FIGURE 8

Figure 8 Identification of quantitative trait loci-hotspot (QTL-hotspot) associated drought responsive genes, proteins and transcription factors (TFs) in drought-tolerant (DT) and drought-sensitive (DS) chickpea genotypes under control (C) and drought (D) conditions. (A) QTL-hotspot region spanning 3Mb (Ca4_11,276,225 to Ca4_14,146,315 bp) harboring several QTLs for drought tolerance related traits in linkage group 04 (CaLG04) in chickpea. QTL-hotspot region (11, 284,553 bp to 14,082,277 bp) comprised of co-expressed genes is considered as co-expression QTL-hotspot region. QTL-hotspot region (11,396,081 to 14,093,770 bp) comprised of co-expressed proteins is considered as protein quantitative trait loci-hotspot (pQTL-hotspot). Differentially abundant transcripts (DATs) and differentially abundant proteins (DAPs) of co-expression QTL-hotspot and pQTL-hotspot, respectively, are shown with their co-ordinates. (B) Heatmap of co-expression QTL-hotspot region associated DATs and DA-TFs identified in different modules of DT(C)/DS(C). (C) Heatmap of pQTL-hotspot region associated DAPs identified in different modules of DT(C)/DS(C), DT(D/C) and DS(D/C). * denotes differentially abundant TF.

We further investigated the differential abundance behavior of QTL-hotspot associated co-expressed genes and proteins. In total, seven (6 up- and 1 down-regulated) DATs including one TF in DT(C)/DS(C) were identified within the co-expression QTL-hotspot. The genes encoding receptor like protein 21 (RLP21; Ca_04471), stabilizer of iron transporter SufD/polynucleotidyl transferase (PNT; Ca_04545), cytochrome P450 family 76 (cyt 450; Ca_04587), copper amine oxidase (CuAOs; Ca_04604) and myosin heavy chain-related protein (Ca_04474) were up-regulated, whereas PLAT/LH2 domain-containing lipoxygenase (Ca_04606) was down-regulated in DT(C)/DS(C) (Figure 8B). In addition, one co-expression QTL-hotspot region associated gene encoding dehydration-responsive element binding (DREB; Ca_04504) TF was up-regulated in DT(C)/DS(C) (Figure 8B). Among the pQTL-hotspot region associated co-expressed proteins, nucleic acid binding protein (Ca_04399) was down-regulated in DT(D/C), whereas PLAT/LH2 domain-containing lipoxygenase family protein (Ca_04606) was up-regulated in DS(D/C). However, oligosaccharyltransferase (OST) complex/magnesium transporter family protein (Ca_04632) was up-regulated, and carboxylesterase 20 (Ca_04524) and membrane-associated progesterone binding protein 3 (Ca_04482) were downregulated in DT(C)/DS(C) (Figure 8C). Overall, the co-expressed/up-regulated genes, proteins and/or TFs located within the QTL-hotspot region represent important candidates for drought tolerance in chickpea.

3.8 Validation of differential abundance of selected genes via RT-qPCR

The differential abundance of selected candidate genes in different comparisons was determined by RT-qPCR. A total of 17 selected genes involved in PI signaling, glutathione metabolism and, glycolysis/gluconeogenesis pathway, and those located in QTL-hotspot and TF related genes that exhibited differential abundance in RNA-seq data were analyzed by RT-qPCR analysis. The expression analysis of the genes revealed a high correlation (Pearson correlation, 0.76) between the results obtained from RT-qPCR and RNA-seq (Figure S9).

4 Discussion

Drought stress significantly affects chickpea growth and productivity via altering the underlying molecular mechanism/response (Nayyar et al., 2006). An integrated multi-omics analysis can elucidate important biological processes, metabolic pathways and regulatory networks in plants (Amiour et al., 2012; Srivastava et al., 2013; Sudre et al., 2013; Zeng et al., 2013 Remmers et al., 2018; Li et al., 2019b; Wang et al., 2019; Yun et al., 2019; Chin et al., 2020; Moreno et al., 2021; Bittencourt et al., 2022; Leão et al., 2022; Shu et al., 2022). However, such integrated analysis to decipher plant response to abiotic stress is lacking in chickpea. In this study, we performed transcriptomics, proteomics and metabolomics analyses of two well-characterized genotypes with contrasting drought response/tolerance (ICC 4958 as DT and ICC 1882 as DS) to gain insights into the molecular mechanisms underlying drought stress in chickpea. Further, integration of multi-omics data was performed to provide a better understanding of drought tolerance in chickpea.

4.1 DATs, DAPs and DAMs participate in specific metabolic pathways/processes

Plant adaptation to abiotic stress is mainly initiated by stress-responsive genes and/or proteins (Kosova et al., 2018; Nawae et al., 2020; Kosova et al., 2021; Kausar et al., 2022). We investigated the differential abundance of genes, proteins and metabolites in DT and DS genotypes under drought and control conditions. The identified DATs and DAPs were found to participate in various metabolic pathways and biological processes. The up-regulated genes and proteins were involved mainly in glycolysis/gluconeogenesis and galactose metabolism in DT genotype under drought stress. On contrary, the DS genotype exhibited down-regulation of glycolysis/gluconeogenesis associated genes and proteins under drought stress. In addition, metabolites involved in carbohydrate metabolism were found to be differentially abundant in both DT and DS genotypes. The carbohydrate metabolism is a major pathway regulating cellular carbon and energy requirement for plant survival under drought stress, and genes and proteins encoding the key enzymes of carbohydrate metabolism were found to be differentially expressed under drought stress in chickpea (Khanna et al., 2014). Indeed, sugars are considered an important player in mitigating abiotic stress tolerance in plants (Keunen et al., 2013; Gangola and Ramadoss, 2018). These results demonstrated the important role of carbohydrate metabolism to withstand drought stress in the DT genotype. The amino acids are the precursors of secondary metabolites and signaling molecules, and promote ATP production and detoxification under abiotic stress (Batista-Silva et al., 2019). In our study, up-regulation of several genes/proteins of amino acid metabolism, and differential abundance of amino acids in DT and DS genotypes was suggested to be involved in drought response. Higher amino acid accumulation is a general attribute to drought stress in the plants (Martinelli et al., 2007). Furthermore, hormone signaling and its cross-talk improve abiotic stress tolerance by inducing stress-responsive genes (Ku et al., 2018). Therefore, up-regulation of hormone signaling related genes and proteins in DT(C)/DS(C) might contribute to encountering drought stress. Overall, the activation of stress-responsive genes, proteins and metabolites might be involved in the better adaptation of DT genotype to drought stress.

4.2 TFs confer genotype-specific response under drought stress

TFs are important regulators contributing to abiotic stress tolerance in the plants (Yoon et al., 2020). In our study, up-regulation of members of GNAT, GRAS, C3H, HB, bZIP, PLATZ, sigma70-like, CCAAT, WRKY, Aux/IAA and C2H2-Dof TF families in DT(C)/DS(C) suggested the genotype-specific involvement of TFs. A significant increase in the expression of GNAT family members, histone acetyltransferase (HAT) and acetylation of histone H3 and H4 has been reported in rice under drought stress (Fang et al., 2014). Importantly, drought-induced genome-wide histone acetylation changes the expression of drought-responsive genes (Li et al., 2021). The over-expression of OsGRAS23 and TaWRKY2 induced drought tolerance in rice and wheat, respectively (Xu et al., 2015; Gao et al., 2018). Likewise, over-expression of homeobox (HB) genes, OsHOX24 and OsWOX13 enhanced abiotic stress tolerance in rice (Bhattacharjee et al., 2016; Minh-Thu et al., 2018). Rice OsbZIP62, involved in ABA signaling, positively regulates the expression of drought-responsive genes (Yang et al., 2019). However, over-expression and RNAi knockdown of OsbZIP71 generated drought-tolerant and sensitive phenotype, respectively (Liu et al., 2014). The C3H ZF-TF (AetTZF1) has been suggested to enhance drought tolerance by promoting root growth in Arabidopsis (Jiang et al., 2014), and C2H2-ZFPs provided abiotic and oxidative stress tolerance (Huang et al., 2009). Likewise, WRKY TF provided adaptation to abiotic stress tolerance by modulating stress-responsive genes (Sen et al., 2017). Therefore, the differential abundance of TFs can contribute to better transcriptional control in multiple regulatory pathways for enhanced drought tolerance in DT genotype.

4.3 Implication of QTL-hotspot region associated factors in drought tolerance

QTL-hotspot region plays a major role in drought tolerance in chickpea, and its introgression in an elite variety (JG 11) improved the root traits and drought tolerance (Varshney et al., 2013b). Integration of QTL information and co-expression network analysis has been exploited successfully for the identification of potential candidate genes associated with the maize kernel starch content (Lin et al., 2019a). We applied a similar strategy for the identification of drought-responsive candidate genes and proteins within the QTL-hotspot. The QTL-hotspot region associated genes and proteins in DT(C)/DS(C) have been investigated for their involvement in drought tolerance/response in previous studies. Among the identified genes of co-expression QTL-hotspot, cytochrome P450 (CYP), OsDSS1 is known to be involved in growth and drought stress response in rice (Tamiru et al., 2015). Drought-responsive miR-114 and its target gene, namely stabilizer of iron transporter SufD/polynucleotidyl transferase, participated in drought tolerance in Sorghum bicolor (Katiyar et al., 2015). Likewise, HORVU2Hr1G023890 encoding myosin-J heavy chain is associated with drought tolerance during seed germination in barley (Thabet et al., 2018). The over-expression of receptor-like kinases (RLKs) enhanced abiotic stress tolerance (Osakabe et al., 2010), and cysteine-rich receptor-like protein kinase 5 (CRK5) improved drought tolerance in Arabidopsis (Lu et al., 2016). Furthermore, over-expression of copper amine oxidase 1 mediates proper xylem development and differentiation in Arabidopsis roots, and xylem morphology determines drought response (Ghuge et al., 2015). Moreover, the co-expression QTL-hotspot region associated up-regulated TF, DREB (Ca_04504) is known to contribute in drought tolerance (Haake et al., 2002; Zhang et al., 2009). Similarly, up-regulated pQTL-hotspot associated protein, oligo-saccharyltransferase complex/magnesium transporter family protein (Ca_04632), has been reported previously to participate in drought tolerance (Farid et al., 2013). These results suggested that the QTL-hotspot region associated drought-responsive genes, proteins and TFs contribute to improved drought tolerance in the DT genotype.

4.4 Lipid signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways are involved in drought tolerance

PI signaling is crucial for regulating cellular homeostasis during abiotic stress (Hou et al., 2016). Under stress conditions, the PI signaling pathway influences membrane integrity and cellular signaling via phosphorylation and de-phosphorylation of its related enzymes by kinases and phosphatases, respectively (Heilmann, 2016). The co-expression of various kinases and phosphatases encoding genes and proteins suggested a more pronounced regulation of PI signaling in DT genotype under drought. It has been demonstrated that the identified kinases and phosphatases are involved in cell cycle regulation, histone modifications, cytoskeleton organization and protein sorting in response to abiotic stress (Williams et al., 2005; Pribat et al., 2011; Dieck et al., 2012; Akhter et al., 2016). Further, FAB1D/PI3P5K allows protein trafficking in cortical and stele cells for proper root development (Hirano and Munnik, 2015), and OsDGK1 restores lateral root (LR) density and seminal root (SR) formation (Yuan et al., 2019). Accordingly, we also suggest the involvement of kinases and phosphatases in better root development and hence drought tolerance in the DT genotype. The myo-inositol acts as an osmoprotectant and maintains plant adaptation to drought stress (Li et al., 2020). The over-expression of IMPase increases myo-inositol content and results in an enhanced abiotic stress tolerance (Zhang et al., 2017). Likewise, up-regulation of IMPase (Ca_05134) leading to accumulation of myo-inositol in DT(D/C) suggested its specific role in drought stress tolerance.

Glutathione metabolism is known to be involved in maintaining cellular redox homeostasis during drought stress (Nahar et al., 2015). This adaptive mechanism encounters oxidative damage by utilizing various ROS scavengers (antioxidants) and redox responsive genes (Aquilano et al., 2014). The glutathione metabolism related genes and proteins are well known for regulating cellular redox homeostasis during abiotic stress (Chen et al., 2003). We observed differential regulation of glutathione metabolism in both the genotypes, and genes and proteins of glutathione metabolism were found to be co-expressed specifically in DT(D). The identified genes have previously been reported to contribute to abiotic stress tolerance. For example, the over-expression of glutathione metabolism related gene/proteins, including GST, G6PDH, PGDH, APX, GSTU and GPX improved drought tolerance in the transgenic plants (Badawi et al., 2004; Miao et al., 2006; Ji et al., 2010; Lin et al., 2013; Srivastava et al., 2019). The peptidases and GCL positively regulate plant tolerance to abiotic stress via regulating cellular redox homeostasis (Hicks et al., 2007; Simova-Stoilova et al., 2009). Likewise, GPx/Prx system efficiency regulates H₂O₂ concentration in balancing the cellular glutathione level (Molavian et al., 2015). Moreover, PGDH and G6PDH maintain cellular redox homeostasis by elevating NADPH/NADP⁺ levels in response to drought and salt stresses (Chen et al., 2003). In accordance, co-expression of glutathione metabolism related gene and proteins in DT(D) might explain, in large extent, the enhanced drought tolerance in the DT genotype. In addition, differential abundance of GST (Ca_12001), GSTU (Ca_05354) and G6PDH (Ca_10123) may further contribute to improved drought tolerance in DT. Higher amino acids level has been suggested to improve drought performance (Hildebrandt, 2018), and regulating meristem activity and root architecture during drought stress (Walch-Liu et al., 2006). Similarly, amino acids accumulation via glutathione metabolism is indicative of stress-adaptive responses in DT. Considering the intricate regulation via stress-responsive genes, proteins and metabolites, an improved glutathione metabolic pathway seems to contribute to the enhanced drought tolerance in the DT genotype.

The glycolysis/gluconeogenesis is an important metabolic pathway that regulates carbohydrate metabolism under drought stress (Zhu et al., 2019). Glycolysis/gluconeogenesis associated co-expressed genes and proteins identified in DT(D) are known to be involved in abiotic stress tolerance (Pan et al., 2016; Lin et al., 2019b; Zeng et al., 2019). Among the identified co-expressed genes and proteins in DT(D), PK, PGAM, LDH, PFK, TPI and GPI have been reported to express differentially under drought (Sharma et al., 2012; Khanna et al., 2014; Pan et al., 2016; Yao and Wu, 2016; Li et al., 2019a). Moreover, ENO is known to promote transcription of glycolysis related genes under abiotic stress (Lee et al., 2002). Likewise, GALM maintains drought adaptation and recovery (D’Andrea et al., 2015), and FBPase undergoes post-translation modification to regulate glycolysis during drought stress (Harn and Daie, 1992). Moreover, over-expression of OsPgk2a-P, ScALDH21, ZmPCK2, LDH and TraeALDH7B1-5A confer improved abiotic stress tolerance (Chen et al., 2015; Joshi et al., 2016; Yang et al., 2016; Jain et al., 2020; Jiang et al., 2022). Notably, the role of co-expressed genes in DT(D), namely Dlat and AAE, have not been reported in drought response/tolerance in plants yet. Therefore, further studies are required to elucidate their role in drought response. The up-regulation of FBPase (Ca_00102), PEPCK1 (Ca_11524), GALM-like (Ca_15348) and PGAM (Ca_09253) in DT(D/C) may further contribute to enhanced drought tolerance in the DT genotype. Glucose is a precursor of glycolysis/gluconeogenesis pathway and, is necessary for coordinate regulation of both glycolysis and gluconeogenesis. Moreover, D-glucose is known to induce the expression of abscisic acid (ABA) signaling related genes (Dekkers et al., 2008; Fukumoto et al., 2013), and certainly ABA is critical for controlling abiotic stress responses (Tuteja, 2007). However, D-mannitol is an important osmolyte and compatible solutes providing enhanced tolerance to salt and drought stress (Pujni et al., 2007). Accordingly, accumulation and differential abundance of D-mannitol and D-glucose in DT genotype is an indicative of improved drought tolerance. These results highlighted that DT genotype possesses an improved carbohydrate metabolism to withstand drought stress. Altogether, the synergistic response of co-expressed genes, proteins and metabolites involved in PI signaling pathway, glutathione metabolism and carbohydrate metabolism circumvent the enhanced drought stress tolerance in the DT genotype.

5 Conclusions

To provide a better understanding of drought tolerance, we performed integrated multi-omics analysis in two chickpea genotypes with contrasting responses to drought stress. The WGCNA analysis revealed the co-expressed genes, proteins and metabolites in DT and DS genotypes under control and/or drought conditions. The integrated transcriptome, proteome, and metabolome analysis identified important stress-responsive pathways, including PI signaling, glutathione metabolism and glycolysis/gluconeogenesis that plausibly, in large part, contribute to the drought tolerance in chickpea. Moreover, up-regulated genes, proteins and TFs associated with the QTL-hotspot region seem to determine drought tolerance in the DT genotype. Overall, these results provide new insights into drought stress response in chickpea and reveal candidate genes/proteins that can serve as potential targets for further functional characterization and improving chickpea drought tolerance via genome engineering approaches.

Data availability statement

The datasets presented in this study can be found in online repositories. The transcriptome data generated in this study have been submitted to the GEO at NCBI under the series accession number GSE193077. Proteome data have been submitted to PRIDE database under the project accession number PXD041434 and metabolome data have been submitted to MetaboLights database with study identifier number MTBLS7641.

Author contributions

MJ and RG conceived, designed, and supervised the study. RG performed stress experiments, collected the tissue materials and performed RNA sequencing. VS performed proteome and metabolome experiments, data analyses, and integrated data analyses. KG performed transcriptome data analysis. SS performed RT-qPCR analysis. VS, MJ, and RG wrote the manuscript with inputs from others. All authors read and approved the final version manuscript. All authors contributed to the article.

Funding

The financial support from the Department of Biotechnology, Government of India, under the National Network Project (BT/PR40261/BTIS/137/55/2023) is gratefully acknowledged. RG acknowledges Science and Engineering Research Board, New Delhi for financial support under the Women Excellence Award scheme. KG and SS acknowledges Shiv Nadar Institution of Eminence for fellowship support.

Acknowledgments

MJ acknowledges the support from the Department of Science & Technology, Government of India under the Fund for Improvement of S&T infrastructure in universities & higher educational institutions (FIST) scheme at SCIS. Metablomics facility of AIRF, JNU is acknowledged for GC-MS analysis of samples.

Conflict of interest

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.

Publisher’s note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

Supplementary material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fpls.2023.1156606/full#supplementary-material

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