Genome-Scale Transcriptomic Insights into Molecular Aspects of Abiotic Stress Responses in Chickpea

Abstract

Chickpea is an important legume crop plant and various abiotic stresses are the major constraints affecting its overall productivity. For discovery of candidate genes involved in abiotic stress responses, we employed RNA sequencing for transcriptome profiling of roots and shoots of chickpea seedlings subjected to desiccation, salinity, and cold stresses. In total, we generated more than 250 million highquality reads from non-stressed and stressed tissue samples. Data analyses provided a comprehensive view of the dynamic transcriptional response of chickpea tissues to different abiotic stresses. Differential expression analysis identified a total of 11,640 chickpea transcripts showing response to at least one of the stress conditions. The reference-based transcriptome assembly was generated and at least 3,536 previously unannotated gene loci differentially expressed under abiotic stress conditions were identified. We observed extensive transcriptional reprogramming of genes involved in transcription regulation, energy metabolism, photosynthesis, hormonal responses, secondary metabolite biosynthesis and osmoprotectant metabolism under stress conditions. In addition, genes involved in post-translational modifications, RNA metabolic processes, and epigenetic regulation were also significantly highlighted. The comprehensive transcriptome analyses presented in this study revealed several potential key regulators of plant response to abiotic stresses and open avenues to carry out functional and applied genomic studies for improving abiotic stress tolerance in chickpea.

The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development

“…In the current dataset, significant number of TFs were identified to be differentially expressed. It has been previously reported that TFs of various gene families perform a crucial function in growth and development via gene regulatory networks (Garg, Bhattacharjee, & Jain, ; Shinozaki & Yamaguchi‐Shinozaki, ). The members of several well‐known TF families implicated in growth and development such as bZIP, GRF, and MYB were significantly differentially expressed suggesting an important role of plant TFs in growth and development of the plant.…”

“…In the current dataset, significant number of TFs were identified to be differentially expressed. It has been previously reported that TFs of various gene families perform a crucial function in growth and development via gene regulatory networks (Garg, Bhattacharjee, & Jain, 2015;Shinozaki & Yamaguchi-Shinozaki, 2007 (Miyashita & Good, 2008). Cysteine and methionine metabolism regulates plant growth and development and are also involved in seed development process.…”

Global analysis of Two Component System (TCS) member of chickpea and other legume genomes implicates its role in enhanced nodulation

“…Tissue specific transcriptomes of chickpea for various tissues and stresses such as leaf (SRX048833), root (SRX048832), flower bud (SRX048834), pod (SRX048835), seed (SRX125162) and nodule (PRJNA214031) were downloaded from SRA (Sequence Read Archive. Stress-specific (salt, desiccation and cold) transcriptome of chickpea root and shoot were retrieved from the SRA database (SRP034839) (Garg et al, 2015). Reads were filtered, trimmed and mapped on the chickpea (desi) genome using TopHat2 (Kim et al, 2013).…”

Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.)

“…Short reads for chickpea root and shoot tissue under three stress conditions- desiccation, salinity and cold, were retrieved from SRA database available under accession number SRP034839 [65]. The reads were mapped onto the predicted gene models in kabuli chickpea genome [23] using BWA-MEM [66] for 454 reads and BWA [67] for Illumina reads.…”