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Transcriptome Sequencing of Chickpea (Cicer arietinum L.) Genotypes for Identification of Drought-Responsive Genes Under Drought Stress Condition

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Abstract

Chickpea (Cicer arietinum L.) is a pulse crop valued for its high protein content, grown in semi-arid tropics and Mediterranean regions. Its yield remains affected by biotic and abiotic stresses with drought alone being responsible for up to 50% annual loss of yield. Transcriptome analysis of a sensitive and a tolerant cultivar of chickpea has been done earlier to unravel the molecular basis for drought and salinity stress responses. In the present study, we performed transcriptome analysis of two drought-tolerant genotypes, BG-362 and P-256, under polyethylene glycol-simulated drought stress to decipher the genes and pathways that are commonly regulated in these genotypes. RNA-Seq using Illumina platform generated 152 million high-quality reads. Reference-guided assembly of genome yielded a total of 37,943 transcripts representing 22,701 genes. Among the 1624 genes that were observed to be differentially expressed under drought, 97 genes were common in both the genotypes. These included the upregulated genes, such as probable mannitol dehydrogenase, serine hydroxymethyltransferase 4-like, 17.5 kDa class I heat shock protein-like, cytochrome P450 81E8-like, and galactinol-sucrose galactosyltransferase-like, and downregulated genes, such as probable xyloglucan endotransglucosylase/hydrolase protein 23, abscisic acid 8′-hydroxylase 1-like, Calmodulin-like protein 11, and proline dehydrogenase 2 mitochondrial-like genes. A major finding was the involvement of transcription factors, including AP2-EREBP, bHLH, bZIP, C3H, MYB, NAC, WRKY, and MADS. The present study is the first comparative analysis of RNA-Seq data for two drought-tolerant chickpea genotypes. These findings would help in improving drought tolerance across chickpea genotypes.

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Funding

This research was financially supported by New Initiative (as a Cross Flow Technology project) “Root Biology and its Correlation to Sustainable Plant Development and Soil Fertility” (Root SF; BSC0204) from the Council of Scientific and Industrial Research (CSIR), New Delhi, India. This manuscript has been assigned a manuscript communication number, IU/R&D/2018-MCN000276, by Dean, Research & Development, Integral University, Lucknow.

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  1. Division of Plant-Microbe Interactions, CSIR-National Botanical Research Institute (NBRI), Rana Pratap Marg, Lucknow, (U.P.), 226001, India

    Manoj Kumar, Abhishek Singh Chauhan, Manoj Kumar & Puneet Singh Chauhan

  2. Department of Biosciences, Integral University, Lucknow, U.P., 226026, India

    Manoj Kumar

  3. Academy of Scientific and Innovative Research, New Delhi, India

    Abhishek Singh Chauhan

  4. Department of Bioengineering, Integral University, Lucknow, U.P., 226026, India

    Mohd Aslam Yusuf

  5. Genetics and Plant Molecular Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, (U.P.), 226001, India

    Indraneel Sanyal

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PSC and MK conceived and designed the research. MK, IS, and ASC conducted the experiments. MK and ASC analyzed the transcriptome data. MK wrote the manuscript. PSC, MK, and MAY critically reviewed the manuscript. All the authors read and approved the manuscript.

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Correspondence to Puneet Singh Chauhan.

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Kumar, M., Chauhan, A.S., Kumar, M. et al. Transcriptome Sequencing of Chickpea (Cicer arietinum L.) Genotypes for Identification of Drought-Responsive Genes Under Drought Stress Condition. Plant Mol Biol Rep 37, 186–203 (2019). https://doi.org/10.1007/s11105-019-01147-4

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