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Whole transcriptome expression profiling and biological network analysis of chickpea during heavy metal stress

  • Birendra Singh Yadav
  • Swati Singh
  • Sameer Srivastava
  • Nand Kumar Singh
  • Ashutosh ManiEmail author
Original Article
  • 40 Downloads

Abstract

Heavy metal stress is a major environmental factor responsible for limiting the production of crops. Whole genome wide expression and functional analysis were performed to investigate the molecular insights of heavy metal/metalloids i.e. Trivalent Arsenic [As(III)], hexavalent Chromium [Cr(VI)] and divalent Cadmium [Cd(II)] mediated stress response in chickpea. Deoxyribonucleic acid microarray-based comparative and functional analysis of transcript revealed the versatility of gene expression in the chickpea genotype. It was found that a total of 490, 238 and 1123 genes were up-regulated as well as 645, 229 and 607 genes were down-regulated during exposure of Arsenic [As(III)], Chromium [Cr(VI)] and Cadmium [Cd(II)], respectively. The key metabolic pathways involved in the stress response during exposure of heavy metals were identified by system biology approach. The pathways which were affected due to over and underexpression of genes during the treatment of heavy metal are glucuronate interconversions, Indole alkaloid biosynthesis, phenylpropanoid, cysteine, and methionine metabolism, and nitrogen metabolism, glycerophospholipid metabolism, protein processing in the endoplasmic reticulum and riboflavin metabolism.

Keywords

Microarray Abiotic stress Chickpea System biology Metabolic pathway 

Abbreviations

ROS

Reactive oxygen species

MG

Methylglyoxal

GPX

Glutathione peroxidase

GEO

Gene Expression Omnibus

DEG’s

Differentially expressed genes

GO

Gene ontology

GSEA

Gene set enrichment analysis

PCC

Pearson’s coefficient correlation

Notes

Acknowledgements

BSY is highly thankful to DST New Delhi for INSPIRE Ph.D. fellowship. AM is highly thankful to MNNIT Allahabad for providing TEQIPII grant.

Author contributions

BSY performed the experiments. AM conceived the project and analyzed the data. BSY, NKS, SS1, and SS2 analyzed the data and helped in writing the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

13562_2019_486_MOESM1_ESM.xlsx (274 kb)
Supplementary material 1 (XLSX 274 kb)
13562_2019_486_MOESM2_ESM.docx (185 kb)
Supplementary material 2 (DOCX 185 kb)

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Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  • Birendra Singh Yadav
    • 1
  • Swati Singh
    • 2
  • Sameer Srivastava
    • 1
  • Nand Kumar Singh
    • 1
  • Ashutosh Mani
    • 1
    Email author
  1. 1.Department of BiotechnologyMotilal Nehru National Institute of Technology AllahabadAllahabadIndia
  2. 2.Center of BioinformaticsUniversity of AllahabadAllahabadIndia

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