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Applied Biochemistry and Biotechnology

, Volume 187, Issue 1, pp 221–238 | Cite as

Genome-Wide Identification and Analysis of Biotic and Abiotic Stress Regulation of C4 Photosynthetic Pathway Genes in Rice

  • Senthilkumar K. Muthusamy
  • Sangram K. Lenka
  • Amit Katiyar
  • Viswanathan Chinnusamy
  • Ashok K. Singh
  • Kailash C. BansalEmail author
Article

Abstract

Photosynthetic fixation of CO2 is more efficient in C4 than in C3 plants. Rice is a C3 plant and a potential target for genetic engineering of the C4 pathway. It is known that genes encoding C4 enzymes are present in C3 plants. However, no systematic analysis has been conducted to determine if these C4 gene family members are expressed in diverse rice genotypes. In this study, we identified 15 genes belonging to the five C4 gene families in rice genome through BLAST search using known maize C4 photosynthetic pathway genes. Phylogenetic relationship of rice C4 photosynthetic pathway genes and their isoforms with other grass genomes (Brachypodium, maize, Sorghum and Setaria), showed that these genes were highly conserved across grass genomes. Spatiotemporal, hormone, and abiotic stress specific expression pattern of the identified genes revealed constitutive as well as inductive responses of the C4 photosynthetic pathway in different tissues and developmental stages of rice. Expression levels of C4 specific gene family members in flag leaf during tillering stage were quantitatively analyzed in five rice genotypes covering three species, viz. Oryza sativa, ssp. japonica (cv. Nipponbare), Oryza sativa, ssp. indica (cv IR64, Swarna), and two wild species Oryza barthii and Oryza australiensis. The results showed that all the identified genes expressed in rice and exhibited differential expression pattern during different growth stages, and in response to biotic and abiotic stress conditions and hormone treatments. Our study concludes that C4 photosynthetic pathway genes present in rice play a crucial role in stress regulation and might act as targets for C4 pathway engineering via CRISPR-mediated breeding.

Keywords

C4 rice Carbonic anhydrase (CA) Phosphoenol pyruvate carboxylase (PEPC) Malate dehydrogenase (MDH)  Malic enzyme (ME) and Pyruvate Orthophosphate dikinase (PPDK) 

Abbreviations

As

arsenic

BAP

6-benzylaminopurine

BSC

bundle sheath cells

Cd

cadmium

CDS

coding DNA sequence

Cr

chromium

GA3

gibberellic acid

IAA

indole-3-acetic acid

MC

mesophyll cell

mdh

malate dehydrogenase

MPSS

massively parallel signature sequencing

NAA

1-naphthaleneacetic acid

nadp-me

malic enzyme

OAA

oxaloacetate

Pb

lead

PEP

phosphoenolpyruvate

PEPC

phosphoenol pyruvate carboxylase

ppdk

pyruvate orthophosphate dikinase

RuBisCo

ribulosebishosphate carboxylase/oxygenase

RUE

radiation use efficiencies

Notes

Acknowledgements

This work was supported by the Indian Council of Agricultural Research (ICAR)-sponsored National Agricultural Innovation Project (NAIP) project. SKM gratefully acknowledges the Indian Agricultural Research Institute (IARI) for IARI-Junior Research Fellowship grant and Department of Science and Technology (DST), Government of India for DST-INSPIRE fellowship grant. The authors acknowledge National Phytotron Facility, IARI, for providing space for growing plants.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

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12010_2018_2809_MOESM5_ESM.pptx (342 kb)
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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Senthilkumar K. Muthusamy
    • 1
    • 2
  • Sangram K. Lenka
    • 1
    • 3
  • Amit Katiyar
    • 1
    • 4
  • Viswanathan Chinnusamy
    • 5
  • Ashok K. Singh
    • 6
  • Kailash C. Bansal
    • 1
    • 3
    Email author
  1. 1.ICAR-National Research Centre on Plant BiotechnologyICAR-Indian Agricultural Research InstituteNew DelhiIndia
  2. 2.Division of Crop ImprovementICAR-Central Tuber Crops Research InstituteThiruvananthapuramIndia
  3. 3.TERI-Deakin Nanobiotechnology CentreGurgaonIndia
  4. 4.ICMR-All India Institute of Medical ScienceNew DelhiIndia
  5. 5.Division of Plant PhysiologyICAR-Indian Agricultural Research InstituteNew DelhiIndia
  6. 6.Division of GeneticsICAR-Indian Agricultural Research InstituteNew DelhiIndia

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