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

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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.

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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

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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.

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  1. Senthilkumar K. Muthusamy

    Present address: Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, 695017, India

  2. Sangram K. Lenka & Kailash C. Bansal

    Present address: TERI-Deakin Nanobiotechnology Centre, Gurgaon, 122 001, India

  3. Amit Katiyar

    Present address: ICMR-All India Institute of Medical Science, Ansari Nagar, New Delhi, 110029, India

Authors and Affiliations

  1. ICAR-National Research Centre on Plant Biotechnology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Senthilkumar K. Muthusamy, Sangram K. Lenka, Amit Katiyar & Kailash C. Bansal

  2. Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Viswanathan Chinnusamy

  3. Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Ashok K. Singh

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  1. Senthilkumar K. Muthusamy
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  2. Sangram K. Lenka
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Correspondence to Kailash C. Bansal.

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Muthusamy, S.K., Lenka, S.K., Katiyar, A. et al. Genome-Wide Identification and Analysis of Biotic and Abiotic Stress Regulation of C4 Photosynthetic Pathway Genes in Rice. Appl Biochem Biotechnol 187, 221–238 (2019). https://doi.org/10.1007/s12010-018-2809-0

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