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Identification and characterization of a grain micronutrient-related OsFRO2 rice gene ortholog from micronutrient-rich little millet (Panicum sumatrense)

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Abstract

Minor millets are considered as nutrient-rich cereals having significant effect in improving human health. In this study, a rice ortholog of Ferric Chelate Reductase (FRO2) gene involved in plant metal uptake has been identified in iron-rich Little millet (LM) using PCR and next generation sequencing-based strategy. FRO2 gene-specific primers designed from rice genome amplified 2.7 Kb fragment in LM genotype RLM-37. Computational genomics analyses of the sequenced amplicon showed high level sequence similarity with rice OsFRO2 gene. The predicted gene structure showed the presence of 6 exons and 5 introns and its protein sequence was found to contain ferric reductase and NOX_Duox_Like_FAD_NADP domains. Further, 3D structure analysis of FCR-LM model protein (494 amino acids) shows that it has 18 helices, 10 beta sheets, 10 strands, 41 beta turn and 5 gamma turn with slight deviation from the FCR-Os structure. Besides, the structures of FCR-LM and FCR-Os were modelled followed by molecular dynamics simulations. The overall study revealed both sequence and structural similarity between the identified gene and OsFRO2. Thus, a putative ferric chelate reductase gene has been identified in LM paving the way for using this approach for identification of orthologs of other metal genes from millets. This also facilitates mining of effective alleles of known genes for improvement of staple crops like rice.

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Abbreviations

LM:

Little millet

Fe:

Iron

FCR-LM:

Ferric chelate reductase-Little millet

FCR-Os:

Ferric chelate reductase-Oryza sativa

FRO2:

Ferric reduction oxidase 2

PCR:

Polymerase chain reaction

NGS:

Next generation sequencing

Zn:

Zinc

MD:

Molecular Dynamics

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Acknowledgements

Seed material provided by ZARS, Jagdalpur and Department of Biotechnology, Ministry of Science and Technology, Govt. of India for providing the financial support are thankfully acknowledged.

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Author notes

  1. Mahima Dubey and Saurabh Gupta are contributed equally to this study.

Authors and Affiliations

  1. Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar, Raipur, 492012, Chattisgarh, India

    Girish Chandel, Mahima Dubey & Arun H. Patil

  2. Department of Bioinformatics, Indian Institute of Information Technology, Deoghat, Jhalwa, Allahabad, 211015, Uttar Pradesh, India

    Saurabh Gupta

  3. Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, Delhi, India

    A. R. Rao

Authors
  1. Girish Chandel
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  2. Mahima Dubey
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  3. Saurabh Gupta
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  4. Arun H. Patil
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  5. A. R. Rao
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Contributions

Execution of experiments and analysis: MD and SG; Experiments designing: MD, SG and GC; Wrote paper: MD, SG, AP, ARR, and GC.

Corresponding author

Correspondence to Girish Chandel.

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The authors do not have any conflict of interest.

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Chandel, G., Dubey, M., Gupta, S. et al. Identification and characterization of a grain micronutrient-related OsFRO2 rice gene ortholog from micronutrient-rich little millet (Panicum sumatrense). 3 Biotech 7, 80 (2017). https://doi.org/10.1007/s13205-017-0656-2

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