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3 Biotech

, 7:80 | Cite as

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

  • Girish ChandelEmail author
  • Mahima Dubey
  • Saurabh Gupta
  • Arun H. Patil
  • A. R. Rao
Original Article

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.

Keywords

Sequencing Ferric Chelate Reductase Little millet Metal homeostasis MD simulation 

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

Notes

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.

Author contributions

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

Compliance with ethical standards

Conflict of interest

The authors do not have any conflict of interest.

Supplementary material

13205_2017_656_MOESM1_ESM.docx (5.9 mb)
Supplementary material 1 (DOCX 6033 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Girish Chandel
    • 1
    Email author
  • Mahima Dubey
    • 1
  • Saurabh Gupta
    • 2
  • Arun H. Patil
    • 1
  • A. R. Rao
    • 3
  1. 1.Department of Plant Molecular Biology and Biotechnology, College of AgricultureIndira Gandhi Krishi VishwavidyalayaRaipurIndia
  2. 2.Department of BioinformaticsIndian Institute of Information TechnologyAllahabadIndia
  3. 3.Centre for Agricultural BioinformaticsICAR-Indian Agricultural Statistics Research InstituteNew DelhiIndia

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