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Mitochondrial markers differentiate two distinct phylogenetic groups in indigenous rice landraces of northeast India: an evolutionary insight

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Abstract

The inheritance of the mitochondria genome and its diversity is unique for genetic and evolutionary studies relative to nuclear genomes. Northeast India and Himalayan regions are considered as one of the centres of indica rice origin. Also, rice diversity in northeast India is very distinct and highly suited for evolutionary studies. Although reports are available on the genetic diversity of indigenous northeast rice landraces, its relationship with the wild relatives is not yet properly explored and understood. In an attempt, mitochondrial markers were used to study the evolutionary relationship between the 68 landraces of northeast India and wild relatives (O. rufipogon and O. nivara) along with IR64 (indica) and Nipponbare (japonica) were taken as reference cultivars. Phylogenetically, the findings include two distinct clusters in the indigenous northeast India landraces representing indica and japonica groups. Further, the wild relatives and ~60% of northeast India landraces were identified to be closely related to the Nipponbare cluster. Besides, landraces of northeast India grouping with the indica group (IR64) are characterized by the absence of wild relatives. This indicates that there are two distinct evolutionary paths in the origin of northeast Indian rice landraces based on mitochondrial markers diversity and it is proposed that the inheritance of mitochondria, mitonuclear genome interactions, and bottleneck events could have genetically separated these two phylogenetically unique groups of northeast rice landraces.

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Acknowledgements

All the authors gratefully acknowledge the financial support provided by the Indian Council of Agricultural Research (ICAR), New Delhi, for supporting this work. Also, we sincerely acknowledge the Director, National Rice Research Institute (ICAR-NRRI), Cuttack for providing the necessary lab facilities for the completion of this work.

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Authors and Affiliations

  1. ICAR-National Rice Research Institute (ICAR-NRRI), Cuttack, 753 006, India

    Madhuchhanda Parida, Gayatri Gouda, Parameswaran Chidambaranathan, Ngangkham Umakanta, Jawahar Lal Katara, Cayalvizhi Balasubramania Sai, Sanghamitra Samantaray, Bhaskar Chandra Patra & Trilochan Mohapatra

  2. ICAR-ICAR Regional Center NEH Region, Manipur Centre, Imphal, 795 004, India

    Ngangkham Umakanta

  3. Indian Council of Agricultural Research (ICAR), New Delhi, 110 001, India

    Trilochan Mohapatra

Authors
  1. Madhuchhanda Parida
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  2. Gayatri Gouda
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  3. Parameswaran Chidambaranathan
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  4. Ngangkham Umakanta
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  5. Jawahar Lal Katara
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  7. Sanghamitra Samantaray
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  8. Bhaskar Chandra Patra
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Contributions

TM: conceptualization; BCP: coordination of work; MP: genotyping, analysis, manuscript preparation; GG: data analysis; PC: analysis, interpretation, validation, manuscript editing and finalization; NU & CBS: data analysis and manuscript editing; SS & JLK: manuscript finalization.

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Correspondence to Parameswaran Chidambaranathan.

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Corresponding editor: Shrish Tiwari

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Parida, M., Gouda, G., Chidambaranathan, P. et al. Mitochondrial markers differentiate two distinct phylogenetic groups in indigenous rice landraces of northeast India: an evolutionary insight. J Genet 102, 26 (2023). https://doi.org/10.1007/s12041-023-01422-0

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  • DOI: https://doi.org/10.1007/s12041-023-01422-0

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