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Exploring the genomic resources of carrot for cross-genera transferability and phylogenetic assessment among orphan spices and vegetables of Apiaceae family

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Abstract

Carrot (Daucus carota L.) is a member of the Apiaceae family that includes economically important medicinal, ornamentals, seed spices and vegetables. However, the genomic resources in these crops are limited compared to carrot, which is enriched with a number of molecular markers that are publicly available. Hence, we studied the usefulness of the 30 carrot molecular markers for eight different genera composed of five seed spices/condiments and three vegetables. The study revealed the transferability of these carrot markers and the genetic diversity across the genera for respective loci were compared by phylogenetic assessment using an un-rooted neighbour joining tree (NJ) and principle coordinate analysis (PCoA). An average of 66.66% amplification with a total of 73 alleles from 30 loci was observed across eight crops with an average of 3.39 alleles/loci. The average polymorphic information content was 0.50, the effective number of alleles was 2.92, gene diversity was 0.56 with a highest fixation index of 0.82 observed among 18 polymorphic markers. These results indicate the practical use of these markers in the respective crops. Interestingly, phylogenetic analysis grouped the eight crops into three clusters, but the PCoA identified four groups in which carrot was out grouped and kept the other cluster composition intact. Comprehensive study of these eight crops with many more molecular markers would help to understand the evolutionary relatedness for distant hybridization among Apiaceae family members to either transfer genes of interest or to create novel crops.

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Acknowledgements

The authors are grateful to the Department of Biotechnology (DBT), Government of India for funding the establishment of the lab facilities under DBT BIO-CARe (File No: 102/IFD/SAN/3308/2014-15). CC is grateful to former Registrar of UHS Bagalkot (Dr A. B. Patil) for providing the opportunity to carry out the research in the PMB Lab and also to KBITS for fellowship assistance under the BTFS scheme.

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Authors and Affiliations

  1. Plant Molecular Biology Laboratory, Department of Biotechnology and Crop Improvement, College of Horticulture, University of Horticultural Sciences, Bagalkot, Karnataka, 587103, India

    Sarvamangala S. Cholin, Chaitra A. Poleshi, D. S. Manikanta & Calvin Christopher

  2. Department of Post Graduate Studies and Research in Biotechnology, St. Aloysius College, Mangaluru, Karnataka, 575003, India

    Calvin Christopher

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  1. Sarvamangala S. Cholin
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  2. Chaitra A. Poleshi
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  3. D. S. Manikanta
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Correspondence to Sarvamangala S. Cholin.

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Cholin, S.S., Poleshi, C.A., Manikanta, D.S. et al. Exploring the genomic resources of carrot for cross-genera transferability and phylogenetic assessment among orphan spices and vegetables of Apiaceae family. Hortic. Environ. Biotechnol. 60, 81–93 (2019). https://doi.org/10.1007/s13580-018-0101-4

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  • DOI: https://doi.org/10.1007/s13580-018-0101-4

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