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Molecular differentiation in Indian Citrus L. (Rutaceae) inferred from nrDNA ITS sequence analysis

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Abstract

Molecular differentiation in 24 accessions representing 19 taxa of Indian Citrus has been examined through sequence analysis of Internal Transcribed Spacer (ITS) region of nrDNA. Sequence length in the 24 accessions of Citrus taxa ranged from 512 to 665 bp (ITS1 & ITS2 partial and 5.8S complete sequence). The ITS sequences were very rich in G+C content ranging from 61.40 to 66.60% with an average of 64.2%. Genetic distance within Citrus group ranged from 0 to 13.4% with an average of 4.6%, showing moderate rate of nucleotide divergence. The phylogeny was inferred using the Maximum parsimony (MP) and Neighbor-Joining (NJ) methods. Both MP and NJ trees separated all the 24 accessions of Citrus into six distinct clusters. The disposition of all the accessions of Citrus in separate clusters in ITS-derived dendrograms was partly in accordance with the morpho-taxonomic affinities of the target taxa. This study supports the concept of Citrus medica (citron), C. reticulata (mandarin), and C. maxima (pummelo) as the basic species of the genus. However, ITS marker could not find any clear cut differentiation between subgenera Citrus and Papeda as proposed in Swingle’s Citrus classification system. The present study also supports the distinctiveness of C. indica (Indian wild orange), C. latipes (Khasi papeda) and C. hystrix (Melanesian papeda) as true species, besides elucidating the probable hybrid origin and relationships among the cultivated species/biotypes, such as Citrus ×aurantiifolia (sour lime) C. ×limon (lemon), C. ×taitensis (Indian rough lemon), C. limettioides (sweet lime), C. ×aurantium (including sour and sweet oranges and grapefruit), and other indigenous varieties of Indian origin: C. megaloxycarpa (sour pummelo), C. karna (karna orange), C. pseudolimon (Hill lemon), ‘Memang athur’, ‘Pummelo-lemon’ and ‘Kathairi nimbu’.

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Acknowledgments

The authors wish to thank the Director, CSIR-National Botanical Research Institute (NBRI) for providing facilities to carry out this work, and the officers & staff of Nokrek Biosphere Reserve (NBR), Tura, Meghalaya for their help and support during exploration trips to NBR. The financial support received from the Department of Biotechnology, New Delhi and the Council of Scientific and Industrial Research (CSIR), New Delhi to carry out this work is gratefully acknowledged.

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Authors and Affiliations

  1. Tissue Culture and Cryopreservation Unit, National Bureau of Plant Genetic Resources, Pusa campus, New Delhi, 110012, India

    Susheel Kumar

  2. Plant Diversity, Systematics and Herbarium Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India

    K. Narayanan Nair

  3. Plant Molecular Biology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India

    Satya Narayan Jena

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  1. Susheel Kumar
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Correspondence to K. Narayanan Nair.

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Kumar, S., Nair, K.N. & Jena, S.N. Molecular differentiation in Indian Citrus L. (Rutaceae) inferred from nrDNA ITS sequence analysis. Genet Resour Crop Evol 60, 59–75 (2013). https://doi.org/10.1007/s10722-012-9814-x

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