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RAPD and ISSR marker assessment of genetic diversity in Citrullus colocynthis (L.) Schrad: a unique source of germplasm highly adapted to drought and high-temperature stress

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Abstract

Citrullus colocynthis (L.) Schrad. (Cucurbitaceae) shows high levels of variation in fruit color, fruit stripe pattern, seed coat color, and size. Thirty-eight accessions of C. colocynthis plants from different parts of semi-arid Rajasthan were collected and genetic diversity was assessed using random-amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Out of 65 RAPD decamer primers, 50 primers produced 549 scorable bands of which 318 were polymorphic. Polymorphic banding patterns with the number of amplified fragments varied from 5 (OPA-08 and OPF-9) to 19 (OPT-20) in the molecular size range of 150–6000 bp. Percent polymorphism ranged from 22.2% (OPA-09) to 83.3% (OPE-12) with 55.14% polymorphism. Out of the 20 ISSR primers screened, 13 primers produced 166 amplification products, of which 99 were polymorphic. The number of bands amplified per primer varied between 9 (UBC-807, 802) and 16 (UBC-803, 812) with average band size between 250 and 4000 bp. Percent polymorphism ranged from 45.4% (UBC-815) to 73.3% (UBC-814) with 65.05% polymorphism. Dendrogram constructed on the basis of RAPD + ISSR polymorphism separated the accessions into four distinct clusters at 72% variation with Jaccard’s similarity coefficient ranging from minimum 0.64 to 0.95. The matrices for RAPD and ISSR were also compared using Mantel’s test and obtained correlation value (r = 0.7947). Discriminating power of RAPD and ISSR markers was assessed by calculating polymorphic information content, multiplex ratio, marker index, and resolving power. Approx. 50% RAPD and ISSR markers showed PIC value and heterozygosity (H) ≥ 0.50, indicating marker as informative. The primers that showed higher polymorphism had higher RP, MR, and MI values.

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Acknowledgements

Authors are thankful to CSIR for financial support and for the award of SRF during Ph.D., Interdisciplinary Program in life Science (IPLS), University with Potential for Excellence Scheme by UGC (UPE Program), DRS-II, Dept. of Botany, Bioinformatics Infrastructure Facility (BIF) by DBT and University of Rajasthan are gratefully acknowledged.

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  1. Department of Botany, University of Rajasthan, Jaipur, India

    Kumar Sambhav Verma, Shamshad ul Haq, Sumita Kachhwaha & S. L. Kothari

  2. Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 302006, India

    Kumar Sambhav Verma & S. L. Kothari

  3. Bioinformatics Infrastructure Facility (BIF), University of Rajasthan, Jaipur, India

    Sumita Kachhwaha

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  1. Kumar Sambhav Verma
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Verma, K.S., ul Haq, S., Kachhwaha, S. et al. RAPD and ISSR marker assessment of genetic diversity in Citrullus colocynthis (L.) Schrad: a unique source of germplasm highly adapted to drought and high-temperature stress. 3 Biotech 7, 288 (2017). https://doi.org/10.1007/s13205-017-0918-z

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