Indian Journal of Biotechnology Vol 16, July 2017, pp 346-356 Molecular markers in assessing genetic variation of Indian citron (Citrus medica L.) cultivars collected from different parts of India Ajit Uchoi 1 , S K Malik 2* , Ravish Choudhary 1 , Susheel Kumar 2 , Digvender Pal 1 , M R Rohini 1 & Rekha Chaudhury 2 1 Indian Agricultural Research Institute, Pusa, New Delhi-110012 India 2 Tissue Culture and Cryopreservation Unit, National Bureau of Plant Genetic Resources (NBPGR), Pusa Campus, New Delhi-110 012, India Received 2 June 2014; revised 28 August 2015; accepted 28 August 2015 Genetic diversity of forty six representative accessions of Citrus medica L. (Rutaceae) was estimated using 17 (RAPD) random amplification of polymorphic DNA and 11 inter simple sequence repeat (ISSR) markers. A total of 213 RAPD and 105 ISSR bands were generated, out of which, 175 (RAPD) and 77 (ISSR) bands were polymorphic. Polymorphism percentage of RAPD (82%) was comparatively higher than ISSR (73%). Genetic similarity value was found in the range of 0.49 to 0.96 (average 0.73), 0.38 to 0.99 (average 0.69) and 0.47 to 0.96 (average 0.72) in RAPD, ISSR and combined data analyses, respectively. Moderately high levels of polymorphism and genetic similarity within C. medica suggested that citron cultivars have a significant level of genetic diversity. A dendrogram generated based on unweighted pair group method of arithmetic- average (UPGMA) separated all the accessions into two main clusters. The placement of C. medica accessions in various sub-clusters and groups in the dendrogram was based on molecular differentiation of individual accessions rather than their geographical origin. Both, RAPD and ISSR analyses were able to identify elite genotypes of C. medica with unique accession specific DNA fragments. Thus, both the markers can be utilized for inferring the extent and distribution of genetic diversity in C. medica. Keywords: Citrus medica, genetic diversity, ISSR, RAPD, UPGMA Introduction The genus Citrus belongs to the sub-tribe Citrineae within the sub-family Aurantioideae of the family Rutaceae and has a pre-dominantly tropical to semi- tropical distributions. It is one of the most important fruit crops in the world with over 122 million tons of international production 1 . Currently, there are two widely used classification systems in Citrus: Swingle 2-3 and Tanaka 4 . The Swingle system included 16 species under two sub- genera - Citrus and Papeda, while the Tanaka system recognized 162 species under the sub-genera ArchiCitrus and MetaCitrus. However, Scora 5 and Barrett & Rhodes 6 suggested that there are only three ‘basic’ true species of Citrus within the sub-genus Citrus i.e., Citron (C. medica L.), Mandarin (C. reticulata Blanco) and Pummelo (C. maxima L. Osbeck). Later, Scora 7 added C. halimi as another true species. Other cultivated species within Citrus were derived from hybridization between these true or closely related genera followed, mainly, by natural mutations. Recently, this idea has gained support from various biochemical and molecular studies 8-11 . There exists a high level of genetic variations among the cultivated Citrus species due to frequent bud mutations, widely sexual compatibility between Citrus genus and related genera, apomixes and the long history of cultivation and the worldwide dispersion 7 . Elucidating relationships, taxonomy, and diversity is important for developing breeding strategies, conserving biodiversity, and improving breeding efficiency. Also understanding of genetic variability in Citrus is critical for characterizing germplasm, controlling genetic erosion and the registration of new cultivars 10,12 . Citrus medica (commonly known as citron) one of the important Citrus fruits of the world, is considered a native of India 5,13 and is found to grow in a wild and semi-wild state in primary as well as secondary forests along the foothills of the Eastern Himalayas and North-East India 4,14,15 . The true citron is called bira- jora or bakol-khowa-tenga (bakol means rind, khowa to eat and tenga stands for sourness) in Assam —————— *Author for correspondence skm@nbpgr.ernet.in Tel: +91-011-25848955