Scientia Horticulturae 190 (2015) 123–127 Contents lists available at ScienceDirect Scientia Horticulturae journal h om epage: www.elsevier.com/locate/scihorti Short communication Retrotransposon based TRAP marker displays diversity among onion (Allium cepa L.) genotypes Sivalingam Anandhan ∗ , Abhilash Nair, Dipali Santosh Kumkar, Jai Gopal ICAR—Directorate of Onion and Garlic Research, Rajgurunagar, Pune 410505, Maharashtra, India a r t i c l e i n f o Article history: Received 4 December 2014 Received in revised form 21 March 2015 Accepted 17 April 2015 Available online 15 May 2015 Keywords: Repeats Insertional polymorphism Diversity Ty1 copia a b s t r a c t Ty1-copia like elements are distributed throughout the onion (Allium cepa) genome, and are actively transcribed. Sequence analysis by LTR finder identified that the copia element in onion is bound by long terminal repeats (LTR) of length 121 bp. Primer binding site and poly purine tract are located on copia element at 193–211 bp and 4593–4607 bp respectively. To exploit the variation at the insertional locus and to explore its further use as a marker, a method using a primer located on the LTR and an arbitrary primer was developed for detecting variation in onion genotypes. This method resulted in the detection of polymorphism in 22 onion genotypes. Thirty-three polymorphic amplicons were detected in these genotypes. The genetic distance between the varieties varied from 0.83 to 0.99. Phylogenetic analysis revealed that the Indian short day onion clustered separately from the exotic varieties indicating that the origin of Indian varieties is distinct. Further, variation observed among Indian varieties was less than that of exotic varieties. The marker was detected across eight species of genus Allium and the genetic distance between the species varied from 0.34 to 0.88. Polymorphism detection was better across the species than within A. cepa. This retrotransposon based method is likely to supplement the marker resources for Allium spp. © 2015 Elsevier B.V. All rights reserved. 1. Introduction Marker resources are limited in onion (Allium cepa), which could be attributed to its large genome size and lack of sequence data. So far, markers such as biochemical and molecular markers (Cramer and Havey, 1999; Arifin et al., 2000) have been used for diver- sity analysis (Roumba et al., 2001; Tanikawa et al., 2002), mapping (Heusden et al., 2000), haploid analysis (Bohanec et al., 1995), and analysis of alien addition lines (Hang et al., 2004). Though consid- erable number of SSR, CAPS, and SNP markers (Kuhl et al., 2004; McCallum et al., 2008; Baldwin et al., 2012; Duangjit et al., 2013) are available, they are not sufficient to cover the entire genome or their density is too low to be used in mapping quantitative traits. Retrotransposons are ubiquitously distributed in all plant species (Voytas et al., 1992) and their copy numbers and genomic locations vary with families. They vary greatly in abundance and chromosomal location between species (Pearce et al., 1996). Since the retrotransposons create permanent loci upon insertion, several ∗ Corresponding author. Tel.: +91 2135 222026 o. E-mail addresses: anandhans@dogr.res.in, anandhans@gmail.com (S. Anandhan). marker systems based upon retrotransposons have been developed (Schulman et al., 2012). In all the reported methods, one primer is located on the retrotransposon sequence. The transposon–plant junction can be amplified through use of microsatellite (REMAP) (Kalender et al., 1999), the retrotransposon sequence itself (IRAP) (Kalender et al., 1999), or through adapter ligation and amplifi- cation (SSAP) (Flavell et al., 1998). Among these, sequence-specific amplification polymorphism (SSAP; Waugh et al., 1997) is the most useful for detecting large numbers of polymorphic loci. Versatil- ity of retrotransposan based markers has been proven in many species like Strawberry (He et al., 2012), Cashew (Syed et al., 2005), Japanese pear (Kim et al., 2012), Peas (Flavell et al., 1998) and Barley (Waugh et al., 1997). Conserved sequences for the copia like element from A. cepa have been reported (Pearce et al., 1996). Retrotransposons consti- tute a major part of repeat elements of A. cepa genome; it also gets transcribed and constitutes around 0.8% of EST data (Kuhl et al., 2004). This is an indication that the retrotransposons are active in the genome, and can create new heritable loci over generations. The insertion sites can be exploited to differentiate the genotypes based on transposon–plant DNA junction. In the present study, we report a novel marker system for A. cepa based on retrotransposon and plant DNA junction that can be utilised in differentiation of A. cepa genotypes. http://dx.doi.org/10.1016/j.scienta.2015.04.024 0304-4238/© 2015 Elsevier B.V. All rights reserved.