Retrotransposon based TRAP marker displays diversity among onion (Allium cepa L.) genotypes

• Copia like element in A. cepa was identified from database and characterised in silico for LTR sequences.
• A TRAP marker was developed based on Retrotransposon–Plant junction using primer located on copia LTR sequence and arbitrary primer.
• The TRAP successfully detected polymorphism between Indian and exotic onion cultivars and also between seven species of genus Allium.
• These markers distinguished the diversity between the onion cultivars and seven species of genus Allium.

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.