Molecular authentication of three Italian melon accessions by ARMS-PCR and ITS1 (internal transcribed spacer 1) secondary structure prediction

Genetic assessment was carried out on three Italian melon accessions by sequence and structural analysis of the internal transcribed spacer 1 (ITS1) from three populations belonging to two Cucumis melo L. varieties (madras and tendral). Alignment of the 18S-5.8S-26S sequences from three melon accessions showed that there were three single-nucleotide polymorphisms (SNPs) and one short insertion-deletion (indel) at the 5'end ITS1. An amplification refractory mutation system (ARMS)-PCR-based analysis was successfully applied to the SNP markers of the ITS1 sequences for the fingerprinting analysis of three melon populations. Secondary structure models for each ITS1 were derived. The prediction of ITS1 RNA secondary structure from each accession was improved by detecting key functional elements shared by all sequences in the alignments. Our results demonstrated that the ITS1secondary structure models can be used to improve the preliminary genetic assessment of the three melon accessions, suggesting a new tool in plant fingerprinting analysis.