Beyond Bioinformatics

Title

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

Authors

Stefania Fantaccione¹, Pasqualina Woodrow¹ and Giovanni Pontecorvo^1, *

Affiliation

Department of Life Science, II University of Naples, via Vivaldi 43, 81100 Caserta, Italy

Email

giovanni.pontecorvo@unina2.it; * Corresponding author

Article Type

Hypothesis

Date

received April 18, 2008; accepted April 19, 2008; published April 28, 2008

Abstract

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.

Keywords

secondary structure prediction; ARMS-PCR; Cucumis melo L.; ITS1; SNP

Citation

Fantaccione et al., Bioinformation 2(7): 311-315 (2008)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics Publishing Group

Copyright

Publisher

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.