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.
Highlights
Melon (Cucumis melo L.) is an outcrossing horticultural crop of worldwide economic importance belonging to the subsp. melo in the Cucurbitaceae family
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
The ITS functionality is related to specific cleavage of the primary transcript within internal transcribed spacer 1 (ITS1) and ITS2 during maturation of the small subunit (SSU), 5.8S, and the large subunit (LSU) ribosomal RNAs
Summary
Melon (Cucumis melo L.) is an outcrossing horticultural crop of worldwide economic importance belonging to the subsp. melo in the Cucurbitaceae family. The understanding genetic diversity is necessary for efficient conservation and management of germplasm collection in agronomically important plants In this preliminary study, we first analyzed and compared the nucleotide sequence of the ITS1-5.8S-ITS2 region from three melon populations belonging to two C. melo varieties (madras and tendral). PCR [10] that could discriminate between the different C. melo cycling program: 35 cycles of 30 s at 94°C, 45 s at 57 or 59 populations To this end, we designed three primers Lowercase letters); common primer sequence: c, 5’- These results demonstrated the feasibility and usefulness of TTAATAATACGACTAGAATGCTCCATCCC-3’; control the ARMS-PCR for the three C. melo ecotype primer sequences: C1, 5’- differentiation, suggesting that the SNPs found in the ITS1. The probability profile for individual bases (W=1) is produced for the region that includes a triplet (the default triplet is GUC) and two flanking sequences of 15 bases each in every site of the selected cleavage triplet
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