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Kalivas A.,Cotton and Industrial Plants Institute | Ganopoulos I.,Institute of Applied Biosciences | Ganopoulos I.,Aristotle University of Thessaloniki | Xanthopoulou A.,Institute of Applied Biosciences | And 4 more authors.
Molecular Biology Reports | Year: 2014

Identification of genotypes in Sideritis is complicated owing to the morphological similarity and common occurrence of natural hybridisation within Sideritis species. Species- and genotype-specific DNA markers are very useful for plant identification, breeding and preservation programs. Herein, a real-time polymerase chain reaction (PCR) of ITS2 barcode region coupled with high resolution melting-curve (HRM) analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on seven Sideritis species growing in Greece. The HRM assay developed in this study is a rapid and straightforward method for the identification and discrimination of the investigated Sideritis species. This assay is simple compared to other genotyping methods as it does not require DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of Sideritis species. © 2014 Springer Science+Business Media. Source


Aliki X.,Institute of Applied Biosciences | Aliki X.,Aristotle University of Thessaloniki | Ioannis G.,Institute of Applied Biosciences | Ioannis G.,Aristotle University of Thessaloniki | And 7 more authors.
Australian Journal of Crop Science | Year: 2015

The conservation and characterization of summer squash (Cucurbita pepo) genetic resources in germplasm banks has been the basis of their use in breeding projects, which resulted in the development of new cultivars. The genetic diversity of thirty six summer squash landraces from Greece was investigated here using start codon targeted (SCoT) polymorphism and inter-simple sequence repeat (ISSR) markers. In this study, we compared the informativeness and efficiency of the SCoT and ISSR molecular markers. ISSR markers were found to be more polymorphic with an average PIC value of 0.237, while SCoT markers showed the highest marker index (1.503). Cluster analysis on combined set of SCoT and ISSR genotyping data classified summer squash landraces in six distinct groups. The obtained PCoA (Principal Coordinate Analysis) scatter plots further supported the dendrogram results in a robust way. To our knowledge, this is the first detailed comparison of performance among the targeted DNA region molecular markers (SCoT) and the ISSR technique on a set of samples of C. pepo. The high genetic diversity existing in the Greek germplasm suggested that it would be beneficial to utilize this pool in summer squash breeding programs and germplasm management activities, in order to maximize genetic diversity in cultivated squash. Source


Ganopoulos I.,Institute of Applied Biosciences | Kalivas A.,Cotton and Industrial Plants Institute | Kavroulakis N.,Institute of Olive Tree and Subtropical Plants of Chania | Xanthopoulou A.,Institute of Applied Biosciences | And 5 more authors.
Plant Gene | Year: 2015

Barbary fig (Opuntia ficus indica) could be an economically important species as it could be an alternative crop extremely tolerant to dry condition and water deficiency. Moreover, it could be used in alternative sustainable cultivation systems and landscape conservation. In this work, we report the analysis of the genetic diversity of Greek Barbary fig genotypes using ISSR molecular markers. Six primers were screened to assess their ability to detect polymorphisms within twenty-two Barbary fig accessions and generated 57 markers (bands), with an average of 9.5 markers per primer. The percentage of polymorphic bands (50.21%) and the resolving power (RP) (28.85) showed the efficiency of the used primers. Mean values for GD (gene diversity) and I (Shannon index) were found as 0.215 and 0.355, respectively. The revealed ISSR markers allow distinguishing all accessions analyzed except for one case. UPGMA dendrogram and PCoA (Principal Coordinate Analysis) were performed to access patterns of diversity among genotypes. The high genetic diversity existing in the Greek germplasm suggests that it would be beneficial to utilize this pool in Barbary fig breeding programs and germplasm management activities. © 2015, Elsevier B.V. All rights reserved. Source


Ganopoulos I.,Institute of Applied Biosciences | Xanthopoulou A.,Institute of Applied Biosciences | Xanthopoulou A.,Aristotle University of Thessaloniki | Molassiotis A.,Aristotle University of Thessaloniki | And 8 more authors.
Trees - Structure and Function | Year: 2015

Key message: The selected germplasm ofFicus caricaestablished in a gene bank collection will be useful for conservation and management and important for fig treebreeding programs.Abstract: Advancement in plant breeding is assisted by accurate information on genetic diversity and structure. A collection of ninety fig tree (Ficus carica L.) cultivars originating from the Mediterranean basin and conserved in an ex situ gene bank collection was genotyped using seven microsatellite markers. A total of 91 alleles were detected presenting an average of 13 alleles per locus. The gene bank fig tree collection preserved a high level of genetic diversity. The mean expected and observed heterozygosities over the seven single locus microsatellites averaged 0.747 and 0.784, respectively. The total value of the probability of identity was 2 × 10−6. The 90 fig tree accessions formed four clusters in the unweighted pair group method using arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the fig tree accessions based on their geographical origin. Moreover, the 90 fig tree accessions could be divided into two clusters based on STRUCTURE analysis. Additionally, microsatellites coupled with high-resolution melting analysis enabled both the distinction, identification and authentication of the ‘Kymis’ fig tree Protected Designation of Origin cultivar and its products. In conclusion, results presented here are significant for the management of gene bank collections, breeding programs and authentication of fig tree cultivars. © 2015 Springer-Verlag Berlin Heidelberg Source


Ganopoulos I.,Institute of Applied Biosciences | Ganopoulos I.,Aristotle University of Thessaloniki | Xanthopoulou A.,Institute of Applied Biosciences | Xanthopoulou A.,Aristotle University of Thessaloniki | And 10 more authors.
Biochemical Systematics and Ecology | Year: 2015

The conservation and characterization of eggplant (Solanum melongena L.) genetic resources in germplasm banks has been the basis of their use in breeding projects, which has resulted in the development of new cultivars. High Resolution Melting (HRM) analysis, combined with eight microsatellite markers, has been integrated in order to facilitate the molecular identification and characterization of the eggplant germplasm, collected from the National Genebank Collection of Greece. The eight microsatellite loci used were highly informative and generated sixty three HRM profiles, which were sufficient to discriminate all eggplant landraces and cultivars studied, highlighting its potential use for cultivar genotyping. The thirty six eggplant genotypes were classified into four clusters. Hence, this assay provided a fast, cost-effective and closed-tube microsatellite genotyping method, well suited for molecular characterization of eggplant cultivars. © 2014 Elsevier Ltd. Source

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