SNP-based markers for discriminating olive (Olea europaea L.) cultivars

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Abstract:

A set of 11 polymorphic markers (1 cleaved amplified polymorphic sequence (CAPS), 2 sequence-characterized amplified regions (SCARs), and 8 single-nucleotide polymorphism (SNP) - derived markers) was obtained for olive cultivar identification by comparing DNA sequences from different accessions. Marker development was more efficient, using sequences from the database rather than cloning arbitrary DNA fragments. Analyses of the sequences of 3 genes from 11 diverse cultivars revealed an SNP frequency of 1 per 190 base pairs in exons and 1 per 149 base pairs in introns. Most mutations were silent or had little perceptible effect on the polypeptide encoded. The higher incidence of transversions (55%) suggests that methylation is not the major driving force for DNA base changes. Evidence of linkage disequilibrium in 2 pairs of markers has been detected. The set of predominantly SNP-based markers was used to genotype 65 olive samples obtained from Europe and Australia, and was able clearly to discriminate 77% of the cultivars. Samples, putatively of the same cultivar but derived from different sources, were revealed as identical, demonstrating the utility of these markers as tools for resolving nomenclature issues. Genotyping data were used for constructing a dendrogram by UPGMA cluster analysis using the simple matching similarity coefficient. Relationships between cultivars are discussed in relation to the route of olive's spread.

Onze marqueurs (1 CAPS, 2 SCAR et 8 SNP) ont été obtenus pour des fins d’identification variétale chez l’olivier en comparant les séquences d’ADN de différentes accessions. Le développement de tels marqueurs s’est avéré plus efficace en faisant appel aux séquences des banques de données qu’en clonant des fragments arbitraires d’ADN. L’analyse de la séquence de trois gènes chez 11 cultivars différents a révélé une fréquence de 1 SNP par 190 pb au sein des exons et de 1 SNP par 149 pb dans les introns. La majorité des mutations étaient silencieuses ou entraînaient peu d’effets perceptibles sur le polypeptide codé. L’incidence supérieure de transversions (55%) suggère que la méthylation n’est pas la force majeure induisant des mutations. Des évidences de déséquilibre de liaison ont été obtenues pour deux paires de marqueurs. Ce jeu de marqueurs, principalement de type SNP, a été employé pour génotyper 65 échantillons d’olivier provenant d’Europe et d’Australie et a permis de différencier 77% des cultivars. Des échantillons, vraisemblablement du même cultivar mais obtenus de différentes sources, se sont montrés identiques ce qui démontre l’utilité de ces marqueurs pour résoudre des problèmes de nomenclature. Les données génotypiques ont été employées pour produire un dendrogramme par groupement UPGMA à l’aide du coefficient de similarité «simple matching». Les relations entre les cultivars sont discutées en relation avec la route qu’aurait suivie l’olivier lors de sa dissémination.

Document Type: Research Article

Publication date: September 1, 2006

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  • From its inception in 1957, this international cytogenetics journal has catered to the research areas of the members of the Genetics Society of Canada; traditionally, these have included agriculture, entomology, genetics/cytogenetics, and evolutionary mechanisms. The contents of the journal have evolved as contributors developed new technologies and interests. A 20-member Editorial Board is composed of scientists from around the world. Reviews and commentary from respected experts are often featured.
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