Open Access Methodology article

Genomic profiling of plastid DNA variation in the Mediterranean olive tree

Guillaume Besnard12*, Pilar Hernández3, Bouchaib Khadari4, Gabriel Dorado5 and Vincent Savolainen16

Author Affiliations

1 Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK

2 CNRS, UPS, ENFA, Laboratoire Evolution & Diversité Biologique, UMR 5174, 31062 Toulouse 4, France

3 Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain

4 INRA, CBNMED, UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP), 34398 Montpellier, France

5 Dep. Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Universidad de Córdoba, 14071 Córdoba, Spain

6 Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK

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BMC Plant Biology 2011, 11:80  doi:10.1186/1471-2229-11-80

Published: 10 May 2011



Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid genomic profiling (by Multiplex PCRs) of cpDNA haplotypes in the Mediterranean olive tree.


Eight complete cpDNA genomes of Olea were sequenced de novo. The nucleotide divergence between olive cpDNA lineages was low and not exceeding 0.07%. Based on these sequences, markers were developed for studying two single nucleotide substitutions and length polymorphism of 62 regions (with variable microsatellite motifs or other indels). They were then used to genotype the cpDNA variation in cultivated and wild Mediterranean olive trees (315 individuals). Forty polymorphic loci were detected on this sample, allowing the distinction of 22 haplotypes belonging to the three Mediterranean cpDNA lineages known as E1, E2 and E3. The discriminating power of cpDNA variation was particularly low for the cultivated olive tree with one predominating haplotype, but more diversity was detected in wild populations.


We propose a method for a rapid characterisation of the Mediterranean olive germplasm. The low variation in the cultivated olive tree indicated that the utility of cpDNA variation for forensic analyses is limited to rare haplotypes. In contrast, the high cpDNA variation in wild populations demonstrated that our markers may be useful for phylogeographic and populations genetic studies in O. europaea.