title: Genomic profiling of plastid DNA variation in the Mediterranean olive tree.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK. gbesnard@cict.fr
authors.forename: Guillaume
authors.initials: G
authors.lastname: Besnard
authors.forename: Pilar
authors.initials: P
authors.lastname: Hernández
authors.forename: Bouchaib
authors.initials: B
authors.lastname: Khadari
authors.forename: Gabriel
authors.initials: G
authors.lastname: Dorado
authors.forename: Vincent
authors.initials: V
authors.lastname: Savolainen
mesh_terms: D002736:Chloroplasts / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods; D018742:DNA, Chloroplast / Q000235:genetics*; D056426:Genetic Loci; D054628:Genome, Chloroplast; D006239:Haplotypes; D054643:INDEL Mutation; D019083:Mediterranean Region; D018895:Microsatellite Repeats; D031658:Olea / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment
chemical_list: D018742:DNA, Chloroplast