Genomic profiling of plastid DNA variation 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.In the last decades, major technical innovations have allowed a rapid development of various methods for genomic analysis. These have led to applications ranging from phylogeographical reconstructions to forensic analyses and species identification [1,2]. In plants, many studies have focused on the organelle genomes (i.e., plastid DNA - cpDNA - and mitochondrial DNA - mtDNA) for six major reasons: (i) these genomes are usually uniparentally inherited (either from the mother or the father) and thus allow for investigations of gene dispersal by seeds or pollen without recombination effect [3]; (ii) their haploid nature facilitates their sequencing and usually does not require cloning; (iii) such genomes are more prone to stochastic events because their effective population size