Genomic profiling of plastid DNA variation in the Mediterranean olive tree

Abstract

BackgroundCharacterisation 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.ResultsEight 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.ConclusionsWe 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.

The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant

“…hotspots of diversity) during previous glaciations [15]. Here, we used a profiling method to characterize variable microsatellites, indels and single nucleotide polymorphisms (SNPs) of the plastid genome [16]. Plastid DNA profiles (haplotypes) were defined by the combination of alleles from 61 loci (see the electronic supplementary material, table S3), and their distribution was represented on a map of the Mediterranean Basin.…”

“…The demographic model (see the electronic supplementary material, figure S1) thus consisted of four populations (E1, E2, E3 and A). Populations E1, E2 and E3 diverge at the same time (T E ) from an ancestral population E (because relationships between the Mediterranean lineages were unresolved based on the complete ptDNA genome suggesting they started diverging from a common ancestor approximately at the same time) [16], and populations A and E diverge at time T AE . Population size changes are allowed for each population; however, they are simultaneous (at time TD E ) and of the same magnitude (from N ancestral to N E ) for populations E1, E2 and E3, but independent for population A at time TD A , from size N ancestral to N A .…”

“…For reconstructing networks at the lineage level, CAPS-XapI was not considered owing to a high homoplasy on this locus [16]. We also computed three diversity parameters: the total diversity (defined as…”

“…Microsatellite data from lineages E1, E2, E3 and A were analysed with DIYABC [21], which implements an approximate Bayesian computation (ABC) method of inference in population genetics. Lineages E1, E2 and E3 were treated as populations to force the coalescence of individuals within the three separate lineages (as defined by SNPs and indels that were not used for this analysis) [10,16]. The demographic model (see the electronic supplementary material, figure S1) thus consisted of four populations (E1, E2, E3 and A).…”

“…This second step consisted of the analysis of all plastid polymorphisms (microsatellites, indels and SNPs), but two loci that were incompatible with unique-event polymorphisms were excluded (i.e. loci CAPS-XapI and 52) [16]. TMRCA was inferred for lineages E1, E2 and E3, and for sublineages with a value of posterior probability of being monophyletic higher than 0.9 (which includes sublineages defined by SNPs and indels, but also some sublineages with characteristic combination of microsatellite alleles).…”