Testing different approaches to construct an olive (Olea europaea L.) core subset suitable for association genetic studies

Evaluation of genetic diversity is of great interest for the management of germplasm collections and breeding programs. Management can be efficient when the evaluation is focused on a subset of accessions that represents the variability observed in the whole germplasm collection. Most core sets have been developed for seed crops using different approaches and sampling size to select entries on the basis of genetic and/or phenotypic data, while few studies on perennial crops have been published. Here, we proposed a core collection for cultivated olive (Olea europaea L.) using both Simple Sequence Repeat (SSR) markers and phenotypic traits by testing different sampling approaches including stratified and non-stratified methods. Twelve SSR markers were used to construct a core subset from an initial collection of 505 single genotypes sourced from 14 Mediterranean countries. Among all the sampling methods, we showed that a sample size of 12.5% was most suitable in capturing all the observed alleles using the M-method approach. Based on both SSR and phenotypic data, we established an initial core set, including the main Mediterranean cultivars, which displayed the highest genetic and phenotypic variability. No obvious genetic structure was indicated when the core subset was analyzed with Principal Coordinate analysis (PCoA). Our results gave an efficient basis as a first step for olive association mapping. The constructed core subset could be further evaluated for traits of agronomic interest, leading to association between the allelic variation and the phenotypic variability

Olive Diversification Process in Southwestern Mediterranean Traditional Agro-Ecosystems

International audienceThe cultivated olive in the west Mediterranean basin seems derived at least from two processes: (i) domestication from their wild relatives and (ii) introgression related to hybridization between introduced cultivars from east Mediterranean and local cultivars. To test this hypothesis, we analysed the genetic structure of 476 Mediterranean olive cultivars using 12 nuclear SSR loci and chloroplast DNA polymorphism. We confirmed the presence of the East and the West gene pools and we showed that the western gene pool has eastern maternal lineage. These results suggest that cultivated olive is a result of selection of olive seedling issued from crossing between introduced cultivars and local populations. This finding was supported by ethnobiological study conducted on current farming practices in principal traditional agro-ecosystems in the north of Morocco. Hence, olive diversification seems to be a dynamic process that mainly arose through sexual reproduction in traditional agro-ecosystems

Testing different approaches to construct an olive ([i]Olea europaea[/i] L.) core subset suitable for association genetic studies

Evaluation of genetic diversity is of great interest for the management of germplasm collections and breeding programs. Management can be efficient when the evaluation is focused on a subset of accessions that represents the variability observed in the whole germplasm collection. Most core sets have been developed for seed crops using different approaches and sampling size to select entries on the basis of genetic and/or phenotypic data, while few studies on perennial crops have been published. Here, we proposed a core collection for cultivated olive (Olea europaea L.) using both Simple Sequence Repeat (SSR) markers and phenotypic traits by testing different sampling approaches including stratified and non-stratified methods. Twelve SSR markers were used to construct a core subset from an initial collection of 505 single genotypes sourced from 14 Mediterranean countries. Among all the sampling methods, we showed that a sample size of 12.5% was most suitable in capturing all the observed alleles using the M-method approach. Based on both SSR and phenotypic data, we established an initial core set, including the main Mediterranean cultivars, which displayed the highest genetic and phenotypic variability. No obvious genetic structure was indicated when the core subset was analyzed with Principal Coordinate analysis (PCoA). Our results gave an efficient basis as a first step for olive association mapping. The constructed core subset could be further evaluated for traits of agronomic interest, leading to association between the allelic variation and the phenotypic variability

Extent of the genetic diversity in Lebanese olive (Olea europaea L.) trees: a mixture of an ancient germplasm with recently introduced varieties

AGAP : équipe Génomique évolutive et gestion des populations (GE²pop)International audienceThe olive tree was primary domesticated in the North-East Levant at least six millennia ago. Nowadays monumental trees are surviving across the Mediterranean Basin. These ancient, traditional varieties testify for the long cultivation of the crop but this germplasm remains incompletely characterized. Here, we investigated the genetic diversity among Lebanese cultivated olives in comparison to accessions from the whole Mediterranean Basin. Seventy-three olive trees including six monumentals were sampled in four main Lebanese areas, and characterized with 12 nuclear microsatellites and 39 plastid DNA markers. These genetic profiles were combined to those previously obtained in the world collection of Marrakech (WOGB) and analyzed with a phenetic approach, a multivariate analysis, and a Bayesian clustering method. Three main genetic clusters were identified in the Mediterranean cultivated olive tree as previously shown. The majority of Lebanese olive trees were assigned to the Eastern Mediterranean gene pool. A few genotypes were however assigned to the Central Mediterranean cluster. Plastid DNA markers revealed the presence of four haplotypes belonging to lineages E1 (72 olive trees) and E2 (one plant). Haplotype E1.1 that originated in the Eastern Mediterranean was found in 68 individuals (93 %). Within the common variety "Baladi", several nuclear microsatellite profiles were identified including closely related olive trees that may correspond to molecular variants due to somatic variation. The six monumentals were remarkably positioned close to the Cypriot accessions and showed three different profiles, one of which matched to the most common profile of the widespread traditional variety "Baladi". Our findings suggest that the Lebanese olive trees were locally selected during the beginning stages of olive growing and served as basic plant material for the current traditional varieties derived by both sexual and clonal propagation. Recent variety introductions from westernmost regions were also evidenced, but only in modern orchards from the Bekaa district

Population genetics of Mediterranean and Saharan olives: geographic patterns of differentiation and evidence for early generations of admixture

BACKGROUND & AIMS : The olive (Olea europaea subsp. europaea) was domesticated in the Mediterranean area but its wild relatives are distributed over three continents, from the Mediterranean basin to South Africa and south-western Asia. Recent studies suggested that this crop originated in the Levant while a secondary diversification occurred in most westward areas. A possible contribution of the Saharan subspecies (subsp. laperrinei) has been highlighted, but the data available were too limited to draw definite conclusions. Here, patterns of genetic differentiation in the Mediterranean and Saharan olives are analysed to test for recent admixture between these taxa.[br/] METHODS : Nuclear microsatellite and plastid DNA (ptDNA) data were compiled from previous studies and completed for a sample of 470 cultivars, 390 wild Mediterranean trees and 270 Saharan olives. A network was reconstructed for the ptDNA haplotypes, while a Bayesian clustering method was applied to identify the main gene pools in the data set and then simulate and test for early generations of admixture between Mediterranean and Saharan olives. [br/] KEY RESULTS : Four lineages of ptDNA haplotypes are recognized: three from the Mediterranean basin and one from the Sahara. Only one haplotype, primarily distributed in the Sahara, is shared between laperrinei and europaea. This haplotype is detected once in Dhokar, a cultivar from the Maghreb. Nuclear microsatellites show geographic patterns of genetic differentiation in the Mediterranean olive that reflect the primary origins of cultivars in the Levant, and indicate a high genetic differentiation between europaea and laperrinei. No first-generation hybrid between europaea and laperrinei is detected, but recent, reciprocal admixture between Mediterranean and Saharan subspecies is found in a few accessions, including Dhokar. [br/] CONCLUSIONS : This study reports for the first time admixture between Mediterranean and Saharan olives. Although its contribution remains limited, Laperrines olive has been involved in the diversification of cultivated olives