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Construction of core collections suitable for association mapping to optimize use of Mediterranean olive (Olea europaea L.) genetic resources.

El Bakkali A, Haouane H, Moukhli A, Costes E, Van Damme P, Khadari B - PLoS ONE (2013)

Bottom Line: The Shannon-Weaver diversity index was found to be the best criterion to be maximized in the first step using the Core Hunter program.Most entries of both core collections (CC50 and CC94) were revealed to be unrelated due to the low kinship coefficient, whereas a genetic structure spanning the eastern and western/central Mediterranean regions was noted.Since they reflect the geographic origin and diversity of olive germplasm and are of reasonable size, both core collections will be of major interest to develop long-term association studies and thus enhance genomic selection in olive species.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR Amélioration Génétique et Adaptation des Plantes (AGAP), Montpellier, France.

ABSTRACT
Phenotypic characterisation of germplasm collections is a decisive step towards association mapping analyses, but it is particularly expensive and tedious for woody perennial plant species. Characterisation could be more efficient if focused on a reasonably sized subset of accessions, or so-called core collection (CC), reflecting the geographic origin and variability of the germplasm. The questions that arise concern the sample size to use and genetic parameters that should be optimized in a core collection to make it suitable for association mapping. Here we investigated these questions in olive (Olea europaea L.), a perennial fruit species. By testing different sampling methods and sizes in a worldwide olive germplasm bank (OWGB Marrakech, Morocco) containing 502 unique genotypes characterized by nuclear and plastid loci, a two-step sampling method was proposed. The Shannon-Weaver diversity index was found to be the best criterion to be maximized in the first step using the Core Hunter program. A primary core collection of 50 entries (CC50) was defined that captured more than 80% of the diversity. This latter was subsequently used as a kernel with the Mstrat program to capture the remaining diversity. 200 core collections of 94 entries (CC94) were thus built for flexibility in the choice of varieties to be studied. Most entries of both core collections (CC50 and CC94) were revealed to be unrelated due to the low kinship coefficient, whereas a genetic structure spanning the eastern and western/central Mediterranean regions was noted. Linkage disequilibrium was observed in CC94 which was mainly explained by a genetic structure effect as noted for OWGB Marrakech. Since they reflect the geographic origin and diversity of olive germplasm and are of reasonable size, both core collections will be of major interest to develop long-term association studies and thus enhance genomic selection in olive species.

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Related in: MedlinePlus

Two-dimensional distribution of the principal coordinate analysis (PCoA) for CC50, CC94 and OWGB Marrakech.Colours indicate the three gene pools (eastern, western and central Mediterranean Basin). The genetic variation of each principal coordinate (PCo1 and PCo2) is indicated. Both core subsets span the range of all genotypes among the three gene pools, whereas the majority of entries were found to occur in the central Mediterranean area.
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pone-0061265-g005: Two-dimensional distribution of the principal coordinate analysis (PCoA) for CC50, CC94 and OWGB Marrakech.Colours indicate the three gene pools (eastern, western and central Mediterranean Basin). The genetic variation of each principal coordinate (PCo1 and PCo2) is indicated. Both core subsets span the range of all genotypes among the three gene pools, whereas the majority of entries were found to occur in the central Mediterranean area.

Mentions: Using model-based Bayesian clustering, the Structure program allowed classification of the 502 genotypes into three gene pools according to their regional origins (western, central, and eastern Mediterranean; Figure 4; Table S1), while the second most likely genetic structure was found at K = 5 (ΔK = 155.12 and H′ = 0.992; Figure S3). Similar results were obtained when the analysis was conducted on genotypes distinguished by more than three dissimilar alleles (457 genotypes; results not shown). In both core collections (CC50 and CC94), the selected genotypes revealed a high level of admixture between gene pools. In fact, among the 50 and 94 genotypes, 23 (46%) and 71 (75.5%) were assigned to more than one gene pool with membership probabilities of less than 0.80, respectively. In addition, principal coordinate analysis (PCoA; Figure 5) revealed that both core collections encompassed the entire range of genotypes in the three gene pools, whereas 32 (64%) and 65 (69.1%) entries were classified into the central Mediterranean gene pool for the CC50 and CC94 core collections, respectively. Low ΔK and H′ scores at K = 3 were noted for both core collections compared to OWGB Marrakech, therefore highlighting the absence of stability in obtaining runs at K = 3. Although high ΔK and H′ scores at K = 5 were obtained for both core collections (Figure S3), no consistency in genetic structure was noted when plotting the Q scores (Figure S4), while the model at K = 3 indicated two subgroups for both CC50 and CC94; the first one contained entries originating from the western and central Mediterranean whereas the second included eastern Mediterranean varieties (Figure 4).


Construction of core collections suitable for association mapping to optimize use of Mediterranean olive (Olea europaea L.) genetic resources.

El Bakkali A, Haouane H, Moukhli A, Costes E, Van Damme P, Khadari B - PLoS ONE (2013)

Two-dimensional distribution of the principal coordinate analysis (PCoA) for CC50, CC94 and OWGB Marrakech.Colours indicate the three gene pools (eastern, western and central Mediterranean Basin). The genetic variation of each principal coordinate (PCo1 and PCo2) is indicated. Both core subsets span the range of all genotypes among the three gene pools, whereas the majority of entries were found to occur in the central Mediterranean area.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646834&req=5

pone-0061265-g005: Two-dimensional distribution of the principal coordinate analysis (PCoA) for CC50, CC94 and OWGB Marrakech.Colours indicate the three gene pools (eastern, western and central Mediterranean Basin). The genetic variation of each principal coordinate (PCo1 and PCo2) is indicated. Both core subsets span the range of all genotypes among the three gene pools, whereas the majority of entries were found to occur in the central Mediterranean area.
Mentions: Using model-based Bayesian clustering, the Structure program allowed classification of the 502 genotypes into three gene pools according to their regional origins (western, central, and eastern Mediterranean; Figure 4; Table S1), while the second most likely genetic structure was found at K = 5 (ΔK = 155.12 and H′ = 0.992; Figure S3). Similar results were obtained when the analysis was conducted on genotypes distinguished by more than three dissimilar alleles (457 genotypes; results not shown). In both core collections (CC50 and CC94), the selected genotypes revealed a high level of admixture between gene pools. In fact, among the 50 and 94 genotypes, 23 (46%) and 71 (75.5%) were assigned to more than one gene pool with membership probabilities of less than 0.80, respectively. In addition, principal coordinate analysis (PCoA; Figure 5) revealed that both core collections encompassed the entire range of genotypes in the three gene pools, whereas 32 (64%) and 65 (69.1%) entries were classified into the central Mediterranean gene pool for the CC50 and CC94 core collections, respectively. Low ΔK and H′ scores at K = 3 were noted for both core collections compared to OWGB Marrakech, therefore highlighting the absence of stability in obtaining runs at K = 3. Although high ΔK and H′ scores at K = 5 were obtained for both core collections (Figure S3), no consistency in genetic structure was noted when plotting the Q scores (Figure S4), while the model at K = 3 indicated two subgroups for both CC50 and CC94; the first one contained entries originating from the western and central Mediterranean whereas the second included eastern Mediterranean varieties (Figure 4).

Bottom Line: The Shannon-Weaver diversity index was found to be the best criterion to be maximized in the first step using the Core Hunter program.Most entries of both core collections (CC50 and CC94) were revealed to be unrelated due to the low kinship coefficient, whereas a genetic structure spanning the eastern and western/central Mediterranean regions was noted.Since they reflect the geographic origin and diversity of olive germplasm and are of reasonable size, both core collections will be of major interest to develop long-term association studies and thus enhance genomic selection in olive species.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR Amélioration Génétique et Adaptation des Plantes (AGAP), Montpellier, France.

ABSTRACT
Phenotypic characterisation of germplasm collections is a decisive step towards association mapping analyses, but it is particularly expensive and tedious for woody perennial plant species. Characterisation could be more efficient if focused on a reasonably sized subset of accessions, or so-called core collection (CC), reflecting the geographic origin and variability of the germplasm. The questions that arise concern the sample size to use and genetic parameters that should be optimized in a core collection to make it suitable for association mapping. Here we investigated these questions in olive (Olea europaea L.), a perennial fruit species. By testing different sampling methods and sizes in a worldwide olive germplasm bank (OWGB Marrakech, Morocco) containing 502 unique genotypes characterized by nuclear and plastid loci, a two-step sampling method was proposed. The Shannon-Weaver diversity index was found to be the best criterion to be maximized in the first step using the Core Hunter program. A primary core collection of 50 entries (CC50) was defined that captured more than 80% of the diversity. This latter was subsequently used as a kernel with the Mstrat program to capture the remaining diversity. 200 core collections of 94 entries (CC94) were thus built for flexibility in the choice of varieties to be studied. Most entries of both core collections (CC50 and CC94) were revealed to be unrelated due to the low kinship coefficient, whereas a genetic structure spanning the eastern and western/central Mediterranean regions was noted. Linkage disequilibrium was observed in CC94 which was mainly explained by a genetic structure effect as noted for OWGB Marrakech. Since they reflect the geographic origin and diversity of olive germplasm and are of reasonable size, both core collections will be of major interest to develop long-term association studies and thus enhance genomic selection in olive species.

Show MeSH
Related in: MedlinePlus