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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

Current study flow chart to construct core collections from OWGB Marrakech.There were two main steps. As a benchmark, a sample size was determined using the Mstrat program to compare different sampling methods and sizes; 80 entries were necessary to capture all alleles. A primary core collection (CC50) was constructed using the Core Hunter program at 8% sample size (step 1). Then CC50 was used as a kernel to select the minimum size required to capture the total diversity using the Mstrat program (step 2). At this step, two procedures were performed, i.e. sampling with nuclear markers and trait classes (A; 94 entries were necessary) or using only nuclear markers (B; 92). For both procedures, a set of 72 genotypes was used in all independent runs while a combination of 22 complement genotypes could be selected from a panel of 106 genotypes to capture all of the allelic and phenotypic diversity (CC94) or 20 genotypes from a panel of 91 genotypes to capture the total allelic diversity (CC92).
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pone-0061265-g001: Current study flow chart to construct core collections from OWGB Marrakech.There were two main steps. As a benchmark, a sample size was determined using the Mstrat program to compare different sampling methods and sizes; 80 entries were necessary to capture all alleles. A primary core collection (CC50) was constructed using the Core Hunter program at 8% sample size (step 1). Then CC50 was used as a kernel to select the minimum size required to capture the total diversity using the Mstrat program (step 2). At this step, two procedures were performed, i.e. sampling with nuclear markers and trait classes (A; 94 entries were necessary) or using only nuclear markers (B; 92). For both procedures, a set of 72 genotypes was used in all independent runs while a combination of 22 complement genotypes could be selected from a panel of 106 genotypes to capture all of the allelic and phenotypic diversity (CC94) or 20 genotypes from a panel of 91 genotypes to capture the total allelic diversity (CC92).

Mentions: To compare the performance of current state-of-the-art methods to construct core subsets, as a benchmark, we estimated the minimum size necessary to capture all the observed alleles using the Mstrat program (Figure 1). The size assessment indicated that 80 entries were necessary to capture the total allelic diversity (16% of OWGB Marrakech). Then, at this sample size, four different sampling methods were first tested:


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)

Current study flow chart to construct core collections from OWGB Marrakech.There were two main steps. As a benchmark, a sample size was determined using the Mstrat program to compare different sampling methods and sizes; 80 entries were necessary to capture all alleles. A primary core collection (CC50) was constructed using the Core Hunter program at 8% sample size (step 1). Then CC50 was used as a kernel to select the minimum size required to capture the total diversity using the Mstrat program (step 2). At this step, two procedures were performed, i.e. sampling with nuclear markers and trait classes (A; 94 entries were necessary) or using only nuclear markers (B; 92). For both procedures, a set of 72 genotypes was used in all independent runs while a combination of 22 complement genotypes could be selected from a panel of 106 genotypes to capture all of the allelic and phenotypic diversity (CC94) or 20 genotypes from a panel of 91 genotypes to capture the total allelic diversity (CC92).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0061265-g001: Current study flow chart to construct core collections from OWGB Marrakech.There were two main steps. As a benchmark, a sample size was determined using the Mstrat program to compare different sampling methods and sizes; 80 entries were necessary to capture all alleles. A primary core collection (CC50) was constructed using the Core Hunter program at 8% sample size (step 1). Then CC50 was used as a kernel to select the minimum size required to capture the total diversity using the Mstrat program (step 2). At this step, two procedures were performed, i.e. sampling with nuclear markers and trait classes (A; 94 entries were necessary) or using only nuclear markers (B; 92). For both procedures, a set of 72 genotypes was used in all independent runs while a combination of 22 complement genotypes could be selected from a panel of 106 genotypes to capture all of the allelic and phenotypic diversity (CC94) or 20 genotypes from a panel of 91 genotypes to capture the total allelic diversity (CC92).
Mentions: To compare the performance of current state-of-the-art methods to construct core subsets, as a benchmark, we estimated the minimum size necessary to capture all the observed alleles using the Mstrat program (Figure 1). The size assessment indicated that 80 entries were necessary to capture the total allelic diversity (16% of OWGB Marrakech). Then, at this sample size, four different sampling methods were first tested:

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