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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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Comparison of sampling size according to average genetic distance (DCE) and Shannon-Weaver diversity index (Sh).Core subsets sampled at different sampling sizes using the four strategies of the ASLS method that was optimal at 16% sample size. (1) When optimizing each parameter independently; “DCE”, “Sh”, and “He strategy”. (2) When optimizing all parameters simultaneously with equal weight given to each parameter; “multi-strategy”. Numbers in brackets and arrows indicate the number of alleles captured and the chosen core subset as starting point for final core collections, respectively.
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pone-0061265-g003: Comparison of sampling size according to average genetic distance (DCE) and Shannon-Weaver diversity index (Sh).Core subsets sampled at different sampling sizes using the four strategies of the ASLS method that was optimal at 16% sample size. (1) When optimizing each parameter independently; “DCE”, “Sh”, and “He strategy”. (2) When optimizing all parameters simultaneously with equal weight given to each parameter; “multi-strategy”. Numbers in brackets and arrows indicate the number of alleles captured and the chosen core subset as starting point for final core collections, respectively.

Mentions: As shown in Figure 3, the sample size was inversely correlated with DCE and Sh, except for the 4% sample size, because of allelic redundancy within the core subset when the core size is increased. Increasing the sample size did not improve the capture of total alleles and trait classes, except for the “multi-strategy” where all alleles had been captured at 24% sample size (Table S3).


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)

Comparison of sampling size according to average genetic distance (DCE) and Shannon-Weaver diversity index (Sh).Core subsets sampled at different sampling sizes using the four strategies of the ASLS method that was optimal at 16% sample size. (1) When optimizing each parameter independently; “DCE”, “Sh”, and “He strategy”. (2) When optimizing all parameters simultaneously with equal weight given to each parameter; “multi-strategy”. Numbers in brackets and arrows indicate the number of alleles captured and the chosen core subset as starting point for final core collections, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0061265-g003: Comparison of sampling size according to average genetic distance (DCE) and Shannon-Weaver diversity index (Sh).Core subsets sampled at different sampling sizes using the four strategies of the ASLS method that was optimal at 16% sample size. (1) When optimizing each parameter independently; “DCE”, “Sh”, and “He strategy”. (2) When optimizing all parameters simultaneously with equal weight given to each parameter; “multi-strategy”. Numbers in brackets and arrows indicate the number of alleles captured and the chosen core subset as starting point for final core collections, respectively.
Mentions: As shown in Figure 3, the sample size was inversely correlated with DCE and Sh, except for the 4% sample size, because of allelic redundancy within the core subset when the core size is increased. Increasing the sample size did not improve the capture of total alleles and trait classes, except for the “multi-strategy” where all alleles had been captured at 24% sample size (Table S3).

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