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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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Frequency distribution of the pairwise relative kinship coefficient.Pairwise relative kinship coefficient for the 457 genotypes of OWGB Marrakech, CC50, and CC94 using 17 SSR loci. Values equal to or greater than 0.45 were grouped as 0.45. The kinship calculation indicated a low level of relatedness between genotypes, with only a few genotypes being more related to each other.
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pone-0061265-g007: Frequency distribution of the pairwise relative kinship coefficient.Pairwise relative kinship coefficient for the 457 genotypes of OWGB Marrakech, CC50, and CC94 using 17 SSR loci. Values equal to or greater than 0.45 were grouped as 0.45. The kinship calculation indicated a low level of relatedness between genotypes, with only a few genotypes being more related to each other.

Mentions: When considering only 457 genotypes distinguished by more than three dissimilar alleles, the LD scores (r2) were significant for 59.5% of the pairwise comparisons (81 among 136 pairwise comparisons), while only 26.5% of the pairwise comparisons displayed a significant LD in CC94 (Figure 6). The relative kinship computed for both core collections showed a high pairwise frequency at 0–0.05 (87.6% for CC50 and 84.9% for CC94), whereas it decreased progressively between 0.05 and 0.45 (7.8% and 10.4% to 0.08% and 0.04% for CC50 and CC94, respectively; Figure 7).


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)

Frequency distribution of the pairwise relative kinship coefficient.Pairwise relative kinship coefficient for the 457 genotypes of OWGB Marrakech, CC50, and CC94 using 17 SSR loci. Values equal to or greater than 0.45 were grouped as 0.45. The kinship calculation indicated a low level of relatedness between genotypes, with only a few genotypes being more related to each other.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0061265-g007: Frequency distribution of the pairwise relative kinship coefficient.Pairwise relative kinship coefficient for the 457 genotypes of OWGB Marrakech, CC50, and CC94 using 17 SSR loci. Values equal to or greater than 0.45 were grouped as 0.45. The kinship calculation indicated a low level of relatedness between genotypes, with only a few genotypes being more related to each other.
Mentions: When considering only 457 genotypes distinguished by more than three dissimilar alleles, the LD scores (r2) were significant for 59.5% of the pairwise comparisons (81 among 136 pairwise comparisons), while only 26.5% of the pairwise comparisons displayed a significant LD in CC94 (Figure 6). The relative kinship computed for both core collections showed a high pairwise frequency at 0–0.05 (87.6% for CC50 and 84.9% for CC94), whereas it decreased progressively between 0.05 and 0.45 (7.8% and 10.4% to 0.08% and 0.04% for CC50 and CC94, respectively; Figure 7).

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