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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 methods according to average genetic distance (DCE) and Shannon-Weaver diversity index (Sh).Core subsets constructed by different sampling methods at 16% sample size. (1) When optimizing each of the four parameters independently; “DCE”, “Sh”, “He”, “Cv strategy”. (2) When a weight of 60% was assigned to DCE and 40% to Cv; “DCECv strategy”. (3) When optimizing all parameters simultaneously with equal weight given to each parameter; “multi-strategy”. Numbers in brackets and dotted lines indicate the number of alleles captured and the four allocation sampling strategies considered optimal, respectively.
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pone-0061265-g002: Comparison of sampling methods according to average genetic distance (DCE) and Shannon-Weaver diversity index (Sh).Core subsets constructed by different sampling methods at 16% sample size. (1) When optimizing each of the four parameters independently; “DCE”, “Sh”, “He”, “Cv strategy”. (2) When a weight of 60% was assigned to DCE and 40% to Cv; “DCECv strategy”. (3) When optimizing all parameters simultaneously with equal weight given to each parameter; “multi-strategy”. Numbers in brackets and dotted lines indicate the number of alleles captured and the four allocation sampling strategies considered optimal, respectively.

Mentions: This comparison was carried out using the 502 SSR profiles with a 16% sample size determined previously by Mstrat. All core sets sampled by different methods outperformed CC9-80 (core chosen randomly) in which the DCE, He, and Sh values were quite similar to those of OWGB Marrakech whereas the allelic richness values were significantly different from those of the whole collection (p<0.05;Table 1; Figure 2). When optimizing each of the four genetic parameters independently with the ASLS method, the sampled core subsets had the highest scores of all the core subsets with respect to the parameter being optimized, whereas other parameters not considered during optimization were highly affected (Table 1). For instance, with the “DCE strategy”, the selected core subset showed the highest DCE (CC2-80; 0.833±0.07), while a low number of alleles was captured compared to the “Cv strategy” (only 234 among 279 alleles). For the MLST method, the CC8-80 core subset revealed higher DCE and similar Sh values as compared to CC6-60 and CC7-80, whereas fewer captured alleles were noted (only 236 alleles). Finally, four sampling strategies using the ASLS method showed better DCE and Sh scores than all other core subsets, including CC7-80, generated by the maximizing method (Table 1; Figure 2).


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 methods according to average genetic distance (DCE) and Shannon-Weaver diversity index (Sh).Core subsets constructed by different sampling methods at 16% sample size. (1) When optimizing each of the four parameters independently; “DCE”, “Sh”, “He”, “Cv strategy”. (2) When a weight of 60% was assigned to DCE and 40% to Cv; “DCECv strategy”. (3) When optimizing all parameters simultaneously with equal weight given to each parameter; “multi-strategy”. Numbers in brackets and dotted lines indicate the number of alleles captured and the four allocation sampling strategies considered optimal, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0061265-g002: Comparison of sampling methods according to average genetic distance (DCE) and Shannon-Weaver diversity index (Sh).Core subsets constructed by different sampling methods at 16% sample size. (1) When optimizing each of the four parameters independently; “DCE”, “Sh”, “He”, “Cv strategy”. (2) When a weight of 60% was assigned to DCE and 40% to Cv; “DCECv strategy”. (3) When optimizing all parameters simultaneously with equal weight given to each parameter; “multi-strategy”. Numbers in brackets and dotted lines indicate the number of alleles captured and the four allocation sampling strategies considered optimal, respectively.
Mentions: This comparison was carried out using the 502 SSR profiles with a 16% sample size determined previously by Mstrat. All core sets sampled by different methods outperformed CC9-80 (core chosen randomly) in which the DCE, He, and Sh values were quite similar to those of OWGB Marrakech whereas the allelic richness values were significantly different from those of the whole collection (p<0.05;Table 1; Figure 2). When optimizing each of the four genetic parameters independently with the ASLS method, the sampled core subsets had the highest scores of all the core subsets with respect to the parameter being optimized, whereas other parameters not considered during optimization were highly affected (Table 1). For instance, with the “DCE strategy”, the selected core subset showed the highest DCE (CC2-80; 0.833±0.07), while a low number of alleles was captured compared to the “Cv strategy” (only 234 among 279 alleles). For the MLST method, the CC8-80 core subset revealed higher DCE and similar Sh values as compared to CC6-60 and CC7-80, whereas fewer captured alleles were noted (only 236 alleles). Finally, four sampling strategies using the ASLS method showed better DCE and Sh scores than all other core subsets, including CC7-80, generated by the maximizing method (Table 1; Figure 2).

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