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Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L).

Motamayor JC, Lachenaud P, da Silva E Mota JW, Loor R, Kuhn DN, Brown JS, Schnell RJ - PLoS ONE (2008)

Bottom Line: Germplasm labeling errors have impeded breeding and confounded the interpretation of diversity analyses.After discarding mislabeled samples, 10 genetic clusters, as opposed to the two genetic groups traditionally recognized within T. cacao, were found by applying Bayesian statistics.The results also provide new insights into the diversification of Amazon species in general, with the pattern of differentiation of the populations studied supporting the palaeoarches hypothesis of species diversification.

View Article: PubMed Central - PubMed

Affiliation: National Germplasm Repository, US Department of Agriculture, Agricultural Research Service, Subtropical Horticulture Research Station, Miami, Florida, USA. juan.motamayor@effem.com

ABSTRACT
Numerous collecting expeditions of Theobroma cacao L. germplasm have been undertaken in Latin-America. However, most of this germplasm has not contributed to cacao improvement because its relationship to cultivated selections was poorly understood. Germplasm labeling errors have impeded breeding and confounded the interpretation of diversity analyses. To improve the understanding of the origin, classification, and population differentiation within the species, 1241 accessions covering a large geographic sampling were genotyped with 106 microsatellite markers. After discarding mislabeled samples, 10 genetic clusters, as opposed to the two genetic groups traditionally recognized within T. cacao, were found by applying Bayesian statistics. This leads us to propose a new classification of the cacao germplasm that will enhance its management. The results also provide new insights into the diversification of Amazon species in general, with the pattern of differentiation of the populations studied supporting the palaeoarches hypothesis of species diversification. The origin of the traditional cacao cultivars is also enlightened in this study.

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Neighbor joining tree from Cavalli-Sforza and Edwards genetic distance [16] matrix among the 36 subclusters identified using Structure (559 clones).Values represent percentages after bootstraps on the 96 loci retained.
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pone-0003311-g002: Neighbor joining tree from Cavalli-Sforza and Edwards genetic distance [16] matrix among the 36 subclusters identified using Structure (559 clones).Values represent percentages after bootstraps on the 96 loci retained.

Mentions: Since more than one clustering scheme was found at K = 10, a complementary graphical cluster analysis was employed to visualize the relatedness among the subclusters identified. The Neighbor Joining method based on the Cavalli-Sforza and Edwards genetic distance [16] among the 36 subclusters (Figure 2) was used. The space between the branches of the subtrees is colored according to the major cluster to which each subcluster belongs (using the same codes as in Figure 1). In Figure 2, the 36 subclusters are grouped under the same clustering pattern observed using Structure, with the exception of the subcluster comprising individuals from the Upper Solimões and Iça River from the Purús cluster and the subcluster including individuals from the Middle Solimões from the Iquitos cluster. These subclusters did not group with other Structure clusters; rather they lie in-between their respective clusters and the next genetically closest cluster. This incongruity between the two clustering methods may be due to the fact that gene flow may occur throughout the Solimões River. Please note, in Table S3, that from the 559 individuals retained for this analysis, only individuals from the Upper Solimões and Iça River subcluster showed three clustering schemes across the 10 runs performed with K = 10 (all the others 1 or 2). The Upper and Middle Solimões are stretches of the Amazon River connecting the Upper Amazon (where other individuals from the Iquitos, Purús and Marañon clusters were collected) to its confluence with the Negro River. Comparing the number of migrants between all combinations of subclusters from different clusters indeed showed that the highest number of migrants was found between the Upper and Middle Solimões subclusters, from the Purus and Iquitos clusters respectively (Table S5). The second highest value was found between the Middle Solimões and Parinari IV from the Marañon cluster (Peruvian Upper Amazon). These results indicate that gene flow is extensive throughout the Amazon River making it difficult to cluster downstream introgressed populations.


Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L).

Motamayor JC, Lachenaud P, da Silva E Mota JW, Loor R, Kuhn DN, Brown JS, Schnell RJ - PLoS ONE (2008)

Neighbor joining tree from Cavalli-Sforza and Edwards genetic distance [16] matrix among the 36 subclusters identified using Structure (559 clones).Values represent percentages after bootstraps on the 96 loci retained.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2551746&req=5

pone-0003311-g002: Neighbor joining tree from Cavalli-Sforza and Edwards genetic distance [16] matrix among the 36 subclusters identified using Structure (559 clones).Values represent percentages after bootstraps on the 96 loci retained.
Mentions: Since more than one clustering scheme was found at K = 10, a complementary graphical cluster analysis was employed to visualize the relatedness among the subclusters identified. The Neighbor Joining method based on the Cavalli-Sforza and Edwards genetic distance [16] among the 36 subclusters (Figure 2) was used. The space between the branches of the subtrees is colored according to the major cluster to which each subcluster belongs (using the same codes as in Figure 1). In Figure 2, the 36 subclusters are grouped under the same clustering pattern observed using Structure, with the exception of the subcluster comprising individuals from the Upper Solimões and Iça River from the Purús cluster and the subcluster including individuals from the Middle Solimões from the Iquitos cluster. These subclusters did not group with other Structure clusters; rather they lie in-between their respective clusters and the next genetically closest cluster. This incongruity between the two clustering methods may be due to the fact that gene flow may occur throughout the Solimões River. Please note, in Table S3, that from the 559 individuals retained for this analysis, only individuals from the Upper Solimões and Iça River subcluster showed three clustering schemes across the 10 runs performed with K = 10 (all the others 1 or 2). The Upper and Middle Solimões are stretches of the Amazon River connecting the Upper Amazon (where other individuals from the Iquitos, Purús and Marañon clusters were collected) to its confluence with the Negro River. Comparing the number of migrants between all combinations of subclusters from different clusters indeed showed that the highest number of migrants was found between the Upper and Middle Solimões subclusters, from the Purus and Iquitos clusters respectively (Table S5). The second highest value was found between the Middle Solimões and Parinari IV from the Marañon cluster (Peruvian Upper Amazon). These results indicate that gene flow is extensive throughout the Amazon River making it difficult to cluster downstream introgressed populations.

Bottom Line: Germplasm labeling errors have impeded breeding and confounded the interpretation of diversity analyses.After discarding mislabeled samples, 10 genetic clusters, as opposed to the two genetic groups traditionally recognized within T. cacao, were found by applying Bayesian statistics.The results also provide new insights into the diversification of Amazon species in general, with the pattern of differentiation of the populations studied supporting the palaeoarches hypothesis of species diversification.

View Article: PubMed Central - PubMed

Affiliation: National Germplasm Repository, US Department of Agriculture, Agricultural Research Service, Subtropical Horticulture Research Station, Miami, Florida, USA. juan.motamayor@effem.com

ABSTRACT
Numerous collecting expeditions of Theobroma cacao L. germplasm have been undertaken in Latin-America. However, most of this germplasm has not contributed to cacao improvement because its relationship to cultivated selections was poorly understood. Germplasm labeling errors have impeded breeding and confounded the interpretation of diversity analyses. To improve the understanding of the origin, classification, and population differentiation within the species, 1241 accessions covering a large geographic sampling were genotyped with 106 microsatellite markers. After discarding mislabeled samples, 10 genetic clusters, as opposed to the two genetic groups traditionally recognized within T. cacao, were found by applying Bayesian statistics. This leads us to propose a new classification of the cacao germplasm that will enhance its management. The results also provide new insights into the diversification of Amazon species in general, with the pattern of differentiation of the populations studied supporting the palaeoarches hypothesis of species diversification. The origin of the traditional cacao cultivars is also enlightened in this study.

Show MeSH