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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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Localization of the origin of individuals analyzed; colors indicate the inferred genetic cluster to which they belong.Approximated location of Amazon ancient ridges (“palaeoarches”) is shown, after [26], in order of apparition clockwise: Fitzcarrald, Marañon, Serra do Moa, Iquitos, Vaupés, Carauari, Purús, Monte Alegre and Gurupa. U: Upper and M: Middle Solimðes.
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pone-0003311-g001: Localization of the origin of individuals analyzed; colors indicate the inferred genetic cluster to which they belong.Approximated location of Amazon ancient ridges (“palaeoarches”) is shown, after [26], in order of apparition clockwise: Fitzcarrald, Marañon, Serra do Moa, Iquitos, Vaupés, Carauari, Purús, Monte Alegre and Gurupa. U: Upper and M: Middle Solimðes.

Mentions: Table S3 shows the highest coefficient of membership and the cluster name for the 735 individuals retained. Figure 1 displays the location where they were originally collected. The same symbol and color were used to display individuals, from a given location, that belonged to the same genetic cluster. Only individuals from the Criollo cluster are found in the Central American primary forests [Mexico [5] and Panama forests], while all ten clusters (including the Criollo one) are represented in the South American forests. Non-Criollo cacao types can be found in Central America (Figure 1, in Costa Rica, as the clone CC 267 or Matina 1–6) but only within existing farms, indicating that they were introduced more recently than the Criollo type. Nevertheless, what now appear as primary forests in Central America may have also been cultivated areas during pre-Columbian times. These data do not support the hypothesis that wild cacao evolved in Central America nor that simultaneous evolution of two subspecies, one in Central America and the other in the Amazon forest [5], occurred. The highest genetic diversity was found in the Upper Amazon region (see below), which is in agreement with the location of the putative center of origin of T. cacao L. [3]. The study of the genetic substructure in the subsample of 735 individuals indicated that the numbers of K identified in each of the 10 clusters (K = 3 to K = 5, with K = 1 to K = 15 tested), roughly corresponded to the number of geographical units and/or traditional cultivars found in each cluster. This correspondence was used to name each subcluster. From the 735 individuals belonging to the aforementioned 10 clusters, 559 had a coefficient of membership equal to or higher than 0.70 for one of the 36 subclusters grouping 5 or more individuals. These were retained for further analyses.


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)

Localization of the origin of individuals analyzed; colors indicate the inferred genetic cluster to which they belong.Approximated location of Amazon ancient ridges (“palaeoarches”) is shown, after [26], in order of apparition clockwise: Fitzcarrald, Marañon, Serra do Moa, Iquitos, Vaupés, Carauari, Purús, Monte Alegre and Gurupa. U: Upper and M: Middle Solimðes.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0003311-g001: Localization of the origin of individuals analyzed; colors indicate the inferred genetic cluster to which they belong.Approximated location of Amazon ancient ridges (“palaeoarches”) is shown, after [26], in order of apparition clockwise: Fitzcarrald, Marañon, Serra do Moa, Iquitos, Vaupés, Carauari, Purús, Monte Alegre and Gurupa. U: Upper and M: Middle Solimðes.
Mentions: Table S3 shows the highest coefficient of membership and the cluster name for the 735 individuals retained. Figure 1 displays the location where they were originally collected. The same symbol and color were used to display individuals, from a given location, that belonged to the same genetic cluster. Only individuals from the Criollo cluster are found in the Central American primary forests [Mexico [5] and Panama forests], while all ten clusters (including the Criollo one) are represented in the South American forests. Non-Criollo cacao types can be found in Central America (Figure 1, in Costa Rica, as the clone CC 267 or Matina 1–6) but only within existing farms, indicating that they were introduced more recently than the Criollo type. Nevertheless, what now appear as primary forests in Central America may have also been cultivated areas during pre-Columbian times. These data do not support the hypothesis that wild cacao evolved in Central America nor that simultaneous evolution of two subspecies, one in Central America and the other in the Amazon forest [5], occurred. The highest genetic diversity was found in the Upper Amazon region (see below), which is in agreement with the location of the putative center of origin of T. cacao L. [3]. The study of the genetic substructure in the subsample of 735 individuals indicated that the numbers of K identified in each of the 10 clusters (K = 3 to K = 5, with K = 1 to K = 15 tested), roughly corresponded to the number of geographical units and/or traditional cultivars found in each cluster. This correspondence was used to name each subcluster. From the 735 individuals belonging to the aforementioned 10 clusters, 559 had a coefficient of membership equal to or higher than 0.70 for one of the 36 subclusters grouping 5 or more individuals. These were retained for further analyses.

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