Adding value to cocoa (Theobroma cacao L.) germplasm information with domestication history and admixture mapping

Marcano, María; Pugh, Tatiana; Cros, Emile; Morales, Sonia; Páez, Elvis A. Portillo; Courtois, B.; Glaszmann, Jean Christophe; Engels, J. M. M.; Phillips, Wilbert; Astorga, Carlos; Risterucci, Ange Marie; Fouet, Olivier; González, Ventura; Rosenberg, Kai; Vallat, Isabelle; Dagert, M.; Lanaud, Claire

doi:10.1007/s00122-006-0486-9

Cited by 23 publications

(19 citation statements)

References 22 publications

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“…It seems necessary the accomplishment of new collections of botanical material of the wild species seeking the enlargement of the conserved variability as well as definition of preservation strategies to avoid losses of genetic variability. Phenotypic information have been used not only for description and characterization purposes but also to derive valuable information about genomic structure and genetic control of useful traits without specifically developing mapping populations for QTL analyses and, thus, saving resources and increasing the scientific value of germplasm-related activities (Clement et al 2003;Marcano et al 2007). Additional studies must be conducted aiming to identify and characterize interesting agronomic traits among Theobroma species for further introgression in T. cacao.…”

Section: General Assessmentmentioning

confidence: 99%

Morphological characterization of leaf, flower, fruit and seed traits among Brazilian Theobroma L. species

Santos

Pires

Corrêa

2011

Genet Resour Crop Evol

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Morphological variability of four wild species, one semi-cultivated and one cultivated species of Theobroma L., indigenous to Brazil and introduced in the Bahian cocoa-growing region, was characterized based on 35 quantitative and 13 qualitative traits. T. cacao, which shows a great diversity of conserved germplasm and many published references for morphological characterization, besides of being one of the most cultivated species in Theobroma, was used for comparison as reference species. Sample size was defined for each organ evaluated and individual data set related to leaf, flower, fruit and seed analyzed by a multivariate approach. The studied species showed a large variation for all morphological traits evaluated. T. grandiflorum (Willd. ex Spreng.) Schum. and T. bicolor Humb. et Bonpl. showed the highest means for quantitative variables but were very divergent from each other considering flower and qualitative traits. These were the only species that presented similar number of seeds in comparison with T. cacao. A species with smaller means for most traits was T. obovatum Klotzsch ex Bernoulli. The four wild species show white seeds while T. cacao shows purple ones. Multivariate analysis of variance indicates significant differences between Theobroma species for individual or grouped morphological fruit traits. The results from a cluster analysis were, in a general way, congruent with botanical classification. The statistical analysis performed here was useful to identify a great variability among evaluated traits and to distinguish the most divergent variables from Theobroma species. This work provided an important contribution to morphological characterization of polymorphic traits from different organs of Theobroma species, which can help breeders in the future on the direction of interspecific crosses attempts.

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Section: General Assessmentmentioning

confidence: 99%

Morphological characterization of leaf, flower, fruit and seed traits among Brazilian Theobroma L. species

Santos

Pires

Corrêa

2011

Genet Resour Crop Evol

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Section: Communicated By D Grattapagliamentioning

confidence: 99%

“…An analysis by Marcano et al (2007) is one of few that highlights the decay of LD in two specific admixed cacao populations. The demographic histories of these two populations reflect continual, if inconsistent, cultivation (Marcano et al 2007;Motamayor et al 2008). While cultivated cacao variation comprises most of cacao's global biomass, they appear to derive from narrow genetic bases (Bartley 2005;Motamayor et al 2003Motamayor et al , 2002.…”

Section: Communicated By D Grattapagliamentioning

confidence: 99%

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping

Stack

Royaert²,

Gutiérrez³

et al. 2015

Tree Genetics & Genomes

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Linkage disequilibrium (LD) measured over the genomes of a species can provide important indications for how future association analyses should proceed. This information can be advantageous especially for slow-growing, perennial crops such as Theobroma cacao, where experimental crosses are inherently time-consuming and logistically expensive. While LD has been evaluated in cacao, previous work has been focused on relatively narrow genetic bases. We use microsatellite marker data collected from a uniquely diverse sample of individuals broadly covering both wild and cultivated varieties to gauge the LD present in the different cacao diversity groups and populations. We find that genome-wide LD decays far more rapidly in the wild and primitive diversity groups of cacao as compared to those representing cultivated varieties. The impact that such differences can have on association analyses is demonstrated using phenotypic data on pod color and genotypic data from two cacao populations with contrasting patterns of LD decay. Our results indicate that the more rapid LD decay in wild and primitive germplasm can lead to higher-resolution mapping intervals when compared to results from cultivated germplasm. Through simulations, we demonstrate how future association mapping analyses, comprising of cacao samples with a wild or primitive background, will likely exhibit lower LD and would be more suitable for fine-scale association mapping analyses. As many traits targeted by cacao breeders are found exclusively in wild and primitive germplasm, association mapping in wild cacao populations holds significant promise for cacao improvement through marker-assisted breeding and emphasize the need to further explore the natural diversity of Amazonian cacao.

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“…All the 257 individuals were evaluated for the quantitative traits and used for the associations analyses. After conducting a structure analysis using the model-based software structure (Pritchard et al 2000), as described by Marcano et al (2007), a subset of 197 individuals among the 257, representing a nonstructured group was selected to study marker/qualitative trait associations.…”

Section: Plant Materialsmentioning

confidence: 99%

“…The admixture mapping approach has proven efficiency for mapping hypertension, a complex trait, in human populations (McKeigue 2005). More recently, this procedure was reported as appropriate to map fruit and seed weight (two important domestication traits) in two "modern Criollo/Trinitario" cacao populations (a germplasm collection and a plantation), after it was demonstrated in these nonstructured populations that large chromosomal fragments (up to 30 cM) were maintained from the ancestors, a situation typical of recent admixture (Marcano et al 2007).…”

Section: Introductionmentioning

confidence: 98%

A genomewide admixture mapping study for yield factors and morphological traits in a cultivated cocoa (Theobroma cacao L.) population

Marcano

Morales

Hoyer

et al. 2008

Tree Genetics & Genomes

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The selection of productive varieties of modern Criollo cocoa, showing fine aromatic qualities in their beans, is of major interest for some producing countries, such as Venezuela. Cultivated populations of Modern Criollo or Trinitario varieties may be suitable for admixture mapping analysis, as large blocks of alleles derived from two identified divergent ancestors, recently admixed, are still preserved, after a few generations of recombination, similar to experimental mapping progenies. Two hundred and fifty-seven individuals from a cultivated population of Modern Criollo were selected and analysed with 92 microsatellite markers distributed along the genome. This population exhibited a wide range of variability for yield factors and morphological features. Population structure analysis identified two main subgroups corresponding to the admixture from the two ancestors Criollo and Forastero. Several significant associations between markers and phenotypic data (yield factors and morphological traits) were identified by a least squares general linear model (GLM) taking into account the population structure and the percentage of admixture of each individual. Results were compared with classical QTL analyses previously reported for other cacao populations. Most markers associated to quantitative traits were very close to QTLs detected formerly for the same traits. Associations were also identified between markers and several qualitative traits including the red pigmentation observed in different organs, mainly associated to common markers in linkage group 4.

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Adding value to cocoa (Theobroma cacao L.) germplasm information with domestication history and admixture mapping

Cited by 23 publications

References 22 publications

Morphological characterization of leaf, flower, fruit and seed traits among Brazilian Theobroma L. species

Morphological characterization of leaf, flower, fruit and seed traits among Brazilian Theobroma L. species

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping

A genomewide admixture mapping study for yield factors and morphological traits in a cultivated cocoa (Theobroma cacao L.) population

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