Skip to main content
Log in

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

  • Original Paper
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Bartley BGD (2005) The genetic diversity of cacao and its utilization. CAB, UK, p 341

    Google Scholar 

  • Borchers AT, Keen CL, Hannum SM, Gershwin ME (2000) Cocoa and chocolate: composition, bioavailability and health implications. J Med Food 3(2):77–105

    Article  CAS  Google Scholar 

  • Braudeau J (1970) El cacao. Técnicas agrícolas y producciones tropicales. Colección Agricultura Tropical. Ed. Blume, Barcelona, España

  • Brown JS, Schnell RJ, Motamayor JC, Lopes U, Kuhn DN, Borrone JW (2005) Resistance gene mapping for witches’ broom disease in Theobroma cacao L. in an F2 population using SSR markers and candidate genes. J Amer Soc Hort Sci 130:366–373

    CAS  Google Scholar 

  • Brown JS, Phillips-Mora W, Power EJ, Krol CA, Cervantes Martinez C, Motamayor JC, Schnell RJ II (2007) Mapping QTL for resistance to frosty pod and black pod diseases, and for horticultural traits in Theobroma cacao L. Crop Sci 47:1851–1858

    Article  Google Scholar 

  • Brown JS, Sautter RT, Tondo CT, Borrone JW, Kuhn DN, Motamayor JC, Schnell RJ II (2008) A composite linkage map from the combination of three crosses made from commercial clones of cacao, T. cacao L. Tropical Plant Biology 1(2):120–130

    Article  Google Scholar 

  • Cakirer MS, Ziegler GR, Guiltinan MJ, Jones AD (2002) Fresh bean colour as an indicator of chocolate flavour potential. In: Le Quere JL, Etievant PX (eds) Flavour research at the dawn of the twenty-first century. Proceedings of the 10th Weurman Flavour Research Symposium. Intercept, London, pp 540–543

    Google Scholar 

  • Cheesman EE (1944) Notes on the nomenclature, classification and possible relationship of cacao populations. Trop Agric 21:144–159

    Google Scholar 

  • Clapperton J, Yow S, Chan J, Lim D, Lockwood R, Romanczyk L, Hammerstone J (1994) The contribution of genotype to cocoa (Theobroma cacao L.) flavor. Trop Agric 71(4):303–308

    Google Scholar 

  • Clément D, Risterucci AM, Motamayor JC, N’Goran J, Lanaud C (2003a) Mapping QTL for yield components, vigour and resistance to Phytophthora palmivora in Theobroma cacao L. Genome 46:204–212

    Article  PubMed  Google Scholar 

  • Clément D, Risterucci AM, Motamayor JC, N’Goran J, Lanaud C (2003b) Mapping quantitative trait loci for bean traits and ovule number in Theobroma cacao L. Genome 46:103–111

    Article  PubMed  Google Scholar 

  • Coe EH, NeuVer MG, Hoisington DA (1988) The genetics of corn. In: Sprague GF, Dudley JW (eds) Corn and corn improvement. 3rd edn. ASA, CSSA, SSSA, Madison, pp 81–258

    Google Scholar 

  • Counet C, Ouwerx C, Rosoux D, Collin S (2004) Relationship between procyanidin and flavor contents of cocoa liquors from different origins. J Agric Food Chem 52:6243–6249

    Article  PubMed  CAS  Google Scholar 

  • Crouzillat D, Lercetau E, Pétiard V, Morera J, Rodríguez H, Walker D, Phillips W, Ronning C, Schnell R, Osei J, Fritz P (1996) Theobroma cacao L.: a genetic linkage map and quantitative trait loci analysis. Theor Appl Genet 93:205–214

    Article  CAS  Google Scholar 

  • Crouzillat D, Ménard B, Mora A, Phillips W, Fritz PJ, Pétiard V (2000a) Quantitative trait loci analysis in Theobroma cacao L. using molecular markers. Euphytica 114:13–23

    Article  CAS  Google Scholar 

  • Crouzillat D, Phillips W, Fritz PJ, Pétiard V (2000b) Quantitative trait loci analysis in Theobroma cacao L. using molecular markers. Inheritance of polygenic resistance to Phytophthora palmivora in two related cacao populations. Euphytica 114:25–36

    Article  CAS  Google Scholar 

  • Darvasi A, Shifman S (2005) The beauty of admixture. Nat Genet 37(2):118–120

    Article  PubMed  CAS  Google Scholar 

  • Engels JMM (1983) A systematic description of cacao clones. III. Relationships between clones, between characteristics and some consequences for the cacao breeding. Euphytica 32:719–733

    Article  Google Scholar 

  • Engels JMM, Bartley BGD, Enríquez GA (1980) Cacao descriptors, their states and modus operandi. Turrialba 30(2):211–218

    Google Scholar 

  • Eskes A, Lanaud C (1997) Cocoa. In: Charrier A (ed) Tropical plant breeding. Montpellier, France, pp 78–105

    Google Scholar 

  • FAO. Anuario Estadístico 2005–2006. http://www.fao.org.statistics/yearbook/

  • Flament MH, Kébé I, Clément D, Pieretti I, Risterucci AM, N’Goran JAK, Cilas C, Despéux D, Lanaud C (2000) Genetic mapping of resistance factors to Phytophthora palmivora in cocoa. Genome 44:79–85

    Article  Google Scholar 

  • Forsyth WCG, Quesnel VC (1957) Cacao polyphenolic substances 4. The anthocyanin pigments. Biochemistry Journal 65:177–179

    CAS  Google Scholar 

  • Gu L, House SE, Wu X, Ou B, Prior RL (2006) Procyanidin and catechin contents and antioxidant capacity of cocoa and chocolate products. J Agric Food Chem 54:4057–4061

    Article  PubMed  CAS  Google Scholar 

  • Jannink JL, Walsh B (2004) Association mapping in plant populations. In: Kang MS (ed) Quantitative genetics, genomics and plant breeding. CAB International, pp 59–68

  • Jeanjean N (1995) Influence du génotype, de la fermentation et de la torréfaction sur le développement de l’arôme cacao. Rôle des précurseurs d’arôme. Thèse de Doctorat, Université de Montpellier II, Montpellier, France, 200 p

  • Kraakman ATW, Niks RE, Van der Berg PMMM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium and mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446

    Article  PubMed  CAS  Google Scholar 

  • Lanaud C, Hamon PC, Duperray C (1992) Estimation of nuclear DNA content of Theobroma cacao L. by flow cytometry. Café, Cacao, Thé 36:3–8

    CAS  Google Scholar 

  • Lanaud C, Kébé I, Risterucci AM, Clément D, N’Goran JKA, Grivet L, Tahi M, Cilas C, Pieretti I, Eskes A, Despréaux D (1999) Mapping quantitative trait loci (QTL) for resistance to Phytophthora palmivora in T. cacao L. 12th International Cocoa Research Conference, November 17–23, Salvador, Bahía, Brazil, pp 99–105

  • Lanaud C, Boult E, Clapperton J, N’Goran JKA, Cros E, Chapelin M, Clément D, Petithugenin P (2003) Identification of QTLs related to fat content, seed size an sensorial traits in Theobroma cacao L. 14th International Cocoa Conference, Accra, Ghana

  • Lewontin R (1964) The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49:49–67

    PubMed  CAS  Google Scholar 

  • López O, Enríquez GA, Soria J (1988) Herencia del número de óvulos por ovario en Theobroma cacao L. Turrialba 38(3):163–167

    Google Scholar 

  • Marcano M, Pugh T, Cros E, Morales S, Portillo Páez E, Courtois B, Glaszmann J, Engels M, Phillips W, Astorga C, Risterucci AM, Fouet O, González V, Rosenberg K, Vallat I, Dagert M, Lanaud C (2007) Adding value to cocoa (Theobroma cacao L) germplasm information with domestication history and admixture mapping. Theor Appl Gen 114:877–884

    Article  Google Scholar 

  • McKeigue P (2005) Prospects for admixture mapping of complex traits. Review article. Am J Hum Genet 76:1–7

    Article  PubMed  CAS  Google Scholar 

  • Motamayor JC, Risterucci AM, López PA, Ortiz CF, Moreno A, Lanaud C (2002) Cacao domestication I: the origin of the cacao cultivated by the Mayas. Heredity 89:380–386

    Article  PubMed  CAS  Google Scholar 

  • Motamayor JC, Risterucci AM, Heat M, Lanaud C (2003) Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar. Heredity 91:322–330

    Article  PubMed  CAS  Google Scholar 

  • N’Goran JAK, Risterucci AM, Clément D, Sounigo O, Lorieux M, Lanaud C (1997) Identification of quantitative trait loci (QTL) in Theobroma cacao L. Agron Afr 9:55–63

    Google Scholar 

  • Paradis L (1979) Le cacao précolombien: monnaie d’échange et breuvage des dieux. J Agric Tradit Bot Appl 26:3–4

    Google Scholar 

  • Pittier H (1935) Degeneration of cacao through natural hybridization. J Heredity 26(10):385–390

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  CAS  Google Scholar 

  • Pugh T (2005) Etude du déséquilibre de liaison chez le cacaoyer appartenant aux groupes Criollo/Trinitario. Application au marquage génétique d’intérêt pour la sélection. Thèse Doctorat, Ecole National Supérieur d’Agonomie, Montpellier, France, 107 p

  • Pugh T, Fouet O, Risterucci AM, Brottier P, Deletrez C, Courtois B, Clément D, Lamande P, N’Goran JAK, Lanaud C (2004) A new codominant markers based cocoa linkage map: Development and integration of 201 new microsatellites markers. Theor Appl Genet 108:1151–1161

    Article  PubMed  CAS  Google Scholar 

  • Quattrocchio F, Wing JF, Leppen H, Mol J, Koes RE (1993) Regulatory genes controlling anthocyanin pigmentation are functionally conserved among plant species and have distinct sets of target genes. Plant Cell 5:1497–1512

    Article  PubMed  CAS  Google Scholar 

  • Queiroz VT, Guimaraes CT, Anhert D, Schuster I, Daher RT, Pereira MG, Miranda VRM, Loguercio LL, Barros EG, Moreira MA (2003) Identification of a major QTL in cocoa (Theobroma cacao L) associated with resistance to witches’ broom disease. Plant Breed 122:268–272

    Article  CAS  Google Scholar 

  • Reddy AR (1996) IRRI International Rice research Institute. Rice genetics III. Proc. of the 3rd International Rice Genetics Symposium. Philippines, 16–20 Oct

  • Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci 20:11479–11484

    Article  Google Scholar 

  • Rife DC (1954) Populations of hybrid origin as source material for the detection of linkage. Am J Hum Gen 6:26–33

    CAS  Google Scholar 

  • Risterucci AM, Paulin D, Ducamp M, N’Goran JAK, Lanaud C (2003) Identification of QTLs related to cocoa resistance to three species of Phytophthora. Theor Appl Genet 108:168–174

    Article  PubMed  CAS  Google Scholar 

  • SAS Institute Inc. (2002) Version 9. SAS Institute Inc., Cary, North Caroline, USA

    Google Scholar 

  • Schnell RJ, Olano CT, Brown JS, Meerow AW, Cervantes-Martínez C (2005) Retrospective determination of the parental population of superior cacao (Theobroma cacao L) seedlings and association of microsatellite alleles with productivity. J Amer Soc Hort Sci 130(2):181–190

    CAS  Google Scholar 

  • Searle SR (1987) Linear models for unbalanced data. Wiley, New York

    Google Scholar 

  • Soria J (1962) “Porcelana” cacao of Venezuela. Cacao 7(4):7–9 Costa Rica

    Google Scholar 

  • Stafford HA (1990) Flavonoid metabolism. CRC, Boca Raton, FL, p 317

    Google Scholar 

  • Stark T, Bareuther S, Hofmann T (2005) Sensory-guided decomposition of roasted cocoa nibs (Theobroma cacao L) and structure determination of taste-active polyphenols. J Agric Food Chem 53:5407–5418

    Article  PubMed  CAS  Google Scholar 

  • Storey JD (2002) A direct approach to false discovery rates. J R Stat Soc Ser B 64:479–498

    Article  Google Scholar 

  • Thornsberry J, Goodman M, Doebley J, Kresovich S, Nielsen D, Buckler E IV (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289

    Article  PubMed  CAS  Google Scholar 

  • Wellensiek SJ (1931) The genetics of cotyledon colour of cocoa as a basis for quality selection. Translated by H. Toxopeus from Archief voor de Koffiecultuur in Nederlandsch-Indië (Buitenzorg, Java)

  • Wollgast J, Anklam E (2000) Polyphenols in chocolate: is there a contribution to human health? Food Res Int 33(6):449–454

    Article  CAS  Google Scholar 

  • Yu J, Pressoir G, Briggs W, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut B, Nielsen DM, Holland JB, Kresovich S, Buckler E (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

We thank the financial support received from FONACIT (Fondo Nacional para la Ciencia y la Tecnología), Venezuela, the FIRC (Fonds Interprofessionnel de la Recherche sur le cacao), the Ministère des Affaires Etrangers, France and VALRHONA/SOCAOVEN for providing the vegetal material and infrastructure needed for this work. We also thank Dr. Surendra SURUJDEO-MAHARAJ for improving the English writing of this manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Maria Marcano.

Additional information

Communicated by F. Gmitter

Rights and permissions

Reprints and permissions

About this article

Cite this article

Marcano, M., Morales, S., Hoyer, M.T. et al. A genomewide admixture mapping study for yield factors and morphological traits in a cultivated cocoa (Theobroma cacao L.) population. Tree Genetics & Genomes 5, 329–337 (2009). https://doi.org/10.1007/s11295-008-0185-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11295-008-0185-6

Keywords

Navigation