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Genetic diversity and structure of farm and GenBank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers

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Abstract

The genetic diversity of 400 accessions collected in cacao farms, 95 GenBank, and 31 reference accessions was analyzed using the 12 microsatellite markers. The GenBank and reference accessions were subdivided into 12 accession groups (AG) that belong to the traditional cacao genetic groups (GG) Lower Amazon Forastero (LA), Upper Amazon Forastero (UA), Trinitario, and Criollo (Cr). The 12-microsatellite loci revealed a total of 125 alleles, 113 of which were present in the farm accession group (FA). The within and between group variation for all AGs accounted respectively for 81% and 19% of the total molecular variation. The average F is for the FA was 0.15 suggesting a moderate level of inbreeding. Significant differences for the level of gene diversity were found between the farm (0.50), GenBank (0.42 to 0.62), and reference (0.10 to 0.60) AGs. Genetic differentiation among AGs was variable with F st values varying between 0.14 and 0.57 for the different AGs. Analysis using a Bayesian model-based method showed the existence of a high level of admixture for the farm accessions group. The LA genes were most represented in the FA (54%), followed by UA (33%) and Cr (7%). The genes of LA were also the most represented in the GenBank (48%), followed by UA (24%) and Cr (14%). Only 14% and 6% of the genes of the GenBank and farm accessions, respectively, could not be attributed to any of the reference GGs. The results suggest the predominating presence of LA genes in the Cameroon farm accessions and a high level of admixture, with apparent presence of genes of more than three GGs in most accessions. The traditional Trinitario types appear to have almost disappeared from farmers fields. The admixture must be the result of hybridization and recombination of these genes from the different GGs in seed gardens and in farmers’ fields. The use of selected farm accessions will depend on the GG that it belongs to and also on their level of heterozygosity. Further implications of the results for breeding and for introduction of new germplasm into the Cameroon GenBank are discussed.

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References

  • Alverson WS, Whitlock BA, Nyffeler R, Bayer C, Baum DA (1999) Phylogeny of the core Malvales: evidence from ndhF sequence data. Am J Bot 86:1474–1486

    Article  PubMed  CAS  Google Scholar 

  • Bartley BGD (2005) The genetic diversity of cacao and its utilization. CABI, Wallingford, UK

    Google Scholar 

  • Bhattacharjee R, Kolesnikova-Allen M, Aikpokpodion P, Taiwo S, Ingelbrecht I (2004) A semi-automated rapid method of extracting genomic DNA for molecular marker analysis in cocoa, Theobroma cacao L. Plant Mol Biol Report 22:435a–435h

    Article  Google Scholar 

  • Braudeau J, Divaret P (1955) Rapport Annuel de la Station Expérimentale du Centre (IRA), Nkoemvone. In: Rapport Annuel de l’Inspection Générale de l’Agriculture, Territoire du Cameroun, pp 60–102

  • Braudeau J, Grimaldi E, Lavabre E (1952) Rapport Annuel de la Station du Cacaoyer de Nkoemvone (IRA). In: Rapport Annuel du Service de l’Agriculture, Territoire du Cameroun, pp 56–12

  • Champaud J (1966) L’économie cacaoyère au Cameroun. Cah ORSTOM Sér Sci hum III(3):105–124

    Google Scholar 

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

    Google Scholar 

  • Cope FW (1984) Cacao Theobroma cacao (Sterculiaceae). In: Simmonds NW (ed) Evolution of crops plants. Longman, London, pp 285–289

    Google Scholar 

  • Cuatrecasas J (1964) Cacao and its allies: a taxonomic revision of the genus Theobroma. Contrib US Natl Herb 35:379–614

    Google Scholar 

  • Efombagn MIB, Nyassé S, Sounigo O, Kolesnikova-Allen M, Eskes AB (2007) Participatory cocoa selection in Cameroon: phytophthora pod rot resistant accessions identified in farmers’ field. Crop Prot 26(10):1467–1473

    Article  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin ver 3.0: an integrated software package for population genetics data analysis. Evol Bioinf Online 1:47–50

    CAS  Google Scholar 

  • Goudet J (1995) FSTAT 1.2: a computer program to calculate F-statistics. J Heredity 86:485–486

    Google Scholar 

  • Hearne CM, Ghosh S, Todd JA (1992) Microsatellites for linkage analysis of genetic traits. Trends Ecol Evol 8:288–294

    CAS  Google Scholar 

  • Kalinowski ST (2005) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187–189

    Article  CAS  Google Scholar 

  • Lanaud C (1987) Nouvelles données sur la biologie du cacaoyer (Theobroma cacao L.): diversité des populations, système d’incompatibilité, haploids spontanées. Leurs conséquences pour l’amélioration génétique de cette espèce. D. Sc. Thesis, Université de Paris Sud, Centre d’Orsay, France

  • Lanaud C, Risterucci AM, Piretti I, Falque M, Bouet A, Lagoda PJL (1999) Isolation and characterization of microsatellites in Theobroma cacao L. Mol Ecol 8:2141–2152

    Article  PubMed  CAS  Google Scholar 

  • Laurent V, Risterucci AM, Lanaud C (1993) Variability for nuclear ribosomal genes within (Theobroma cacao). Heredity 71:96–103

    Article  CAS  Google Scholar 

  • Laurent V, Risterucci AM, Lanaud C (1994) Genetic diversity in cocoa revealed by cDNA probes. Theor Appl Genet 88:193–198

    Article  CAS  Google Scholar 

  • Leberg PL (2002) Estimating allelic richness: effects on sample sizes and bottlenecks. Mol Ecol 11:2445–2449

    Article  PubMed  CAS  Google Scholar 

  • Lerceteau E, Robert T, Pétiard V, Crouzillat D (1997) Evaluation of the extent genetic variability among Theobroma cacao L. accessions using RAPD and RFLP markers. Theor Appl Genet 95:10–19

    Article  CAS  Google Scholar 

  • Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655

    Article  PubMed  CAS  Google Scholar 

  • Motamayor JC, Risterucci AM, Lopez PA, 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, Heath M, Lanaud C (2003) Cocoa domestication II. Progenitor germplasm of the Trinitario cacao cultivar. Heredity 91:322–330

    Article  PubMed  CAS  Google Scholar 

  • N’Goran JAK, Laurent V, Risterucci AM, Lanaud C (2000) Comparative genetic diversities studies of Theobroma cacao L. using RFLP and RAPD markers. Heredity 73:589–597

    Article  Google Scholar 

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glazmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield, Montpellier, pp 43–76

    Google Scholar 

  • Preuss P (1901) Expedition nach central und Sudamerika 1899/900. Verlag des Kolonial-Wirtschaftlichen Komitees, Berlin

    Google Scholar 

  • Pound JF (1943) Cacao and witches broom diseases (Marasmius pernicious). Report on a recent visit to the Amazon territory of Peru, September 1942–February 1943. Government Printer, Port of Spain, Trinité and Tobago

    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 

  • Risterucci AM, Eskes AB, Fargeasm D, Motamayor JC, Lanaud C (2001) Use of microsatellite markers for germplasm identity analysis in cocoa. In: Bekele F, End M, Eskes A (eds) Proceedings of the international workshop on new technologies in cocoa breeding, INGENIC, 16–17 October 2000. Kota, Malaysia, pp 25–33

    Google Scholar 

  • Russell JR, Hosein F, Johnson E, Waugh R, Powell W (1993) Genetic differentiation of cocoa (Theobroma cacao L.) populations revealed by RAPD analysis. Mol Ecol 2:89–97

    Article  PubMed  CAS  Google Scholar 

  • Saunders AJ, Mischke S, Leamy EA, Hemeida AA (2004) Selection of international molecular standards for DNA fingerprinting of Theobroma cacao. Theor Appl Genet 110:41–47

    Article  PubMed  CAS  Google Scholar 

  • Sounigo O, Umaharan R, Christopher Y, Sankar A, Ramdahin S (2005) Assessing the genetic diversity in the International Cocoa Genebank, Trinidad (ICG,T) using isozyme electrophoresis and RAPD. Genet Resour Crop Evol 52:1111–1120

    Article  CAS  Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  • Zhang D, Arevalo-Gardini E, Mischke S, Zuniga-Cerdanes L, Barreto-Chavez A, Adriazola del Aguila J (2006) Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru. Ann Bot 98:647–655

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank the Institute of Agricultural Research for Development (IRAD), Cameroon which authorized the publication of this paper. The study was partially financed by the West Africa Cacao Diversity Project (IITA/USAID), the CFC/ICCO/Bioversity project titled ‘Cacao Productivity and Quality Improvement, a Participatory Approach’ and MARS, Inc. We thank Nanette Langevin (USDA–ARS–SHRS, Miami, FL, USA), Sunday Taiwo (IITA-CBL, Ibadan, Nigeria), François Edoa, Innocent Badjeck, Essomo Ngomba, and K. Daniel Vefonge (IRAD, Cameroon) for their technical support in the present work.

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Authors and Affiliations

  1. Institute of Agricultural Research for Development (IRAD), P.O. Box 2067 or 2123, Yaoundé, Cameroon

    Ives Bruno M. Efombagn & Salomon Nyassé

  2. MARS, Inc, c/o USDA–ARS–SHRS, 13601 Old Cutler Road, Miami, FL, 33158, USA

    Juan C. Motamayor, Ray Schnell & Maria Kolesnikova-Allen

  3. CIRAD, UPR31, 34398, Montpellier, France

    Olivier Sounigo, Albertus B. Eskes & Christian Cilas

  4. Agrocampus Rennes APBV, UMR INRA, BP35327, 35653, Le Rheu, France

    Maria J. Manzanares-Dauleux

  5. Central Biotechnology Laboratory, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria

    Maria Kolesnikova-Allen

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  1. Ives Bruno M. Efombagn
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  2. Juan C. Motamayor
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  3. Olivier Sounigo
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  4. Albertus B. Eskes
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  5. Salomon Nyassé
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  6. Christian Cilas
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  7. Ray Schnell
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  8. Maria J. Manzanares-Dauleux
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  9. Maria Kolesnikova-Allen
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Correspondence to Ives Bruno M. Efombagn.

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Communicated by D. Grattapaglia

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Efombagn, I.B.M., Motamayor, J.C., Sounigo, O. et al. Genetic diversity and structure of farm and GenBank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers. Tree Genetics & Genomes 4, 821–831 (2008). https://doi.org/10.1007/s11295-008-0155-z

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