Hostname: page-component-586b7cd67f-rcrh6 Total loading time: 0 Render date: 2024-11-30T15:17:14.511Z Has data issue: false hasContentIssue false
  • English
  • Français

Elucidation of genetic identity and population structure of cacao germplasm within an international cacao genebank

Published online by Cambridge University Press:  23 October 2012

Lambert A. Motilal ,
Dapeng Zhang ,
Pathmanathan Umaharan ,
Michel Boccara ,
Sue Mischke ,
Antoinette Sankar  and
Lyndel W. Meinhardt
Lambert A. Motilal*
Affiliation:
Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad, Republic of Trinidad and Tobago, West Indies
Dapeng Zhang
Affiliation:
USDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD20705, USA
Pathmanathan Umaharan
Affiliation:
Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad, Republic of Trinidad and Tobago, West Indies
Michel Boccara
Affiliation:
Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad, Republic of Trinidad and Tobago, West Indies Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Biological Systems Department, Unité Mixte de Recherche Développement et Amélioration des Plantes (UMR DAP) TA A 96/03-34,398, Montpellier, France
Sue Mischke
Affiliation:
USDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD20705, USA
Antoinette Sankar
Affiliation:
Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad, Republic of Trinidad and Tobago, West Indies
Lyndel W. Meinhardt
Affiliation:
USDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD20705, USA
*
*Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Theobroma cacao L., or cacao, is the source of cocoa products used in the making of chocolate. These tropical trees are conserved in living genebanks. The International Cocoa Genebank, Trinidad is one of the largest ex situ collections in the public domain. Mislabelling is a critical problem and the correction of this problem is vital to improve the accuracy and efficiency of genebank management. Using microsatellite DNA markers, we assessed the level of mislabelling in a group of Refractario cacao that originated from Ecuador and determined their population memberships through Bayesian clustering analysis. The microsatellite data revealed a synonymous rate of 7.5% and an error rate of 39.4% in this germplasm subset. The analysis of the population structure grouped the Refractario accessions into four subclusters, indicating intra-population heterogeneity in this germplasm group. Based on the results, we recommend that when the assignment test is used for cacao genotype identification, it should (a) use duplicated samples as internal checks, (b) choose suitable reference accessions, including a known homogeneous group and (c) employ subclustering checks to obtain reliable results. The information framework generated is discussed in relation to the management of the collection, population enhancement and future research of the collection.

Keywords

cocoaconservationfield genebankmislabellingpopulation structuretree identity
Type
Research Article
Information
Plant Genetic Resources , Volume 10 , Issue 3 , December 2012 , pp. 232 - 241
Copyright
Copyright © NIAB 2012

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Aikpokpodion, PO, Kolesnikova-Allen, M, Adetmirin, VO, Guiltinan, MJ, Eskes, AB, Motamayor, JC and Schnell, RC (2010) Population structure and molecular characterization of Nigerian field genebank collections of cacao, Theobroma cacao L. Silvae Genetica 59: 273–285.CrossRefGoogle Scholar
Aradhya, MK, Stover, E, Velasco, D and Koehmstedt, A (2010) Genetic structure and differentiation in cultivated fig (Ficus carica L.). Genetica 138: 681–694.Google Scholar
Bartley, B (2000) The nomenclature of the accessions derived from Dr. F.J. Pound's collection in Ecuador in 1937. INGENIC Newsletter 5: 4–6.Google Scholar
Bartley, BGD (2005) The Genetic Diversity of Cacao and its Utilization. Wallingford: CABI Publishing, 341 pp.CrossRefGoogle Scholar
Bekele, F and Bekele, I (1996) A sampling of the phenetic diversity of cacao in the International Cocoa Gene Bank of Trinidad. Crop Science 36: 57–64.Google Scholar
Bekele, F, Butler, DR, et al. (2000) Proposed short list of descriptors for characterization. In: (ed.) Working Procedures for Cocoa Germplasm Evaluation and Selection: Proceedings of the CFC/ICCO/IPGRI Project Workshop, 1–6 February 1998, Montpellier, France. Rome: IPGRI.Google Scholar
Bekele, F, Bekele, I, Butler, DR and Bidaisee, GG (2006) Patterns of morphological variation in a sample of cacao (Theobroma cacao L.) germplasm form the International Cocoa Genebank, Trinidad. Genetic Resources and Crop Evolution 53: 933–948.Google Scholar
Chang, A (2001) Group differences program v.3.0. Available athttp://department.obg.cuhk.edu.hk/researchsupport/download/downloads.asp.Google Scholar
Christopher, Y, Mooleedhar, V, Bekele, F and Hosein, F (1999) Verification of accessions in the ICG,T using botanical descriptors and RAPD analysis. Annual Report 1998. St. Augustine: Cocoa Research Unit, The University of the West Indies, pp. 15–18.Google Scholar
Dawson, KJ and Belkhir, K (2009) An agglomerative hierarchical approach to visualization in Bayesian clustering problems. Heredity 103: 32–45.CrossRefGoogle ScholarPubMed
Earl, DA and von Holdt, BM (2011) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method Conservation Genetics Resources. doi:10.1007/s12686-011–9548-7. Available at http://taylor0.biology.ucla.edu/structureHarvester/.Google Scholar
Efombagn, IBM, Motamayor, JC, Sounigo, O, Eskes, AB, Nyassé, S, Cilas, C, Schnell, R, Manzanares-Dauleux, MJ and Kolesnikova-Allen, M (2008) Genetic diversity and structure of farm and GenBank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers. Tree Genetics & Genomes 4: 821–823.Google Scholar
Engels, JMM, Bartley, BGD and Enriquez, GA (1980) Cacao descriptors, their states and modus operandi. Turrialba (Costa Rica) 30: 209–218.Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.Google Scholar
Falush, D, Stephens, M and Pritchard, JK (2003) Inference of population structure: extensions to linked loci and correlated allele frequencies. Genetics 164: 1567–1587.Google Scholar
Hurka, H, Neuffer, B and Friesen, N (2004) Plant genetic resources in botanical gardens. In: Forkmann G and Michaelis S (eds) Proceedings of the 21st International Symposium on Breeding Ornamentals, Part II. Acta Horticulturae 651: 35–44.CrossRefGoogle Scholar
Irish, BM, Goenaga, R, Zhang, D, Schnell, R, Brown, JS and Motamayor, JC (2010) Microsatellite fingerprinting of the USDA-ARS Tropical Agriculture Research Station cacao (Theobroma cacao L.) germplasm collection. Crop Science 50: 656–667. doi:10.2135/cropsci2009.06.0299.Google Scholar
Iwaro, AD, Bekele, FL and Butler, DR (2003) Evaluation and utilisation of cacao (Theobroma cacao L.) germplasm at the International Cocoa Genebank, Trinidad. Euphytica 130: 207–221.Google Scholar
Jakobsson, M and Rosenberg, NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801–1806.CrossRefGoogle ScholarPubMed
Johnson, SE, Mora, A and Schnell, RJ (2007) Field guide efficacy in the identification of reallocated clonally propagated accessions of cacao. Genetic Resources and Crop Evolution 54: 1301–1313.Google Scholar
Kaeuffer, R, Réale, D, Coltman, DW and Pontier, D (2007) Detecting population structure using STRUCTURE software: effect of background linkage disequilibrium. Heredity 99: 374–380. doi:10.1038/sj.hdy.6801010.Google Scholar
Kalinowski, ST, Taper, ML and Marshall, TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16: 1099–1106. doi:10.1111/j.1365–294X.2007.03089.x.Google Scholar
Kennedy, AJ and Mooleedhar, V (1993) Conservation of cocoa in field genebanks – the International Cocoa Genebank, Trinidad. pp. 21–23. Proceedings of International Workshop on Conservation, Characterisation and Utilisation of Cocoa Genetic Resources in the 21st Century, 13–17 September, 1992, Port of Spain, Trinidad. Port of Spain: Cocoa Research Unit, The University of the West Indies.Google Scholar
Lanaud, C, Risterucci, AM, Pieretti, I, Falque, M, Bouet, A and Lagoda, PJL (1999) Isolation and characterization of microsatellites in Theobroma cacao L. Molecular Ecology 8: 2141–2143. doi:10.1046/j.1365–294x.1999.00802.x.Google Scholar
Leão, PCS, Riaz, S, Graziani, R, Dangl, GS, Motoike, SY and Walker, MA (2009) Characterization of a Brazilian grape germplasm collection using microsatellite markers. American Journal of Enology and Viticulture 60: 517–524.CrossRefGoogle Scholar
Motamayor, JC, Lachneaud, P, da Silva e Mota, JW, Loor, R, Kuhn, DN, Brown, JS and Schnell, RJ (2008) Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L.). PLoS ONE 3: e3311. doi:10.1371/journal.pone.0003311.Google Scholar
Motilal, L and Butler, D (2003) Verification of identities in global cacao germplasm collections. Genetic Resources and Crop Evolution 50: 799–807. doi:10.1023/A:1025950902827.Google Scholar
Motilal, LA, Zhang, D, Umaharan, P, Mischke, S, Boccara, M and Pinney, S (2009) Increasing accuracy and throughput in large-scale microsatellite fingerprinting of cacao field germplasm collections. Tropical Plant Biology 2: 23–27. doi:10.1007/s12042-008-9016-z.CrossRefGoogle Scholar
Motilal, LA, Zhang, D, Umaharan, P, Mischke, S, Mooleedhar, V and Meinhardt, LW (2010) The relic Criollo cacao in Belize – genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank Trinidad. Plant Genetic Resources: Characterization and Utilization 8: 106–115. doi:10.1017/S1479262109990232.Google Scholar
Motilal, LA, Zhang, D, Umaharan, P, Mischke, S, Pinney, S and Meinhardt, LW (2011) Microsatellite fingerprinting in the International Cocoa Genebank Trinidad: accession and plot homogeneity information for germplasm management. Plant Genetic Resources: Characterization and Utilization 9: 430–438. doi:10.1017/S147926211100058X.Google Scholar
Nei, M (1972) Genetic distance between populations. American Naturalist 106: 283–392.Google Scholar
Nei, M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583–590.Google Scholar
Onofri, A (2007) Routine statistical analyses of field experiments by using an Excel extension In: Proceedings 6th National Conference Italian Biometric Society: “La statistica nelle scienze della vita e dell'ambiente”, 20–22 June 2007, Pisa, pp. 93–96, version 1.1 (update 18 March 2011). Available at http://www.unipg.it/~onofri/DSAASTAT/DSAASTAT.htm.Google Scholar
Park, SDE (2001) Trypanotolerance in West African cattle and the population genetic effects of selection. PhD Thesis, University of Dublin.Google Scholar
Peakall, R and Smouse, PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295.Google Scholar
Pound, FJ (1938) Cacao and witches' broom disease (Marasmius perniciosus) of South America. In: (ed.) Archives Cacao Research. vol 1. Washington, DC/Brussels: American Cacao Research Institute/International Office of Cacao and Chocolate, pp. 20–72.Google Scholar
Pound, FJ (1943) Cacao and witches' broom disease (Marasmius perniciosa). In: Report on a recent visit to the Amazon territory of Peru, September 1942–February 1943. Port of Spain: Yuille's Printery.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
Pugh, T, Fouet, O, Risterucci, AM, Brottier, P, Abouladze, M, Deletrez, C, Courtois, B, Clement, D, Larmande, P, N'Goran, JAK and Lanaud, C (2004) A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers. Theoretical and Applied Genetics 108: 1151–1161. doi:10.1007/s00122-003-1533-4.Google Scholar
Saunders, JA, Mischke, S, Leamy, EA and Hemeida, AA (2004) Selection of international molecular standard for DNA fingerprinting of Theobroma cacao. Theoretical and Applied Genetics 110: 41–47. doi:10.1007/s00122-004-1762-1.CrossRefGoogle ScholarPubMed
Schmidt, JI, Hundertmark, KJ, Bowyer, RT and McCraken, KG (2009) Population structure and genetic diversity of moose in Alaska. Journal of Heredity 100: 170–180. doi:10.1093/jhered/esn076.Google Scholar
Sounigo, O, Christopher, Y, Bekele, F, Mooleedhar, V and Hosein, F (2001) The detection of mislabelled trees in the International Cocoa Genebank, Trinidad (ICG,T). In: Proceedings of the Third International Group for Genetic Improvement of Cocoa (INGENIC) International Workshop on the New Technologies and Cocoa Breeding, 16–17. October 2000. Malaysia: Kota Kinabalu, pp. 34–39.Google Scholar
Sounigo, O, Umaharan, R, Christopher, Y, Sankar, A and Ramdahin, S (2005) Assessing the genetic diversity in the International Cocoa Genebank. Trinidad (ICG,T) using isozyme electrophoresis and RAPD. Genetic Resources and Crop Evolution 52: 1111–1120.CrossRefGoogle Scholar
SPSS, Inc. (1986–2001) SigmaPlot 2002 for Windows, version 8.02. Chicago, IL: SPSS, Inc.Google Scholar
Toxopeus, H (1985) Botany, types and populations. In: (eds) Cocoa. 4th edn.London: Longman Group Ltd, pp. 11–37.Google Scholar
Valière, N (2002) GIMLET: a computer program for analyzing genetic individual identification data. Molecular Ecology Notes 2: 377–379. doi:10.1046/j.1471–8286.2002.00228.x-i2.Google Scholar
van Treuren, R, de Groot, EC, Boukema, IW, van de Wiel, CCM and van Hintum, ThJL (2010) Marker-assisted reduction of redundancy in a genebank collection of cultivated lettuce. Plant Genetic Resources: Characterization and Utilization 8: 95–105. doi:10.1017/S1479262109990220.CrossRefGoogle Scholar
Waits, LP, Luikart, G and Taberlet, P (2001) Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Molecular Ecology 10: 249–256. doi:10.1046/j.1365–294X.2001.01185.x.CrossRefGoogle ScholarPubMed
Zhang, D, Boccara, M, Motilal, L, Butler, DR, Umaharan, P, Mischke, S and Meinhardt, L (2008) Microsatellite variation and population structure in the “Refractario” cacao of Ecuador. Conservation Genetics 9: 327–337. doi:10.1007/s10592-007-9345-8.CrossRefGoogle Scholar
Zhang, D, Boccara, M, Motilal, L, Mischke, S, Johnson, ES, Butler, DR, Bailey, B and Meinhardt, L (2009 a) Molecular characterization of an earliest cacao (Theobroma cacao L.) collection from Upper Amazon using microsatellite DNA markers. Tree Genetics & Genomes 5: 595–607. doi:10.1007/s11295-009-0212-2.CrossRefGoogle Scholar
Zhang, D, Mischke, S, Johnson, ES, Phillips-Mora, W and Meinhardt, L (2009 b) Molecular characterization of an international cacao collection using microsatellite markers. Tree Genetics & Genomes 5: 1–10. doi:10.1007/s11295-008-0163-z.CrossRefGoogle Scholar
Supplementary material: File

Motilal Supplementary Material

Figure S1

Download Motilal Supplementary Material(File)
File 302.6 KB
Supplementary material: File

Motilal Supplementary Material

Table S1

Download Motilal Supplementary Material(File)
File 69.6 KB
Supplementary material: File

Motilal Supplementary Material

Table S2

Download Motilal Supplementary Material(File)
File 70.1 KB
Supplementary material: File

Motilal Supplementary Material

Table S3

Download Motilal Supplementary Material(File)
File 19.5 KB