Molecular characterization of an earliest cacao (Theobroma cacao L.) collection from Upper Amazon using microsatellite DNA markers

Tree Genetics and Genomes

Volumn 5, Issue 4, 2009, Pages 595-607

  Zhang, Dapeng ^a   Boccara, Michel ^b,c   Motilal, Lambert ^b   Mischke, Sue ^a   Johnson, Elizabeth S ^a   Butler, David R ^b   Bailey, Bryan ^a   Meinhardt, Lyndel ^a  

^a USDA ARS PSI   (United States)

^b UNIVERSITY OF THE WEST INDIES   (Trinidad and Tobago)

^c CIRAD   (France)

Author keywords

Amazon; Conservation; Genetic diversity; Germplasm; Peru; Population structure; Theobroma cacao; Tropical tree

Indexed keywords

ANACARDIUM OCCIDENTALE; THEOBROMA CACAO;

EID: 70349515547     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-009-0212-2     Document Type: Article

References (48)

1. Aikpokpodion PO, Adetimirin VO, Ingelbrecht I, Schnell RJ, Kolesnikova-Allen M (2005) Assessment of Genetic diversity of cacao, Theobroma cacao L., Collections in Nigeria using simple sequence repeat markers. In: Malaysian Intl Cocoa Conf Sustainable Cocoa Economy through Increase in Productivity, Efficiency and Quality, pp 83-86
2. Bartley BGD (1994) A review of cacao improvement: fundamentals, methods and results. Proc Intl Workshop Cocoa Breeding Strategies, pp 3-16. Available at http://ingenic.cas.psu.edu/proceedings.htm
3. Bartley BGD (2005) The genetic diversity of cacao and its utilization. CAB International, Wallingford, Oxfordshire
4. Boccara M and Zhang D (2006) Progress in resolving identity issues among the Parinari accessions held in Trinidad: the contribution of the collaborative USDA/CRU project. CRU Annu Rpt 2005, Cacao Research Unit, The University of the West Indies, St. Augustine, Trinidad and Tobago
5. Bowers JH, Bailey BA, Hebbar PK, Sanogo S, Lumsden RD (2001) The impact of plant diseases on world chocolate production. Plant Health Progress (online). doi:10.1094/PHP-2001-0709-01-RV
6. Cheesman EE (1944) Notes on the nomenclature, classification and possible relationships of cocoa populations. Trop Agric 21:144-159
7. Cryer NC, Fenn MGE, Turnbull CJ, Wilkinson MJ (2006) Allelic size standards and reference genotypes to unify international cocoa (Theobroma cacao L.) microsatellite data. Genet Resour Crop Evol 53:1643-1652. doi:10.1007/s10722-005-1286-9
8. Cuatrecasas J (1964) Cacao and its allies: A taxonomic revision of the genus Theobroma. Contributions from the United States National Herbarium, vol. 35. Smithsonian Institution Press, Washington, DC, pp 375-614
9. Dias LAS (2001) Genetic improvement of cacao. Editora Folha de Vicosa Ltda. Trans. Abreu-Reichart CE, Vicosa, MG, Brazil, supported by FAO (2005). Available at http://ecoport.org/ep?SearchType=earticleView&earticleId=197
10. Efombagan IB, Motamayor JC, Sounigo O, Eskes AB, Nyasse S, Cilas C, Schnell RJ, Manzanares-Dauleux M, Kolesnikova-Allen M (2008) Genetic diversity and structure of farm and genebank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers. Tree Genetics & Genomics 4:821-831. doi:10.1007/s11295-008-0155-z
11. Evett IW, Weir BS (1998) Interpreting DNA evidence: statistical genetics for forensic scientists. Sinauer, Sunderland, MA
12. Gómez-Pompa A, Flores JS, Fernandez MA (1990) The sacred cacao groves of the Maya. Latin Am Antiq 1:247-257. doi:10.2307/972163
13. Henderson JS, Joyce RA, Hall GR, Hurst WJ, McGovern PE (2007) Chemical and archaeological evidence for the earliest cacao beverages. Proc Natl Acad Sci U S A 104:18937-18940
14. Hunter RJ (1990) The status of cocoa (Theobroma cacao, Sterculiaceae) in the western hemisphere. Econ Bot 44:425-439
15. Iwaro AD, Bekele FL, Butler DR (2003) Evaluation and utilization of cacao (Theobroma cacao L.) germplasm at the International Cocoa Genebank, Trinidad. Euphytica 130:207-221
16. Johnson ES, Mora A, Schnell RJ (2007) Field guide efficacy in the identification of reallocated clonally propagated accessions of cacao (Theobroma cacao L.). Genet Resour Crop Evol 54:1301-1313
17. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099-1006
18. Kennedy AJ, Mooleedhar V (1993) Conservation of cocoa in field genebanks-the International Cocoa Genebank, Trinidad. In: Proceedings of the International Workshop on Conservation, Characterization and Utilization of Cocoa Genetic Resources in the 21st Century. The University of the West Indies, Cocoa Research Unit, Port-of-Spain, Trinidad and Tobago, pp 21-23
19. Kobayashi N, Horikoshi T, Katsuyama H, Handa T, Takayanagi K (1998) A simple and efficient DNA extraction method for plants, especially woody plants. Plant Tissue Cult Biotechnol 4:76-80
20. Lanaud C, Motamayor JC, Risterucci AM (2001) Implications of new insight into the genetic structure of Theobroma cacao L. for breeding strategies. In: Proceedings of the International Workshop on New Technologies for Cocoa Breeding. Ingenic Press, Kota Kinabalu, Malaysia, London, pp 89-107
21. Lanaud C, Risterucci AM, Pieretti I, Falque M, Bouet A, Lagoda PJL (1999) Isolation and characterization of microsatellites in Theobroma cacao L. Mol Ecol 8:2141-2143
22. Liu J, Muse S (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics Applications Note 21:2128-2129 (doi:10.1093/bioinformatics/bti282) (Free Program, v 3.23, distributed by author, available at http://www.powermarker.net)
23. Lockwood C, End M (1993) History, technique and future needs for cacao collection. In: Proceedings of the Workshop on the Conservation, Characterization and Utilization of Cacao Genetic Resources in the 21st Century, 13-17 September, 1992, Port-of-Spain. Trinidad and Tobago, The University of the West Indies, The Cacao Research Unit, pp 1-14
24. Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639-655
25. Motamayor JC, Lopez PA, Ortiz CF, Moreno A, Lanaud C (2002) Cacao domestication. I. The origin of the cacao cultivated by the Mayas. Heredity 89:380-386
26. Motamayor JC, Lachenaud P, Wallace J, Loor G, Kuhn DN, Brown JS, Schnell Ii RJ (2008) Geographic and genetic population differentiation of the Amazonian chocolate tree. PLoS One 3:e3311. doi:10.1007/s12042-008-9011-4
27. Peakall R, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6:288-295
28. Posnette AF (1986) Fifty years of cocoa research in Trinidad and Tobago. Cocoa Research Unit, University of the West Indies, St. Augustine, Trinidad
29. Pound FJ (1938) Cacao and witches' broom disease (Marasmius perniciosus) of South America. Arch Cacao Res 1:20-72
30. Pound FJ (1943) Cacao and witches' broom disease (Marasmius perniciosus). Report on a recent visit to the Amazon territory of Peru, September, 1942-February, 1943. Yuille's Printery, Port of Spain, Trinidad and Tobago
31. Pound FJ (1945) A note on the cocoa population of South America. In: Report and Proceedings of the 1945 Cocoa Conference. London, pp 131-133
32. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure from multilocus genotype data. Genetics 155:945-959
33. Risterucci AM, Grivet L, Ngoran JA, Pieretti I, Flamen MH et al (2000) A high-density linkage map of Theobroma cacao L. Theor Appl Genet 101:948-955
34. Risterucci AM, Eskes B, Fargeas D, Motamayor JC, Lanaud C (2001) Use of microsatellite markers for germplasm identity analysis in cocoa. In: Proc Intl Workshop on New Technologies and Cocoa Breeding, pp 25-33. Available via http://ingenic.cas.psu.edu/proceedings.htm.
35. SAS Institute Incorporated (1999) SAS Version 8.02: SAS/STAT Software: Changes and enhancements through Release 8.02. SAS Institute Inc., Cary, NC, USA
36. Saunders JA, Hemeida AA, Mischke S (2001) USDA DNA fingerprinting programme for identification of Theobroma cacao accessions. In: Bekele F, End M, Eskes AB (eds) Proceeding of the International Workshop on New Technologies and Cocoa Breeding, 16-17 October 2000, Kota Kinabalu, Sabah, Malaysia. INGENIC Press, Malaysia, pp 108-114
37. Saunders JA, Mischke S, Leamy EA, Hemeida AA (2004) Selection of international molecular standards for DNA fingerprinting of Theobroma cacao. Theor Appl Genet 110:41-47
38. Schnell RJ, Olano CT, Brown JS, Meerow AW, Cervantes-Martinez C, Nagai C, Motamayor JC (2005) Retrospective determination of the parental population of superior cacao (Theobroma cacao L.) seedlings and association of microsatellite alleles with productivity. J Am Soc Hortic Sci 130:181-190
39. Sereno ML, Albuquerque PSB, Vencovsky R, Figueira A (2006) Genetic diversity and natural population structure of cacao (Theobroma cacao L.) from the Brazilian Amazon evaluated by microsatellite markers. Conserv Genet 7:13-24
40. Sounigo O, Christopher Y, Ramdahin S, Umaharan R, Sankar A (2000) Evaluation and use of the genetic diversity present in the International Cacao Genebank (ICG,T), in Trinidad. In: Proceedings of the 3rd INGENIC International Workshop on the New Technologies and Cocoa Breeding, Kota Kinabalu, Sabah, Malaysia.
41. Wadsworth RM, Ford CS, End MJ, Hadley P (eds) (1997) International cacao germplasm database. The London International Financial Futures and Options Exchange (LIFFE), London, UK.
42. Waits LP, Luikart G, Taberlet P (2001) Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol 10:249-256
43. Wang J (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166:1963-1979
44. Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19:395-420
45. Zhang D, Mischke S, Goenaga R, Hemeida AA, Saunders JA (2006a) Accuracy and reliability of high-throughput microsatellite genotyping for cacao clone identification. Crop Sci 46:2084-2092
46. Zhang D, Arevalo-Gardini E, Mischke S, Zúñiga-Cernades L, Barreto-Chavez A et al (2006b) Genetic diversity and structure of managed and semi-natural populations of cacao (Theobroma cacao) in the Huallaga and Ucayali valleys of Peru. Ann Bot 98:647-655
47. Zhang D, Boccara M, Motilal L, Butler DR, Umaharan P, Mischke S, Meinhardt L (2008) Microsatellite variation and population structure in the "refractario" cacao of Equador. Conserv Genet 9:327-337. doi:10.1007/s10592-007-9345-8
48. Zhang D, Mischke S, Johnson ES, Phillips-Mora W, Meinhardt L (2009) Molecular characterization of an International cocoa collection using microsatellite markers. Tree Genetics & Genomes 5:1-10. doi:10.1007/s11295-008-0163-z