Accuracy and reliability of high-throughput microsatellite genotyping for cacao clone identification

Crop Science

Volumn 46, Issue 5, 2006, Pages 2084-2092

  Zhang, Dapeng ^a   Mischke, Sue ^a   Goenaga, Ricardo ^b   Hemeida, Alaa A ^c   Saunders, James A ^d  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c MENOUFIA UNIVERSITY   (Egypt)

^d TOWSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

THEOBROMA CACAO;

EID: 33748029866     PISSN: 0011183X     EISSN: None     Source Type: Journal    
DOI: 10.2135/cropsci2006.01.0004     Document Type: Article

References (36)

1. Bonin, A., E. Bellemain, P. Bronken, F. Eidesen, C. Pompanon, C. Brochmann, and P. Taberlet. 2004. How to track and assess genotyping errors in population genetic studies. Mol. Ecol. 13:3261-3273.
2. Broquet, T., and E. Petit. 2004. Quantifying genotyping errors in non-invasive population genetics. Mol. Ecol. 13:3601-3608.
3. Christopher, Y., V. Mooleedhar, F. Bekele, and F. Hosein. 1999. Verification of accession in the ICG, T using botanical descriptors and RAPD analysis. p. 15-18. In Annual Report 1998, Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad and Tobago.
4. Coe, S.D., and M.D. Coe. 1996. p. 16-34. In The true history of chocolate. Thames & Hudson, Ltd., London.
5. Cryer, N.C., M.G.E. Fenn, C.J. Turnbull, and M.J. Wilkinson. 2006. Allelic size standards and reference genotypes to unify international cocoa (Theobroma cacao L.) microsatellite data. Genet. Resour. Crop Evol. Available at: http://dx.doi.org/10.1007/s10722-005-1286-9; verified 18 July 2006.
6. Cuatrecasas, J. 1964. Cacao and its allies. A taxonomic revision of the genus Theobroma. Contrib. U.S. Nat. Herbarium 35(6). Smithsonian Institution, Washington, DC.
7. Evett, I.W., and B.S. Weir. 1998. Interpreting DNA evidence: Statistical genetics for forensic scientists. Sinauer, Sunderland, MA.
8. Griffiths, L.A. 1958. Phenolic acids and flavonoids of Theobroma cacao L. Separation and identification by paper chromatography. Biochem. J. 70:120-125.
9. Hoffman, J.I., and W. Amos. 2005. Microsatellite genotyping errors: Detection approaches, common sources and consequences for paternal exclusion. Mol. Ecol. 14:599-612.
10. John, M.E. 1992. An efficient method for isolation of RNA and DNA from plants containing polyphenolics. Nucleic Acids Res. 20:2381.
11. Kalinowski, S.T., M. Sawaya, and M. Taper. 2006. Individual identification and distributions of genotypic differences between individuals. J. Wildlife Manage. (In press).
12. Katterman, F.R.H., and V.I. Shattuck. 1983. An effective method of DNA isolation from the mature leaves of Gossypium species that contain large amounts of phenolic terpenoids and tannins. Prep. Biochem. 13:347-359.
13. Kennedy, A.J., and V. Mooleedhar. 1993. Conservation of cocoa in field genebanks - The International Cocoa Genebank, Trinidad, p. 21-23. In Proc. Int. Workshop on Conservation, Characterization and Utilization of Cocoa Genetic Resources in the 21st Century. 13-17 Sep. 1992. The University of the West Indies, St. Augustine, Trinidad and Tobago.
14. Lanaud, C., A.M. Risterucci, I. Pieretti, M. Falque, A. Bouet and P.J.L. Lagoda. 1999. Isolation and characterization of microsatellites in Theobroma cacao L. Mol. Ecol. 8:2141-2143.
15. Lanaud, C., J.C. Motamayor, and A.M. Risterucci. 2001. Implications of new insight into the genetic structure of Theobroma cacao L. for breeding strategies. p. 89-107. In Proceedings of the international workshop on new technologies and cocoa breeding. INGENIC, London.
16. Liu, K., and S.V. Muse. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129.
17. Lockwood, C., and M. End. 1993. History, technique and future needs for cacao collection. p. 1-14. In Proc. Int. Workshop on Conservation, Characterization and Utilization of Cocoa Genetic Resources in the 21st Century. 13-17 Sep. 1992. The University of the West Indies, St. Augustine, Trinidad and Tobago.
18. McKelvey, K. S., and M.K. Schwartz. 2004. Genetic errors associated with population estimation using non-invasive molecular tagging: Problems and new solutions. J. Wildlife Manage. 68:439-448.
19. Motamayor, J.C., A.M. Risterucci, P.A. Lopez, C.F. Ortiz, A. Moreno, and C. Lanaud. 2002. Cacao domestication I: The origin of the cacao cultivated by the Mayas. Heredity 89:380-386.
20. Motamayor, J.C., A.M. Risterucci, M. Heath, and C. Lanaud. 2003. Cacao domestication II: Progenitor germplasm of the Trinitario cacao cultivar. Heredity 91:322-30.
21. Paetkau, D. 2003. An empirical exploration of data quality in DNA-based population inventories. Mol. Ecol. 12:1375-1387.
22. Paetkau, D. 2004. The optimal number of markers in genetic capture-mark-recapture studies. J. Wildlife Manage. 68:449-452.
23. Perry, M.D., M.R. Davey, J.B. Power, K.C. Lowe, H.F.J. Bligh, P.S. Roach, and C. Jones. 1998. DNA isolation and AFLP genetic fingerprinting of Theobroma cacao (L.). Plant Mol. Biol. Rep. 16:49-59.
24. Powell, W., M. Morgante, C. Andre, M. Hanafey, J. Vogel, S. Tingey, and A. Rafalski. 1996. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed. 2:225-238.
25. Pugh, T., O. Fouet, A.M. Risterucci, P. Brottier, M. Abouladze, C. Deletrez, B. Courtois, D. Clement, P. Larmande, J.A.K. N'Goran, and C. Lanaud. 2004. A new cacao linkage map based on codominant markers: Development and integration of 201 new microsatellite markers. Theor Appl. Genet. 108:1151-1161.
26. Saunders, J.A., A.A. Hemeida, and S. Mischke. 2001. USDA DNA fingerprinting programme for identification of Theobroma cacao accessions. p. 108-114. In F. Bekele et al (ed.) Proc. Int. Workshop on new technologies and cocoa breeding. Kota Kinabalu, Sabah, Malaysia. 16-17 Oct. 2000. INGENIC Press, London.
27. Saunders, J.A., S. Mischke, E.A. Leamy, and A.A. Hemeida. 2004. Selection of International molecular standard for DNA fingerprinting. Theor. Appl. Genet. 110:41-47.
28. Schnell, R.J., C.T. Olano, J.S. Brown, A.W. Meerow, C. Cervantes-Martinez, C. Nagai, and J.C. Motamayor. 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. 130:181-190.
29. Sounigo, O., Y. Christopher, F. Bekele, V. Mooleedhar, and F. Hosein. 2001. The detection of mislabelled trees in the International Cocoa Genebank, Trinidad (ICG,T) and options for a global strategy for identification of accessions. p. 34-39. In F. Bekele et al (ed.) Proc Int. Workshop on new technologies and cocoa breeding. Kota Kinabalu, Sabah, Malaysia. 16-17 Oct. 2000. INGENIC Press, London.
30. Taberlet, P., S. Griffin, B. Goossens, S. Questiau, V. Manceau, N. Escaravage, L. Waits, J. Bouvet. 1996. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res. 24:3189-3194.
31. Taberlet, P., and G. Luikart. 1999. Non-invasive genetic sampling and individual identification. Biol. J. Linn. Soc. 68:41-55.
32. Turnbull, C.J., D.R. Butler, N.C. Cryer, C. Lanaud, D. Zhang, A.J. Daymond, and P. Hadley. 2004. Tackling mislabelling in cocoa germplasm collections. INGENIC Newsl. 9:8-11.
33. Valière, N. 2002. GIMLET: A computer program for analysing genetic individual identification data. Mol. Ecol. Notes 2:377-379.
34. Valière, N., P. Berthier, D. Mouchiroud, D. Pontier. 2002. GEMINI: Software for testing the effects of genotyping errors and multitube approach for individual identification. Mol. Ecol. Notes 2:83-86.
35. Waits, L.P., G. Luikart, and P. Taberlet. 2001. Estimating the probability of identity among genotypes in natural populations: Cautions and guidelines. Mol. Ecol. 10:249-256.
36. Young, A.M. 1994. The chocolate tree, A natural history of cacao. Smithsonian Institution Press, Washington, DC.