Population Structure and Molecular Characterization of Nigerian Field Genebank Collections of Cacao, Theobroma cacao L.

AIKPOKPODION, P. O. (2007): Genetic diversity in Nigerian cacao, Theobroma cacao L. collections as revealed by phenotypic and simple sequence repeats marker. PhD Thesis submitted to the University of Ibadan, Nigeria. 147 pp.Search in Google Scholar

AIKPOKPODION, P. O., J. C. MOTAMAYOR, V. O. ADETIMIRIN, Y. ADU-AMPOMAH, I. INGELBRECHT, A. B. ESKES, R. J. SCHNELL and M. KOLESNIKOVA-ALLEN (2009): Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L. collections in West Africa using simple sequence repeats marker. Tree Genetics & Genomes 5: 699-711.10.1007/s11295-009-0221-1Open DOISearch in Google Scholar

ALVERSON, W. S., B. A. WHITLOCK, R. NYFELLER, C. BAYER and D. A. BAUM (1999): Phylogeny of the core Malvales: Evidence from ndhF sequence data. American Journal of Botany 86: 1474-1486.10.2307/2656928Open DOISearch in Google Scholar

ATANDA, O. A. (1975): Assessment of WACRI Series I and II varieties of cocoa in Nigeria. 2. Pod value, butter fat content and flavour assessment. Ghana Journal of Agricultural Science 8: 3-10.Search in Google Scholar

BARTLEY, B. G. D. (2005): The genetic diversity of cacao and its utilization CABI Publishing, United Kingdom 341pp.10.1079/9780851996196.0000Search in Google Scholar

BELKHIR, K., P. BORSA, L. CHIKHI, N. RAUFASTE and F. BONHOMME (2001): GENETIX 4.02, logiciel sous Windows TM pour la génétique des populations, Laboratoire Génome, Populations, Interactions: CNRS UMR. 5,000, Université de Montpellier II, Montpellier, FranceSearch in Google Scholar

BHATTACHARJEE, R., M. KOLSNIKOVA-ALLEN, P. O. AIKPOK - PODION, S. TAIWO and I. INGELBRECHT (2004): An improved semi-automated rapid method of extracting genomic DNA for molecular marker analysis in cocoa, Theobroma cacao L. Plant Molecular Biology Reporter22: 435a-435h.10.1007/BF02772686Open DOISearch in Google Scholar

BOCCARA, M. and D. ZHANG (2006): Progress in resolving identity issues among the Parinari accessions held in Trinidad: the contribution of the collaborative USDA/CRU project. In: Proceedings of the CRU annual report 2005, Cacao Research Unit, The University of the West Indies, St. Augustine, Trinidad and Tobago.Search in Google Scholar

CHEESMAN, E. E. (1944): Notes on nomenclature, classification and possible relationships of cacao populations. Tropical Agriculture 21: 144-159.Search in Google Scholar

CUATRECASAS, J. (1964): Cacao and its allies: A taxonomic revision of the genus Theobroma. Contributions to the U.S. Natural Herbarium 35(6): 379-614.Search in Google Scholar

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. Genetic Resources and Crop Evolution 53: 1643-1652.10.1007/s10722-005-1286-9Search in Google Scholar

EFRON, B. (1982): The jackknife, the bootstrap and other resampling plans. NSF-CBMS Regional Conference Series in Applied Mathematics, Monograph 38. Society for Industrial and Applied Mathematics (SIAM), Philadelphia, Pennsylvania.10.1137/1.9781611970319Search in Google Scholar

EXCOFFIER, L., P. E. SMOUSE and J. M. QUATTRO (1992): Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.10.1093/genetics/131.2.47912050201644282Search in Google Scholar

GOUDET, J. (2001): FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Updated from Goudet (1995) Available from http://www.unilch/izea/softwares/fstat.html.Search in Google Scholar

GUILTINAN, M. J. (2007): Cacao. Biotechnology in Agriculture and Forestry, Vol. 60. In: Transgenic Crops V (ed.Search in Google Scholar

PUA, E. C., DAVEY, M. R.). Springer-Verlag Berlin Heidelberg HAYATI, A., R. WICKNESWARI, I. MAIZURA and N. RAJANAIDU (2004): Genetic diversity in oil palm (Elaeis guineensis Jacq.) germplasm collections from Africa: implications for improvement and conservation of genetic resources. Theoretical and Applied Genetics 108: 1274-1284.10.1007/s00122-003-1545-014676949Search in Google Scholar

HOLM, S. (1979): A simple sequentially rejective multiple test procedure. Scand J. Stat 6: 65-70.Search in Google Scholar

ICCO: INTERNATIONAL COCOA ORGANIZATION (2008): Quarterly Bulletin Cocoa Statistics. Vol. XXXIV. 2007/2008.Search in Google Scholar

JACOBS, V. J., O. A. ATANDA and L. K. OPEKE (1971): Cacao breeding in Nigeria. In: CRIN Commemorative Publication - Progress in Tree Crops Research in Nigeria pp. 9-12.Search in Google Scholar

JAKOBSSON, M. and N. A. ROSENBERG (2007): CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure, Bioinformatics 23: 1801-1806.10.1093/bioinformatics/btm23317485429Open DOISearch in Google Scholar

JOHNSON, E. S., F. L. BEKELE, S. J. BROWN, Q. SONGE, D. ZHANG, L. MEINHARDT and R. J. SCHNELL (2009): Population structure and genetic diversity of the Trinitario cacao (Theobroma cacao L.) from Trinidad and Tobago. Crop Sci 49: 564-572.10.2135/cropsci2008.03.0128Search in Google Scholar

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. Molecular Ecology 8: 2141-2143.10.1046/j.1365-294x.1999.00802.xSearch in Google Scholar

LOCKWOOD, G. and M. M. O. GYAMFI (1979): The CRIG cocoa germplasm collection with notes on codes used in the breeding programme at Tafo and elsewhere. Cocoa Research Institute, Ghana Technical Bulletin No. 10 Tafo.Search in Google Scholar

MARSHALL, T. (1998): CERVUS v.2.0. University of Edinburgh 1998-2001.Search in Google Scholar

MILLER, M. P. (1997): Tools for Population Genetics analysis (TFPGA) version 1.3: a window program for the analysis of allozyme and molecular population genetic data©. Flagstaff Northern Arizona University, Flagstaff, AZ.Search in Google Scholar

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: 380-386.10.1038/sj.hdy.6800156Search in Google Scholar

MOTAMAYOR, J.-C., A. M. RISTERUCCI, M. HEATH and C. LANAUD (2003): Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar. Heredity 91: 322-330.10.1038/sj.hdy.6800298Open DOISearch in Google Scholar

MOTAMAYOR, J.-C., P. LACHENAUD, J. WALLACE, G. LOOR, D. N. KUHN, J. S. BROWN and R. J. SCHNELL II. (2008): Geographic and genetic population differentiation of the Amazonian chocolate tree. PLoS One 3: e3311. doi:10.1007/s12042-008-9011-4Search in Google Scholar

MOTILAL, L. and D. BUTLER (2003): Verification of identities in global cacao germplasm collections. Genet Resour Crop Evol 50: 799-807.10.1023/A:1025950902827Search in Google Scholar

MOTILAL, L., D. ZHANG, P. UMAHARAN, S. MISCHKE, V. MOOLEEDHAR and L. MEINHARDT (2009): 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.10.1017/S1479262109990232Search in Google Scholar

NEI, M. (1978): Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.10.1093/genetics/89.3.583Search in Google Scholar

OHTSUKA, A., M. WATANABE and T. YAHARA (2005): Inbreeding coefficients in six species of Ainsliaea and two species of Pertya (Asteraceae). Plant Syst. Evol. 251: 143-151.Search in Google Scholar

OJO, A. A., J. O. SANWO and E. B. ESAN (1991): Early results of evaluation of Nanay and Parinari Theobroma cacao double cross progenies in Nigeria. Field Crops Research 27: 257-266.10.1016/0378-4290(91)90065-4Open DOISearch in Google Scholar

OLATOYE, S. T. and E. B. ESAN (1992): Recent innovation in cacao genetic resources conservation in Nigeria. In: Proceedings of the International Workshop on Conservation, Characterization and Utilization of Cacao Genetic Resources in the 21st Century. Cocoa Research Unit, Port of Spain, Trinidad 13-17 September, 1992 pp. 281-291.Search in Google Scholar

PEAKALL, R. and P. E. SMOUSE (2006): Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6: 288-295.10.1111/j.1471-8286.2005.01155.xOpen DOISearch in Google Scholar

POSNETTE, A. F. and J. M. A. TODD (1951): Virus diseases of cacao in West Africa. VIII. The search for virus resistant cacao. Annals of Applied Biology 38: 785-800.10.1111/j.1744-7348.1951.tb07850.xOpen DOISearch in Google Scholar

POWELL, W., M. MORGANTE, C. ANDRE, M. HANATEY, J. VOGEL, S. TINGEY and A. RAFALSKI (1996): The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 2: 225-238.10.1007/BF00564200Open DOISearch in Google Scholar

PRITCHARD, J. K., M. STEPHENS and P. DONNELLY (2000): Inference of population structure from multilocus genotype data. Genetics 155: 945-959.10.1093/genetics/155.2.945146109610835412Search in Google Scholar

PUGH, T., O. FOUET, A. M. RISTERUCCI, P. BROTTIER, M. ABOULADZE, C. DELETREZ, B. COURTOIS, D. CLEMENT, P. LARMANDE, J. A. K. NGORAN 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: 1151-1161.10.1007/s00122-003-1533-414760486Search in Google Scholar

PURSEGLOVE, J.W. (1974): Tropical crops, dicotyledons. John Wiley & Sons, New York.Search in Google Scholar

QUENOILLE, M. (1956): Notes on bias in estimation. Biometrika 43: 253-260.Search in Google Scholar

RICE, W. R. (1989): Analyzing tables of statistical tests. Evolution 43: 223-225.28568501Search in Google Scholar

RICE, R. A. and R. GREENBERG (2000): Cacao cultivation and the conservation of biological diversity. Ambio 29(3): 167-173.10.1579/0044-7447-29.3.167Open DOISearch in Google Scholar

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.Search in Google Scholar

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.Search in Google Scholar

SERENO, M., P. P. ALBUQUERQUE, R. VENCOVSKY and A. FIGUERA (2006): Genetic diversity and natural population structure of cacao, Theobroma cacao L. from the Brazilian Amazon evaluated by microsatellite markers. Conservation Genetics 7: 13-24.10.1007/s10592-005-7568-0Search in Google Scholar

SWEIGART, A., K. KAROLY, A. JONES and J. H. WILLIS (1999): The distribution of individual inbreeding coefficients and an pairwise relatedness in a population of Mimulus guttatus. Heredity 83: 625-632.10.1038/sj.hdy.688602010620036Open DOISearch in Google Scholar

TOXOPEUS, H. (1964): F3 Amazon cacao in Nigeria. Rep. Cacao Res. Inst. Nigeria, 1963/64, pp.13-22.Search in Google Scholar

WEIR, B. S. and C. C. COCKERHAM (1984): Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.Search in Google Scholar

WRIGHT, S. (1965): The interpretation of genetic structure by F-statistics with special regard to systems of mating. Evolution 19: 355.10.1111/j.1558-5646.1965.tb01731.xSearch in Google Scholar

ZHANG, D., E. AREVALO, B. MISCHKE, L. ZUNIGA and A. BARRETO (2006a): Genetic diversity and population structure of cocoa, Theobroma cacao L. in the Hullaga and Ucayali valleys of Peru. Annals of Botany 98: 647-655.10.1093/aob/mcl146329205616845139Open DOISearch in Google Scholar

ZHANG, D., E. AREVALO, S. MISCHKE, R. GOENAGA, A. A. HEMEIDA and J. A. SAUNDERS (2006b): Accuracy and reliability of high-throughput microsatellite genotyping for cacao clone identification. Crop Science 46: 2084-2092.10.2135/cropsci2006.01.0004Open DOISearch in Google Scholar

ZHANG, D., M. BOCCARA, L. MOTILAL, D. R. BUTLER, P. UMAHARAN, S. MISCHKE and L. MEINHARDT (2008): Microsatellite variation and population structure in the “refractario” cacao of Equador. Conserv Genet 9: 327-337.10.1007/s10592-007-9345-8Open DOISearch in Google Scholar

ZHANG, D., S. MISCHKE, E. S. JOHNSON, W. PHILLIPS-MORA and L. MEINHARDT (2009): Molecular characterization of an International cocoa collection using microsatellite markers. Tree Genetics & Genomes 5: 1-10.10.1007/s11295-008-0163-zOpen DOISearch in Google Scholar