Back Article

Cope FW. 1984. Cacao Theobroma cacao (Sterculiaceae). In Evolution of Crop Plants, ed. SimmondsNW. London, UK: Longman. pp. 285–89

Bartley BGD. 2005. The genetic diversity of cacao and its utilization. Wallingford: CABI https://doi.org/10.1079/9780851996196.0000

Zarrillo S, Gaikwad N, Lanaud C, Powis T, Viot C, et al. 2018. The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon. Nature Ecology & Evolution 2:1879−88

ICCO. 2021. ICCO Quarterly Bulletin of Cocoa Statistics, Vol. XLVII, No. 2, Cocoa year 2020/21. https://www.icco.org/statistics/#tab-id-1

Whitlock BA, Baum DA. 1999. Phylogenetic relationships of Theobroma and Herrania (Sterculiaceae) based on sequences of the nuclear gene Vicilin. Systematic Botany 24:128

Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, et al. 2011. The genome of Theobroma cacao. Nature Genetics 43:101−8

Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, Livingstone D, et al. 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biology 14:r53

Cheesman EE. 1932. The economic botany of cacao. A critical survey of the literature to the end of 1930. Tropical. Agriculture. 9:16 pp

Cuatrecasas J. 1964. Cacao and its allies. A taxonomic revision of the genus Theobroma. Contributions from the United States National Herbarium 35:379−605

Motamayor JC, Lachenaud P, da Silva E Mota JW, Loor R, Kuhn DN, et al. 2008. Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L). PLoS ONE 3:e3311

Motamayor JC, Lachenaud P, Da Silva E Mota JW, Loor RG, Martinez WJ, et al. 2010. No mas forastero: a new protocol for meaningful cacao germplasm classification. Proc. 16th International Cocoa Research Conference, Bali, Indonesia. 2010: 179−85. Indonesia: Cocoa Producers' Alliance

Zhang D, Martínez WJ, Johnson ES, Somarriba E, Phillips-Mora W, et al. 2012. Genetic diversity and spatial structure in a new distinct Theobroma cacao L. population in Bolivia. Genetic Resources and Crop Evolution 59:239−52

Motilal L, Butler D. 2003. Verification of identities in global cacao germplasm collections. Genetic Resources and Crop Evolution 50:799−807

Olasupo FO, Adewale DB, Aikpokpodion PO, Muyiwa AA, Bhattacharjee R, et al. 2018. Genetic identity and diversity of Nigerian cacao genebank collections verified by single nucleotide polymorphisms (SNPs): a guide to field genebank management and utilization. Tree Genetics & Genomes 14:32

Padi FK, Ofori A, Takrama J, Djan E, Opoku SY, et al. 2015. The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao. Tree Genetics & Genomes 11:44

DuVal A, Gezan SA, Mustiga G, Stack C, Marelli JP, et al. 2017. Genetic parameters and the impact of off-types for Theobroma cacao L. in a breeding program in Brazil. Frontiers in Plant Science 8:2059

Cornejo OE, Yee MC, Dominguez V, Andrews M, Sockell A, et al. 2018. Population genomic analyses of the chocolate tree,Theobroma cacao L., provide insights into its domestication process. Communications Biology 1:167

Hämälä T, Wafula EK, Guiltinan MJ, Ralph PE, dePamphilis CW, et al. 2021. Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree. PNAS 118:e2102914118

Livingstone D, Royaert S, Stack C, Mockaitis K, May G, et al. 2015. Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao. DNA Research 22:279−91

Livingstone D, Stack C, Mustiga GM, Rodezno DC, Suarez C, et al. 2017. A larger chocolate chip − development of a 15K Theobroma cacao L. SNP array to create high-density linkage maps. Frontiers in Plant Science 8:2008

Turnbull CJ, Hadley P. 2021. International Cocoa Germplasm Database (ICGD). CRA Ltd./ICE Futures Europe/University of Reading, UK.

Livingstone DS, Motamayor JC, Schnell RJ, Cariaga K, Freeman B, et al. 2011. Development of single nucleotide polymorphism markers in Theobroma cacao and comparison to simple sequence repeat markers for genotyping of Cameroon clones. Molecular Breeding 27:93−106

Takrama J, Kun J, Meinhardt L, Mischke S, Opoku SY, et al. 2014. Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers. African Journal of Biotechnology 13:2127−36

Dadzie AM, Livingstone DS, Opoku SY, Takrama J, Padi F, et al. 2013. Conversion of microsatellite markers to single nucleotide polymorphism (SNP) markers for genetic fingerprinting of Theobroma cacao L. Journal of Crop Improvement 27:215−41

Fang W, Meinhardt LW, Mischke S, Bellato CM, Motilal L, et al. 2014. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication. Journal of Agricultural and Food Chemistry 62:481−87

Ji K, Zhang D, Motilal LA, Boccara M, Lachenaud P, et al. 2013. Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by single nucleotide polymorphism (SNP) markers. Genetic Resources and Crop Evolution 60:441−53

Li Y, Zhang D, Motilal LA, Lachenaud P, Mischke S, et al. 2021. Traditional varieties of cacao (Theobroma cacao) in Madagascar: their origin and dispersal revealed by SNP markers. Beverage Plant Research 1:4

Mahabir A, Motilal LA, Gopaulchan D, Ramkissoon S, Sankar A, et al. 2019. Development of a core SNP panel for cacao (Theobroma cacao L.) identity analysis. Genome 63:103−14

Takrama J, Dadzie AM, Opoku SY, Padi FK, Adomako B, et al. 2012. Applying SNP marker technology in the cacao breeding programme in Ghana. African Crop Science Journal 20:67−75

Wang B, Motilal LA, Meinhardt LW, Yin J, Zhang D. 2020. Molecular characterization of a cacao germplasm collection maintained in Yunnan, China using single nucleotide polymorphism (SNP) markers. Tropical Plant Biology 13:359−70

Mata-Quirós A, Arciniegas-Leal A, Phillips-Mora W, Meinhardt L, Zhang D. 2017. Understanding the genetic structure and parentage of the clonal series of cacao UF, CC, PMCT and ARF preserved in the International Cacao Collection at CATIE (IC3). Proc. International Symposium on Cocoa Research (ISCR), Lima, Peru. pp. 13−17

Gutiérrez OA, Puig AS, Phillips-Mora W, Bailey BA, Ali SS, et al. 2021. SNP markers associated with resistance to frosty pod and black pod rot diseases in an F1 population ofTheobroma cacao L. Tree Genetics & Genomes 17:28

Peakall R, Smouse PE. 2006. GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6:288−95

Peakall R, Smouse PE. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research − an update. Bioinformatics 28:2537−39

Golden Helix, Inc. 2021. SNP & Variation Suite^TM. Bozeman, MT, USA.

Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567−87

Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945−59

Pritchard JK, Wen X, Falush D. 2010. Documentation for structure software: Version 2. 3

Li Y, Liu J. 2018. StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods. Molecular Ecology Resources 18:176−77

Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14:2611−20

Puechmaille SJ. 2016. The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem. Molecular Ecology Resources 16:608−27

Jakobsson M, Rosenberg NA. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801−6

Rosenberg NA. 2004. DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes 4:137−38

Nei M. 1972. Genetic distance between populations. The American Naturalist 106:283−92

Dieringer D, Schlötterer C. 2003. Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes 3:167−69

Sokal RR, Michener CD. 1958. A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin 38:1409−38

Felsenstein J. 1989. PHYLIP - phylogeny inference package, (version 3.2). Cladistics 5:164−66

Rambaut A. 2014. FigTree-v1.4.2. A graphical viewer of phylogenetic trees. http://tree.bio.ed.ac.uk/software/figtree2014

Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479−91

Kalinowski ST. 2011. The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure. Heredity 106:625−32

Arevalo-Gardini E, Meinhardt LW, Zuñiga LC, Arévalo-Gardni J, Motilal L, et al. 2019. Genetic identity and origin of "Piura Porcelana" − a fine-flavored traditional variety of cacao (Theoborma cacao) from the Peruvian Amazon. Tree Genetics & Genomes 15:11

Zhang D, Motilal L. 2016. Origin, Dispersal, and Current Global Distribution of Cacao Genetic Diversity. In Cacao Diseases: A History of Old Enemies and New Encounters, ed. Bailey BA, Meinhardt LW. Switzerland: Springer, Cham. pp. 3−31 https://doi.org/10.1007/978-3-319-24789-2_1