Genetic diversity of ecuadorian cocoa from the germplasm bank of tenguel-guayas ecuador based in SNP’S
Keywords:
Genetic diversity, germplasm, molecular markers, SNPsAbstract
The genetic diversity and structure of 80 cocoa introductions of Theobroma cacao L. Nacional variety existing in the farm “La Buseta”, Tenguel-Guayas, Ecuador, was studied. The characterization included 19 controls and the use of 96 markers of simple nucleotide polymorphisms (SNPs), in the Fluidigm EP1 system platform. The SNPs showed to be informative, with a mean content of polymorphic information of 0.289, and an average observed heterozygosity of 0.479 and expected heterozygosity of 0.378. The genetic profiles of the introductions were obtained from which 16 groups of identical introductions were identified. The identity probability analysis, including siblings (PIsib), concluded that the SNPs were enough to differentiate the introductions. The average of heterozygosity of the samples was 0.432 being higher in the group F (0.646) and lower in the group P (0.253). The Criollo and Contamana genotyping controls showed greater genetic distance than the Trinitario, Forastero and Ecuadorian Criollo controls. The maximum genetic distance between the introductions was 0.167. The results are consistent with the history of cultivation of the Nacional cacao, which over time received genetic contributions from other varieties. The present study constitutes a significant advance in the knowledge of the genetic diversity of Ecuador's Nacional cacao.
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References
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38. Scheltema, T. 1989. La autoincompatibilidad en los híbridos de cacao del CATIE. San José (Costa Rica): CATIE 43: 1-90.
39. Thomas, E., M. van Zonneveld, J. Loo, T. Hodgkin, G. Galluzzi and J. van Etten. 2012. Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in pleistocene refugia followed by human-influenced dispersal. PLoS One 7(10): 1-17.
40. Wilde, J., R. Waugh and W. Powell. 1992. Genetic fingerprinting of Theobroma clones using randomly amplified polymorphic DNA markers. Theoretical and Applied Genetics 83(6): 871-77.
41. Zapata, Y. 2016. Protocolo para extracción de ADN de cacao. Manual interno del Laboratorio de Genética Molecular y Cultivo de Tejidos. CIAT. Cali, Colombia.
42. Zarrillo, S., N. Gaikwad, C. Lanaud, T. Powis, C. Viot, I. Lesur et al. 2018. The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon. Nature Ecology and Evolution 2(12): 1879-1888.
43. Zhang, D., W. Martínez, E. Johnson, E. Somarriba, W. Phillips-Mora, C. Astorga et al. 2012. Genetic diversity and spatial structure in a new distinct Theobroma cacao L. population in Bolivia. Genetic Resources and Crop Evolution 59(2): 239-52.
2. Asociación Nacional de Exportadores de Cacao e Industrializados del Ecuador. 2010. Cacao Nacional, Un producto emblemático del Ecuador. http://www.anecacao.com/es/quienes-somos/cacao-nacional (retrieved Mar 19, 2019).
3. Argout, X., O. Fouet, P. Wincker, K. Gramacho, T. Legavre, X. Sabau et al. 2008. Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions. BMC Genomics 9(1): 512.
4. Argout, X., J. Salse, J. Aury, M. Guiltinan, G. Droc, J. Gouzy, M. Allegre et al. 2011. The genome of Theobroma cacao. Nature genetics 43(2): 101-8.
5. Arvelo, M., D. Gonzáles, S. Maroto, T. Delgado and P. Montoya. 2017. Manual Técnico del Cultivo de Cacao Prácticas Latinoamericanas. San José Costa Rica: IICA.
6. Beerli, P. 2005. Pairwise distance methods. Computacional Evolucionary Biology, No BSC5936-Fall: 1-7.
7. Cornejo, O., M. Yee, V. Dominguez, M. Andrews, A. Sockell, E. Strandberg and J. Motamayor. 2018. Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process. Communications Biology 1(1): 1-12.
8. Corporation Fluidigm. 2018. Biomark/EP1 Software v4. fluidigm.com/software.
9. Cosme, S., H. Cuevas, D. Zhang, T. Oleksyk and B. Irish. 2016. Genetic diversity of naturalized cacao (Theobroma cacao L.) in Puerto Rico. Tree Genetics and Genomes 12(5): 88.
10. Danial, D. and J. Rojas-Beltran. 2007. Uso de marcadores moleculares en el mejoramiento genético de plantas. Quito-Ecuador: Instituto Nacional de Investigaciones Agropecuarias [INIAP]. 199 p.
11. DuVal, A., S. Gezan, G. Mustiga, D. Livingstone, J. Chaparro, J. Marelli 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: 1-12.
12. Earl, D.A. and B.M. VonHoldt. 2012. Structure Harvester: A website and program for visualizing Structure output and implementing the Evanno method. Conservation Genetics Resources 4(2): 359-361.
13. Fang, W., L. Meinhardt, S. Mischke, C. Bellato, L. Motilal and D. Zhang. 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(2): 481-87.
14. Illic, K., D. Zhang, X. Wang, R. Jones, L. Meinhardt and L. Wang. 2012. Cacao Germplasm Characterization with 48-SNP Genotyping Panel using Fluidigm SNPtypeTM Assays and Dynamic ArrayTM Integrated Fluidic Circuits. San Diego California (https://pag.confex.com/pag).
15. Ji, K., M. Boccara, L. Motilal, D. Zhang, P. Lachenaud and L. Meinhardt. 2012. 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(2): 441-453.
16. Laliberté, B. 2012. A Global Strategy for the Conservation and use of Cacao Genetic Resources, as the Foundation for a Sustainable Cocoa Economy. Bioversity Internacional 66: 186.
17. Lanaud C., O. Fouet, K. Gramacho and X. Argout. 2006. A large EST resource for Theobroma cacao including cDNAs isolated from various organs and under various biotic and abiotic stresses. Proc. 15th International Cocoa Research Conference. pp. 185-191.
18. Lerceteau, E., S. Flipo, J. Quiroz, J. Soria, V. Pétiard and D. Crouzilat. 1997. Genetic differentiation among Ecuadorian Theobroma cacao L. accessions using DNA and morphological analyses. Euphytica 95(1): 77-87.
19. Liu, K. and S. Muse. 2005. PowerMaker: An integrated analysis environment for genetic maker analysis. Bioinformatics 21(9): 2128-2129.
20. Livingstone, D., C. Stack, G. Mustiga, D. Rodezno, C. Suarez, F. Amores 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: 1-18.
21. Lindo, A.A., D. Robinson, P. Tennant, L. Meinhardt and D. Zhang. 2018. Molecular characterization of cacao (Theobroma cacao) germplasm from Jamaica using single nucleotide polymorphism (SNP) markers. Tropical Plant Biology 11(3-4): 93-106.
22. Loor, R., A. Risterucci, B. Courtois, O. Fouet, M. Jeanneau, E. Rosenquist et al. 2009. Tracing the native ancestors of the modern Theobroma cacao L. population in Ecuador. Tree Genetics and Genomes 5(3): 421-33.
23. Mata-Quiroz, A., A. Arciniegas-Leal, W. Phillips-Mora, S. Mischke, A. Mata-Quirós, L. Motilal et al. 2018. Assessing hidden parentage and genetic integrity of the “united fruit clones” of cacao (Theobroma cacao) from Costa Rica using SNP markers. Breeding Science 68(5): 545-53.
24. Michiels, A., W. Ende, M. Tucker and L. Riet. 2003. Extraction of high-quality genomic DNA from latex-containing plants. Analytical Biochemistry 315(1): 85-89.
25. Motamayor, J., P. Lachenaud, J. da Silva e Mota, R. Loor, D. Kuhn, J. Brown and R. Schnell. 2008. Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L.). PLoS One 3(10): 8.
26. Motamayor, J., A. Risterucci, P. Lopez, C. Ortiz, A. Moreno and C. Lanaud. 2002. Cacao domestication I: the origin of the cacao cultivated by the Mayas. Heredity 89(5): 380-86.
27. Motamayor, J., R. Schnell, D. Kuhn, W. Phillips, N. Haiminen, D. Livingstone 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(6): 2-24.
28. Osorio-Guarín, J., R. Yockteng, C. Quintero, Y. Zapata, R. Coronado, G. Gallego-Sánchez and J. Berdugo-Cely. 2017. Colombia a source of cacao genetic diversity as revealed by the population structure analysis of the Germplasm Bank of Theobroma cacao L. Frontiers in Plant Science 8(11): 1-13.
29. Peakall, R. and P. Smouse. 2012. GenALEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28(19): 2537-2539.
30. Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
31. Pound, F. 1945. A note on the cocoa population of South America. Reprinted in 1982 in Arch. Cacao Res. 1: 96-97.
32. Rambaut, A. 2016. FigTree V1.4.2: Tree figure drawing tool. Institute of Evolutionary Biology, University of Edinburgh. http://tree.bio.ed.ac.uk.
33. Reif, J., A. Melchinger and M. Frisch. 2005. Assessing the genetic diversity in crops with molecular markers: theory and experimental results with CIMMYT wheat and maize elite germplasm and genetic resources. Crop Science 45: 1-7.
34. Rogers, J. 1972. Measures of genetic similarity and genetic distance. Studies in genetics. University of Texas Pub. 7213: 145-153.
35. Romero, C., J. Bonilla., E. Santos., E. Peralta and X. Zhong. 2010. Identificación varietal de 41 plantas seleccionadas de cacao (Theobroma cacao L.) provenientes de cuatro cultivares distintos de la región amazónica ecuatoriana, mediante el uso de marcadores microsatélites. Revista Tecnológica 23(1): 121-28.
36. Ruiz, X., M. Almanza, Y. Morillo, A. Morillo, A. Gonzalez, Ä. Caicedo and J. Muñoz. 2015. Comparación genética de tres fuentes del cacao Theobroma cacao L. mediante el uso de marcadores microsatélites. Biotecnología en el Sector Agropecuario 13(1): 10-18.
37. Sánchez-Mora, F., M. Medina-Jara, G Díaz-Coronel, R. Ramos-Remache, J. Vera-Chang, V. Vásquez-Morán et al. 2015. Potencial sanitario y productivo de 12 clones de cacao en Ecuador. Revista Fitotecnia Mexicana 38(3): 265-74.
38. Scheltema, T. 1989. La autoincompatibilidad en los híbridos de cacao del CATIE. San José (Costa Rica): CATIE 43: 1-90.
39. Thomas, E., M. van Zonneveld, J. Loo, T. Hodgkin, G. Galluzzi and J. van Etten. 2012. Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in pleistocene refugia followed by human-influenced dispersal. PLoS One 7(10): 1-17.
40. Wilde, J., R. Waugh and W. Powell. 1992. Genetic fingerprinting of Theobroma clones using randomly amplified polymorphic DNA markers. Theoretical and Applied Genetics 83(6): 871-77.
41. Zapata, Y. 2016. Protocolo para extracción de ADN de cacao. Manual interno del Laboratorio de Genética Molecular y Cultivo de Tejidos. CIAT. Cali, Colombia.
42. Zarrillo, S., N. Gaikwad, C. Lanaud, T. Powis, C. Viot, I. Lesur et al. 2018. The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon. Nature Ecology and Evolution 2(12): 1879-1888.
43. Zhang, D., W. Martínez, E. Johnson, E. Somarriba, W. Phillips-Mora, C. Astorga et al. 2012. Genetic diversity and spatial structure in a new distinct Theobroma cacao L. population in Bolivia. Genetic Resources and Crop Evolution 59(2): 239-52.
Published
2020-05-16
How to Cite
Carranza, M. S., Zapata, Y. P., Gallego, G., Nieto Rodríguez, J., Morante Carriel, J., Cruz Rosero, N., Medina Jara, S., & Muñoz, J. E. (2020). Genetic diversity of ecuadorian cocoa from the germplasm bank of tenguel-guayas ecuador based in SNP’S. Bioagro, 32(2), 75-86. Retrieved from https://revistas.uclave.org/index.php/bioagro/article/view/2691
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