Genetic population structure of cacao plantings within a young production area in Nicaragua

PLoS ONE

Volumn 6, Issue 1, 2011, Pages

  Trognitz, Bodo ^a   Scheldeman, Xavier ^b   Hansel Hohl, Karin ^a   Kuant, Aldo ^c   Grebe, Hans ^c   Hermann, Michael ^d  

^a AIT AUSTRIAN INSTITUTE OF TECHNOLOGY   (Austria)

^b BIOVERSITY INTERNATIONAL   (Italy)

^c Pro Mundo Humano   (Nicaragua)

^d CROPS FOR THE FUTURE   (Malaysia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CACAO; FRUIT; GENETIC DISTANCE; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHY; GERMPLASM; HETEROZYGOSITY; MICROSATELLITE MARKER; NICARAGUA; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PLANT PRODUCT; POPULATION GENETIC STRUCTURE; POPULATION GENETICS; POPULATION STRUCTURE; SIMPLE SEQUENCE REPEAT; BIODIVERSITY; ECONOMICS; FOUNDER EFFECT; GENETICS; TREE;

THEOBROMA CACAO;

MICROSATELLITE DNA;

BIODIVERSITY; CACAO; FOUNDER EFFECT; GENETIC STRUCTURES; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; MICROSATELLITE REPEATS; NICARAGUA; TREES;

EID: 79251553765     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016056     Document Type: Article

References (27)

1. Motamayor JC, Lachenaud P, Wallace da Silva e Mota J, Loor R, Kuhn DN, et al. (2008) Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L). PloS ONE 3(10): e3311. Available: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003311.
2. Motamayor JC, Risterucci AM, Lopez PA, Ortiz CF, Moreno A, et al. (2002) Cacao domestication I: the origin of the cacao cultivated by the Mayas. Heredity 89: 380-386.
3. Motilal LA, Zhang D, Umaharan P, Mischke S, Mooleedhar V, et al. (2009) The relic Criollo cacao in Belize - genetic diversity and relationship with Trinitario and other cacao clones held at the International Cocoa Genebank, Trinidad. Plant Genetic Resources: Characterization and Utilization. doi: 10.1017/S1479262109990232.
4. Motamayor JC, Risterucci AM, Heath M, Lanaud C (2003) Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar. Heredity 91: 322-330.
5. Johnson ES, Bekele FL, Brown SJ, Song Q, Zhang D, et al. (2009) Population structure and genetic diversity of the Trinitario cacao (Theobroma cacao L.) from Trinidad and Tobago. Crop Sci 49: 564-572.
6. Lanaud C, Sounigo O, Amefia YK, Paulin D, Lachenaud P, et al. (1987) Nouvelles données sur la fonctionement du systéme d'incompatibilité du cacaoyer et ses consequences pour la selection. Café Cacao Thé 31(4): 267-277.
7. Merrill T (1994) Pre-Colonial Period. In: Merrill T, ed. Nicaragua: a country study (3rd edition). Washington DC: Library of Congress, Available: http:// lcweb2.loc.gov/frd/cs/nitoc.html#ni0013.
8. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. Intl J Climatol 25: 1965-1978.
9. Kalinowski ST (2004) Counting alleles with rarefaction: Private alleles and hierarchical sampling designs. Conservation Genet 5: 539-543.
10. Peakall R, Smouse PE (2006) GenAlEx 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288-295.
11. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
12. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
13. Pritchard JK, Wen X, Falush D (2010) Documentation for structure software: Version 2.3. Chicago, USA: Univ Chicago. pp 15-17. Available: http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/structure_doc.pdf.
14. Motilal LA, Zhang D, Umaharan P, Mischke S, Boccara M, et al. (2008) Increasing accuracy and throughput in large-scale microsatellite fingerprinting of cacao field germplasm collections. Tropical Plant Biol online 2(1). Available: http://www.springerlink.com/content/120913/?k=Motilal.
15. Zhang D, Mischke S, Johnson ES, Phillips-Mora W, Meinhardt L (2009) Molecular characterization of an international cacao collection using microsatellite markers. Tree Genet & Genomes 5: 1-10.
16. Irish BM, Goenaga R, Zhang D, Schnell R, Brown JS, et al. (2010) Microsatellite fingerprinting of the USDA-ARS Tropical Agriculture Research Station cacao (Theobroma cacao L.) germplasm collection. Crop Sci 50: 656-667.
17. Zhang D, Arevalo-Gardini E, Mischke S, Zún ̃ iga-Cernades L, Barreto-Chavez A, et al. (2006) Genetic diversity and structure of managed and seminatural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali valleys of Peru. Ann Bot, doi: 10.1093/aob/mcl146. Available: http://www.aob.oxfordjournals.org.
18. Zhang D, Mischke S, Goenaga R, Hemeida AA, Saunders JA (2006) Accuracy and reliability of high-throughput microsatellite genotyping for cacao clone identification. Crop Sci 46: 2084-2092.
19. Zhang D, Boccara M, Motilal L, Butler DR, Umaharan P, et al. (2008) Microsatellite variation and population structure in the ''Refractario'' cacao of Ecuador. Conserv Genet 9: 327-337.
20. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
21. Wood GAR, Lass RA (1985) Cocoa. 4th edn. London: Longman. 620 p.
22. Li Y-C, Röder MS, Fahima T, Kirzhner VM, Beiles A, et al. (2002) Climatic effects on microsatellite diversity in wild emmer wheat (Triticum dicoccoides) at the Yehudiyya microsite, Israel. Heredity 89: 127-132.
23. Hübner S, Höffken M, Oren E, Haseneyer G, Stein N, et al. (2009) Strong correlation of wild barley (Hordeum spontaneum) population structure with temperature and precipitation variation. Mol Ecol 18: 1523-1536.
24. Muir G, Fleming CC, Schlötterer Ch (2000) Species status of hybridizing oaks. Nature 405: 1016.
25. 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.
26. MARENA (2005) Atlas de la Reserva de la Biosfera Bosawas. Managua, Nicaragua: Ministerio del Ambiente y los Recursos Naturales (MARENA). 65 p.
27. Risterucci AM, Grivet L, N'Goran JAK, Pieretti I, Flament MH, et al. (2000) A high-density linkage map of Theobroma cacao L. Theor Appl Genet 101: 948-955.