Ambiguous genetic relationships among coconut (Cocos nucifera L.) cultivars: The effects of outcrossing, sample source and size, and method of analysis

Genetic Resources and Crop Evolution

Volumn 57, Issue 2, 2010, Pages 203-217

  Mauro Herrera, Margarita ^a   Meerow, Alan W ^a   Perera, Lalith ^b   Russell, Joanne ^c   Schnell, Raymond J ^a  

^a U S DEPARTMENT OF AGRICULTURE   (United States)

^b Coconut Research Institute ^*  (Sri Lanka)

^c SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

Author keywords

'Atlantic Tall'; 'Panama Tall'; Clustering method; Coconut; Cocos nucifera; Microsatellite DNA; Population structure; Sample size; WRKY

Indexed keywords

CULTIVAR; DNA; DOMESTICATION; GENETIC MARKER; GENETIC STRUCTURE; GENOTYPE; HYBRIDIZATION; OUTCROSSING; POPULATION STRUCTURE; RELATEDNESS;

COCOS NUCIFERA;

EID: 75549084189     PISSN: 09259864     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10722-009-9463-x     Document Type: Article

References (52)

1. Ashburner GR, Thompson WK, Halloran GM (1997) RAPD analysis of South Pacific coconut palm populations. Crop Sci 37: 992-997.
2. Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge, MA.
3. Avise JC (2009) Phylogeography: retrospect and prospect. Journal of Biogeography 36: 3-15.
4. Baudouin L, Lebrun P (2009) Coconut (Cocos nucifera L.) DNA studies support the hypothesis of an ancient Austronesian migration from Southeast Asia to America. Genet Resour Crop Evol 56: 257-262.
5. Baudouin L, Lebrun P, Berger A, Myrie W, Been B, Dollet M (2008) The Panama Tall and the Maypan hybrid coconut in Jamaica: did genetic contamination cause a loss of resistance to lethal yellowing? Euphytica 161: 353-360.
6. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331.
7. Bruman HJ (1944) Some observations on the early history of the coconut in the new world. Acta Americana 2: 220-243.
8. Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Amer J Hum Genet 19: 233-257.
9. Devakumar K, Jayadev K, Rajesh MK, Chandrasekar A, Manimekalai R, Kumaran PM, Parthasarathy VA (2006) Assessment of the genetic diversity of Indian coconut accessions and their relationship to other cultivars, using microsatellite markers. Plant Gen Res Newsletter FAO-Bioversity 145: 38-45.
10. El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree Argania spinosa (L.) Skeels endemic to Morocco. Theor Appl Genet 92: 832-839.
11. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14: 2611-2620.
12. 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.
13. Glaubitz JC (2004) Convert: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol Ecol Notes 4: 309-310.
14. Goudet J (2002) FSTAT (vers. 2. 9. 3. 2), a program to estimate and test gene diversities and fixation indices. Available from http://www.unil.ch/izea/softwares/fstat. html.
15. Harries HC (1977) The cape verde region (1499-1549); the key to coconut culture in the western hemisphere? Turrialba 27: 227-231.
16. Harries HC (1978) The evolution, dissemination and classification of Cocos nucifera L. Bot Rev 44: 265-320.
17. Harries HC (2001) The coconut palm (Cocos nucifera L.). In: Last FT (ed) Tree crop ecosystems. Elsevier, New York, pp 321-338.
18. Harries H, Baudouin L, Cardeña R (2004) Floating, boating and introgression: Molecular techniques and the ancestry of coconut palm populations on Pacific islands. Ethnobotany Res Appl [online] 2: 37-53 http://128.171.206.29/ojs/index.php/era/article/view/36/24.
19. Kalinowski ST (2007) TreeFit, a computer program for evaluating how well evolutionary trees fit genetic distance data. Available for download at http://www.montana.edu/kalinowski/Software/TreeFit2.htm.
20. Langella O (2002) Populations 1. 2. 28: population genetic software (individuals or populations distances, phylogenetic trees). Available from http://www.cnrs-gif.fr/pge.
21. Lebrun P, N'cho YP, Seguin M, Grivet L, Baudouin L (1998) Genetic diversity in coconut (Cocos nucifera L.) revealed by restriction fragment length polymorphism (RFLP) markers. Euphytica 101: 103-108.
22. Lebrun P, Berger A, Hodgkin T, Baudouin L (2005) Biochemical and molecular methods for characterizing coconut diversity. In: Batugal P, Ramanatha R, Oliver J (eds) Coconut genetic resources. International plant genetic resources Institute-regional office for Asia, the Pacific and Oceania (IPGRI-APO). Serdang, Selangor, pp 225-247.
23. Lebrun P, Baudouin L, Myrie W, Berger A, Dollet M (2008) Recent lethal yellowing outbreak: why is the malayan yellow dwarf coconut no longer resistant in Jamaica? Tree Genet Genomes 4: 125-131.
24. Lewis PO, Zaykin D (2001) GENETIC DATA ANALYSIS: computer program for the analysis of allelic data. Version 1. 1. Free program distributed by the authors over the internet from http://hydrodictyon.eeb.uconn.edu/people/plewis/software. php.
25. Liu K, Muse SV (2005) Powermarker: Integrated analysis environment for genetic marker data. Bioinformatics 21: 2128-2129.
26. Manimekalai R, Nagarajan P (2006a) Interrelationships among coconut (Cocos nucifera L.) accessions using RAPD technique. Genet Resour Crop Evol 53: 1137-1144.
27. Manimekalai R, Nagarajan P (2006b) Assessing genetic relationships among coconut (Cocos nucifera L.) accessions using inter simple sequence repeat markers. Sci Hort 108: 49-54.
28. Mauro-Herrera M, Meerow AW, Borrone JW, Kuhn DN, Schnell RJ (2006) Ten informative markers developed from WRKY sequences in coconut (Cocos nucifera). Mol Ecol Notes 6: 904-906.
29. Mauro-Herrera M, Meerow AW, Borrone JW, Kuhn DN, Schnell RJ (2007) Usefulness of WRKY gene-derived markers for assessing genetic population structure: an example with Florida coconut cultivars. Sci Hort 115: 19-26.
30. Meerow AW, Wisser RJ, Brown JS, Kuhn DN, Schnell RJ, Broschat TK (2003) Analysis of genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm using microsatellite DNA, with special emphasis on the Fiji Dwarf cultivar. Theor Appl Genet 106: 715-726.
31. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York.
32. Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19: 153-170.
33. Perera L, Russell JR, Provan J, McNicol JW, Powell W (1998) Evaluating genetic relationships between indigenous coconut (Cocos nucifera L.) accessions from Sri Lanka by means of AFLP profiling. Theor Appl Genet 96: 545-550.
34. Perera L, Russell JR, Provan J, Powell W (1999) Identification and characterization of microsatellite loci in coconut (Cocos nucifera L.) and the analysis of coconut populations in Sri Lanka. Mol Ecol Notes 8: 344-346.
35. Perera L, Russell JR, Provan J, Powell W (2000) Use of microsatellite DNA markers to investigate the level of genetic diversity and population genetic structure of coconut (Cocos nucifera L.). Genome 43: 15-21.
36. Perera L, Russell JR, Provan J, Powell W (2003) Studying genetic relationships among coconut varieties/populations using microsatellite markers. Euphytica 132: 121-128.
37. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12: 844-855.
38. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
39. Purseglove JW (1985) Tropical crops: monocotyledons, 5th edn. Longman, London.
40. Rivera R, Edwards KJ, Barker JHA, Arnold GM, Ayad G, Hodgkin T, Karp A (1999) Isolation and characterization of polymorphic microsatellites in Cocos nucifera L. Genome 42: 668-675.
41. Rohde W, Kullaya A, Rodriguez J, Ritter E (1995) Genome analysis of Cocos nucifera L. by PCR amplification of spacer sequences separating a subset of copia-like EcoR1 repetitive elements. J Genet Breed 49: 179-186.
42. Rosenberg NA (2004) Distruct: a program for the graphical display of population structure. Mol Ecol Notes 4: 137-138.
43. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
44. Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. WH Freeman, San Francisco.
45. Takezaki N, Nei M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144: 389-399.
46. Teulat B, Aldam C, Trehin R, Lebrun P, Barker JHA, Arnold GM, Karp A, Baudouin L, Rognon F (2000) An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence-tagged microsatellites (SSRs) and AFLPs. Theor Appl Genet 100: 764-771.
47. Upadhyay A, Jayadev K, Manimekalai R, Parthasarathy VA (2004) Genetic relationship and diversity in Indian coconut accessions based on RAPD markers. Sci Hort 99: 353-362.
48. van den Berg RG, Jacobs MMJ (2007) Molecular taxonomy. In: Vreugdenhil D (ed) Potato biology and biotechnology. Elsevier, New York, pp 55-76.
49. Whitehead RA (1965) Speed of germination, a characteristic of possible taxonomic significance in Cocos nucifera L. Trop Agric (Trinidad) 42: 369-372.
50. Whitehead RA (1966) Sample survey and collection of coconut germplasm in the Pacific Islands (30 May-5 September 1964). Ministry of Overseas Development, HMSO, London.
51. Whitehead RA (1976) Coconut. In: Simmonds NW (ed) Evolution of crop plants. Longman, London, pp 221-225.
52. Zizumbo-Villarreal D, Ruiz-Rodriguez M, Harries H, Colunga-GarcíaMarín P (2006) Population genetics, lethal yellowing disease, and relationships among Mexican and imported coconut ecotypes. Crop Sci 46: 2509-2516.