Tree Genetics & Genomes

, 12:116 | Cite as

SSR markers reveal the population structure of Sri Lankan yellow dwarf coconuts (Cocos nucifera L.)

  • L. C. J. Kamaral
  • P. N. Dassanayaka
  • K. L. N. S. Perera
  • S. A. C. N. Perera
Original Article
Part of the following topical collections:
  1. Population structure


World coconut germplasm has been classified broadly as tall and dwarf coconuts based on palm stature. Dwarf coconuts are predominantly self-breeding purelines hypothesised to have derived from tall coconuts. Dwarfs are categorized as yellow, green, red and brown on the colour of epicarp and are important as parents in hybridization of coconuts for desirable traits. Sri Lankan yellow dwarfs (SLYD) were observed to have uncommon phenotypes which were not previously reported for dwarf coconuts in the world, and this study was conducted to elucidate the population structure of SLYD. One hundred and two randomly selected SLYD individuals were categorized into three morphological groups and their genotypes were derived at 30 SSR loci. Genotypic data were analysed in PowerMarker 3.2.5 and Structure 2.3.4 software to derive the genetic diversity and the population structure. Unexpectedly high numbrs of alleles, genotypes, gene diversity and heterozygosity values were recorded for SLYD. Four populations were identified within SLYD under admixture model and their morphological variations were determined. Cross pollination between the dwarf and tall coconut varieties followed by the fixing of alleles by subsequent self-pollination was hypothesised to be the cause for the emergence of new genetic groups within dwarf populations. The study demonstrated the formation of new genotypes upon limited cross pollination of even naturally self-pollinating tree crops. The information will be useful for developing strategies for germplasm conservation, practical coconut breeding and determining the domestication and evolution of dwarf coconuts.


Dwarf coconuts Evolution Genetic diversity Self-pollination Cross pollination 



This research was funded by the National Research Council of Sri Lanka under grant no. 11-042. Authors wish to thank Mrs. W. B. S. Fernando of the Coconut Research Institute of Sri Lanka for assistance provided in extraction of DNA.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

Genotypic data will be submitted to database DRYAD if the manuscript is accepted for publication in the tree genetics and genomes prior to publication.


  1. Anolles GC, Petter MG (1994) Staining nucleic acids with silver: an alternative to radio isotopic and fluorescent labelling. Promega Notes Magazine 45:13Google Scholar
  2. Baudouin L, Lebrun P (2002) The development of a microsatellite kit and dedicated software for use with coconuts. Burotrop bull 17:16–20Google Scholar
  3. Dasanayaka PN, Everard JMDT, Karunanayaka EH, Nanadasa HG (2009) Analysis of coconut (Cocos nucifera L.) diversity using microsatellite markers with emphasis on management and utilization of genetic resources. Journal of National Science Foundation of Sri Lanka 37(2):99–109CrossRefGoogle Scholar
  4. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissues. Focus 12:13–15Google Scholar
  5. Gunn BF, Baudouin L, Olsen KM (2011) Independent origins of cultivated coconut (Cocos nucifera L.) in the old world tropics. PLoS One 6(6):e21143CrossRefPubMedPubMedCentralGoogle Scholar
  6. Hamrick JL, Godt MJW, Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New For 6:95–124CrossRefGoogle Scholar
  7. Lebrun P, Baudouin L, Myrie W, Burger A, Dollet M (2008) Recent lethal yellowing outbreak: why is the Malayan yellow dwarf coconut no longer resistant in Jamaica? Tree Genet Genomes 4(1):125–131CrossRefGoogle Scholar
  8. Liu K, Muse SV (2005) PowerMarker; integrated analysis environment for genetic marker data. Bioinformatics 21(9):2128–2129CrossRefPubMedGoogle Scholar
  9. 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 and Appl Genet 106:715–726CrossRefGoogle Scholar
  10. Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170CrossRefPubMedGoogle Scholar
  11. 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. and Appl. Genet. 96:545–550CrossRefGoogle Scholar
  12. 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 43:15–21CrossRefPubMedGoogle Scholar
  13. Perera L, Russell JR, Provan J, Powell W (2003) Studying genetic relationships among coconut varieties/populations using microsatellite markers. Euphytica 132:121–128CrossRefGoogle Scholar
  14. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  15. 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 42:668–675CrossRefPubMedGoogle Scholar
  16. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138CrossRefGoogle Scholar
  17. Weising K, Kahl G (1997) Hybridization-based microsatellite fingerprinting of plants and fungi. In: Casteno-Anolles G, Gresshoff PM (eds) DNA markers; protocols, applications and overviews. Wiley-VCH, p 27–53Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Coconut Research Institute of Sri LankaLunuwilaSri Lanka
  2. 2.University of Sri JayawardenepuraNugegodaSri Lanka
  3. 3.Genetech Molecular DiagnosticsColombo 08Sri Lanka

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