Advertisement

Biologia

, Volume 63, Issue 2, pp 227–235 | Cite as

Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity

  • Rajinder SinghEmail author
  • Noorhariza Mohd Zaki
  • Ngoot-Chin Ting
  • Rozana Rosli
  • Soon-Guan Tan
  • Eng-Ti Leslie Low
  • Maizura Ithnin
  • Suan-Choo Cheah
Full Paper

Abstract

A total of 5,521 expressed sequence tags (ESTs) from oil palm were used to search for type and frequency of simple sequence repeat (SSR) markers. Dimeric repeat motifs appeared to be the most abundant, followed by tri-nucleotide repeats. Redundancy was eliminated in the original EST set, resulting in 145 SSRs in 136 unique ESTs (114 singletons and 22 clusters). Primers were designed for 94 (69.1%) of the unique ESTs (consisting of 14 consensus and 80 singletons). Primers for 10 EST-SSRs were developed and used to evaluate the genetic diversity of 76 accessions of oil palm originating from seven countries in Africa, and the standard Deli dura population. The average number of observed and effective alleles was 2.56 and 1.84, respectively. The EST-SSR markers were found to be polymorphic with a mean polymorphic information content value of 0.53. Genetic differentiation (F ST) among the populations studied was 0.2492 indicating high level of genetic divergence. Moreover, the UPGMA (unweighted pair-group method with arithmetic mean) analysis revealed a strong association between genetic distance and geographic location of the populations studied. The germplasm materials exhibited higher diversity than Deli dura, indicating their potential usefulness in oil palm improvement programmes. The study also revealed that the populations from Nigeria, Congo and Cameroon showed the highest diversity among the germplasm evaluated in this study. The EST-SSRs further demonstrated their worth as a new source of polymorphic markers for phylogenetic analysis, since a high percentage of the markers showed transferability across species and palm taxa.

Key words

oil palm EST-SSR germplasm 

Abbreviations

EST

expressed sequence tags

MPOB

Malaysian Palm Oil Board

PIC

polymorphic information content

RAPD

random amplified polymorphic DNA

RFLP

restriction fragment length polymorphism

SSR

simple sequence repeat

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Anderson J.A., Churchill G.A., Autrique J.E., Tanksley S.D. & Sorrells M.E. 1993. Optimizing parental selection for genetic linkage maps. Genome 36: 181–186.Google Scholar
  2. Aggarwal R.K., Hendre P.S., Varshney R.K., Bhat P.R., Krishnakumar V. & Singh L. 2007. Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor. Appl. Genet. 114: 359–372.PubMedCrossRefGoogle Scholar
  3. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J. & Wheeler D.L. 2007. GenBank. Nucleic Acids Res. 35(Database Issue): D21–D25.CrossRefGoogle Scholar
  4. Bakoume C.R. 2006. Genetic diversity of natural oil palm (Elaeis guineensis Jacq.) populations using microsatellite markers. PhD. Thesis, Universiti Kebangsaan Malaysia, Kuala Lumpur.Google Scholar
  5. Billotte N., Risterucci A.M., Barcelos E., Noyer J.L., Amblard P. & Baurens F.C. 2001. Development, characterisation, and across-taxa utility of oil palm (Elaeis guineensis Jacq.) microsatellite markers. Genome 44: 413–425.PubMedCrossRefGoogle Scholar
  6. Cardle L., Ramsay L., Milbourne D., Macaulay M., Marshall D. & Waugh R. 2000. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156: 847–854.PubMedGoogle Scholar
  7. Chabane K., Ablett G.A., Cordeiro G.M., Valkoun J. & Henry R.J. 2005. EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley. Genet. Resour. Crop Evol. 52: 903–909.CrossRefGoogle Scholar
  8. Doyle J.J. & Doyle J.L. 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13–15.Google Scholar
  9. Ewing B. & Green P. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8: 186–194.PubMedGoogle Scholar
  10. Ewing B., Hillier L., Wendl M.C. & Green P. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8: 175–185.PubMedGoogle Scholar
  11. Hamrick J.L. & Godt M.J.W. 1989. Allozyme diversity in plant species, pp. 43–63. In: Brown A.H.D, Clegg M.J, Kahler A.L & Weir B.S (eds), Plant Population Genetics, Breeding and Genetic Resources, Sinauer Associates Inc., Sunderland.Google Scholar
  12. Hartley C.W.S. 1988. The Oil Palm (Elaeis guineensis Jacq.). Longman Scientific and Technical Publication, New York, 761 pp.Google Scholar
  13. Hayati A., Wickneswari R., Maizura I. & Rajanaidu N. 2004. Genetic diversity of oil palm (Elaeis guineensis Jacq.) germplasm collections from Africa: implications for improvement and conservation of genetic resources. Theor. Appl. Genet. 108: 274–1284.CrossRefGoogle Scholar
  14. Kularatne R.S. 2000. Assessment of genetic diversity in natural oil palm (Elaeis guineensis Jacq.) populations using amplified fragment length polymorphism markers. PhD. Thesis, Universiti Kebangsaan Malaysia, Kuala Lumpur.Google Scholar
  15. Loveless M.D. & Hamrick, J.L. 1984. Ecological determinants of genetic structure in plant population. Annu. Rev. Ecol. Syst. 15: 65–95.CrossRefGoogle Scholar
  16. Maizura I., Rajanaidu N., Zakri A.H. & Cheah S.C. 2006. Assessment of genetic diversity in oil palm (Elaeis guineensis Jacq.) using Restriction Fragment Length Polymorphism (RFLP). Genet. Res. Crop Evol. 53: 187–195.CrossRefGoogle Scholar
  17. Mantovani A., Morellato L.P.C. & Reis M.S. 2006. Internal genetic structure and outcrossing rate in natural population of Araucaria angustifolia (Bert) O. Kuntze. J. Hered. 97: 466–472.CrossRefGoogle Scholar
  18. Manimekalai R. & Nagarajan P. 2006. Interrelationships among coconut (Cocos nucifera L.) accessions using RAPD technique. Genet. Res. Crop Evol. 53: 1137–1144.CrossRefGoogle Scholar
  19. Maria M., Clyde M.M. & Cheah S.C. 1995. Cytological analysis of Elaeis guineensis (tenera) chromosomes. Elaeis 7: 122–134.Google Scholar
  20. Miller R.T., Christoffels A.G., Gopalakrishnan C., Burke J., Ptitsyn A.A., Broveak T.R. & Hide W.A. 1999. A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res. 9: 1143–1155.PubMedCrossRefGoogle Scholar
  21. Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individual. Genetics 89: 583–590.PubMedGoogle Scholar
  22. Purseglove J.W. 1972. Tropical Crops, Monocotyledons. London, Longman, 607 pp.Google Scholar
  23. Rajanaidu N. 1985. The oil-palm (Elaeis guineensis) collections in Africa, pp 59–83. In: International Workshop on Oil Palm Germplasm and Utilization, PORIM, Bangi, Selangor, Malaysia.Google Scholar
  24. Rajanaidu N. & Jalani B.S. 1994. Oil palm genetic resources — collection, evaluation, utilization and conservation. In: PORIM Colloquium on Oil Palm Genetic Resources, 13 September 1994, PORIM, Bangi, Malaysia.Google Scholar
  25. Rice P., Longden I. & Bleasby A. (2000) EMBOSS: the European molecular biology open software suite. Trends Genet. 16: 276–277.PubMedCrossRefGoogle Scholar
  26. Rival A., Beule T., Barre P., Hamon S., Duval Y. & Noirot M. 1997. Comparative flow cytometric estimation of nuclear DNA content in oil palm (Elaeis guineensis, Jacq.) tissue cultures and seed derived plants. Plant Cell Reports 16: 884–887.CrossRefGoogle Scholar
  27. Rozen S. & Skaletsky H. 2000. Primer3 on the www for general users and for biologist programmers. Methods Mol. Biol. 132: 365–386.PubMedGoogle Scholar
  28. Rungis D., Berube Y., Zhang J., Ralph S., Ritland C.E., Ellis B.E., Douglas C., Bohlmann J. & Ritland K. 2004. Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags. Theor. Appl. Genet. 109: 1283–1294.PubMedCrossRefGoogle Scholar
  29. Shah F.H., Rasid O., Simons A.J. & Dunsdon A. 1994. The utility of RAPD markers for the determination of genetic variation in oil palm (Elaeis guineensis). Theor. Appl. Genet. 89: 713–718.CrossRefGoogle Scholar
  30. Sneath P.H.A. & Sokal R.R. 1973. Numerical Taxonomy: The Principles and Practice of Numerical Classification. Freeman, San Francisco, CA.Google Scholar
  31. Soltis D.E. & Soltis P.S. 1989. Polyploidy, breeding systems and genetic differentiation in homosporous pteridophytes, pp. 241–258. In: Soltis D.E & Soltis P.S. (eds), Isozymes in Plant Biology, Dioscorides Press, Portland, Ore.Google Scholar
  32. Temnykh S., Park W.D., Ayres N., Cartinhour S., Hauck N., Lipovich L., Cho Y.G., Ishii T. & McCouch S.R. 2000. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100: 698–712.CrossRefGoogle Scholar
  33. Thiel T., Michalek W., Varshney R.K. & Graner A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106: 411–422.PubMedGoogle Scholar
  34. Varshney R.K., Chabane K., Hendre P.S., Aggrawal R.K. & Graner A. 2007. Comparative assessment of EST-SSR, ESTSNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci. 173: 638–649.CrossRefGoogle Scholar
  35. Varshney R.K., Sorrells M.E. & Graner A. 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23: 48–55.PubMedCrossRefGoogle Scholar
  36. Varshney R.K., Thiel T., Stein N., Langridge P. & Graner A. 2002. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell. Mol. Biol. Lett. 7: 537–546.PubMedGoogle Scholar
  37. Wang H.Y., Wei Y.M., Yan Z.H. & Zheng Y.L. 2007. EST-SSR DNA polymorphism in durum wheat (Triticum durum L.) collections. J. Appl. Genet. 48: 35–42.PubMedGoogle Scholar
  38. Yeh F.C & Boyle T. 1999. Popgene version 1.32. The user-friendly software for population genetic analysis. University of Alberta and CIFOR, Calgary.Google Scholar
  39. Zeven A.C. 1967. The semi-wild oil palm and its industry in Africa. Agricultural Research Report 698. Agricultural University, Wageningen, The Netherlands.Google Scholar
  40. Zhang L.Y., Ravel C., Bernard M., Balfourier F., Leroy P., Feuillet C. & Sourdille P. 2006. Transferable bread wheat EST-SSRs can be useful for phylogenetic studies among Triticeae species. Theor. Appl. Genet. 113: 407–418.PubMedCrossRefGoogle Scholar

Copyright information

© Versita 2008

Authors and Affiliations

  • Rajinder Singh
    • 1
    Email author
  • Noorhariza Mohd Zaki
    • 1
  • Ngoot-Chin Ting
    • 1
  • Rozana Rosli
    • 1
  • Soon-Guan Tan
    • 2
  • Eng-Ti Leslie Low
    • 1
  • Maizura Ithnin
    • 1
  • Suan-Choo Cheah
    • 1
  1. 1.Advanced Biotechnology and Breeding CentreMalaysian Palm Oil Board (MPOB)Kuala LumpurMalaysia
  2. 2.Biology Department, Faculty of ScienceUniversity Putra MalaysiaUPM SerdangMalaysia

Personalised recommendations