Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Biologia

12 Issues per year


IMPACT FACTOR 2016: 0.759
5-year IMPACT FACTOR: 0.803

CiteScore 2016: 0.85

SCImago Journal Rank (SJR) 2016: 0.300
Source Normalized Impact per Paper (SNIP) 2016: 0.476

Online
ISSN
1336-9563
See all formats and pricing
More options …
Volume 63, Issue 2 (Apr 2008)

Issues

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

Rajinder Singh
  • Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Noorhariza Zaki
  • Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Ngoot-Chin Ting
  • Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Rozana Rosli
  • Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Soon-Guan Tan / Eng-Ti Low
  • Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Maizura Ithnin
  • Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Suan-Choo Cheah
  • Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2008-03-27 | DOI: https://doi.org/10.2478/s11756-008-0041-z

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.

Keywords: oil palm; EST-SSR; germplasm

  • [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. CrossrefGoogle 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. http://dx.doi.org/10.1007/s00122-006-0440-xWeb of ScienceCrossrefGoogle 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. http://dx.doi.org/10.1093/nar/gkl986CrossrefGoogle 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. http://dx.doi.org/10.1139/gen-44-3-413CrossrefGoogle 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. Google 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. http://dx.doi.org/10.1007/s10722-003-6112-7CrossrefGoogle 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. Google 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. CrossrefGoogle 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. http://dx.doi.org/10.1007/s00122-003-1545-0CrossrefGoogle 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. http://dx.doi.org/10.1146/annurev.es.15.110184.000433CrossrefGoogle 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. http://dx.doi.org/10.1007/s10722-004-4004-0CrossrefGoogle 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. http://dx.doi.org/10.1093/jhered/esl031CrossrefGoogle Scholar

  • [18] Manimekalai R. & Nagarajan P. 2006. Interrelationships among coconut (Cocos nucifera L.) accessions using RAPD technique. Genet. Res. Crop Evol. 53: 1137–1144. http://dx.doi.org/10.1007/s10722-005-1303-zCrossrefGoogle 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. http://dx.doi.org/10.1101/gr.9.11.1143CrossrefGoogle Scholar

  • [21] Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individual. Genetics 89: 583–590. Google 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. http://dx.doi.org/10.1016/S0168-9525(00)02024-2CrossrefGoogle 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. http://dx.doi.org/10.1007/s002990050339CrossrefGoogle Scholar

  • [27] Rozen S. & Skaletsky H. 2000. Primer3 on the www for general users and for biologist programmers. Methods Mol. Biol. 132: 365–386. Google 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. http://dx.doi.org/10.1007/s00122-004-1742-5CrossrefGoogle 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. http://dx.doi.org/10.1007/BF00223710CrossrefGoogle 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. http://dx.doi.org/10.1007/s001220051342CrossrefGoogle 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. Google 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. http://dx.doi.org/10.1016/j.plantsci.2007.08.010Web of ScienceCrossrefGoogle Scholar

  • [35] Varshney R.K., Sorrells M.E. & Graner A. 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23: 48–55. http://dx.doi.org/10.1016/j.tibtech.2004.11.005CrossrefGoogle 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. Google 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. CrossrefGoogle 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. http://dx.doi.org/10.1007/s00122-006-0304-4CrossrefGoogle Scholar

About the article

Published Online: 2008-03-27

Published in Print: 2008-04-01


Citation Information: Biologia, ISSN (Online) 1336-9563, ISSN (Print) 0006-3088, DOI: https://doi.org/10.2478/s11756-008-0041-z.

Export Citation

© 2008 Slovak Academy of Sciences. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

[2]
Eng-Ti L. Low, Rozana Rosli, Nagappan Jayanthi, Ab Halim Mohd-Amin, Norazah Azizi, Kuang-Lim Chan, Nauman J. Maqbool, Paul Maclean, Rudi Brauning, Alan McCulloch, Roger Moraga, Meilina Ong-Abdullah, Rajinder Singh, and Gen Hua Yue
PLoS ONE, 2014, Volume 9, Number 1, Page e86728
[3]
Alireza Valdiani, Daryush Talei, Surrinder K. Lattoo, Rodomiro Ortiz, Søren Kjærsgaard Rasmussen, Jacqueline Batley, Mohd Yusop Rafii, Mahmood Maziah, Kallevettankuzhy K. Sabu, Rambod Abiri, Suchirat Sakuanrungsirikul, and Soon Guan Tan
Critical Reviews in Biotechnology, 2017, Volume 37, Number 6, Page 803
[4]
Carlos Felipe González Chavarro, Marlon Eduardo León Lozano, Ana Cruz Morillo Coronado, Erick Iván Ochoa, and Yacenia Morillo Coronado
Acta Agronómica, 2016, Volume 65, Number 3, Page 276
[5]
Maxwell N. Okoye, Michael I. Uguru, Claude Bakoumé, Rajinder Singh, and Christy O. Okwuagwu
American Journal of Plant Sciences, 2016, Volume 07, Number 01, Page 218
[7]
Qian Ding, Jingjuan Li, Fengde Wang, Yihui Zhang, Huayin Li, Jiannong Zhang, and Jianwei Gao
International Journal of Genomics, 2015, Volume 2015, Page 1
[8]
May Lee, Jun Hong Xia, Zhongwei Zou, Jian Ye, Rahmadsyah, Yuzer Alfiko, Jingjing Jin, Jessica Virginia Lieando, Maria Indah Purnamasari, Chin Huat Lim, Antonius Suwanto, Limsoon Wong, Nam-Hai Chua, and Gen Hua Yue
Scientific Reports, 2015, Volume 5, Number 1
[9]
Emad Omer Hama-Ali, Sharifah Shahrul Rabiah Syed Alwee, Soon Guan Tan, Jothi Malar Panandam, Ho Chai Ling, Parameswari Namasivayam, and Hoh Boon Peng
Molecular Biology Reports, 2015, Volume 42, Number 5, Page 917
[10]
C. Bakoumé, R. Wickneswari, S. Siju, N. Rajanaidu, A. Kushairi, and N. Billotte
Genetic Resources and Crop Evolution, 2015, Volume 62, Number 3, Page 349
[11]
Noorhariza Mohd Zaki, Rajinder Singh, Rozana Rosli, and Ismanizan Ismail
International Journal of Molecular Sciences, 2012, Volume 13, Number 12, Page 4069
[12]
Diana Arias, Iván Ochoa, Fernando Castro, and Hernán Romero
Plant Genetic Resources, 2014, Volume 12, Number 03, Page 341
[13]
Diana Arias, Carmenza Montoya, and Hernán Romero
Plant Genetic Resources, 2013, Volume 11, Number 02, Page 140
[15]
Chatchawan Jantasuriyarat, Savitree Ritchuay, Pawat Pattarawat, Pattana Srifah Huehne, and Sureeporn Kate-Ngam
Biochemical Systematics and Ecology, 2012, Volume 45, Page 57
[16]
Xia Lu, Hongxia Wang, Baozhong Liu, and Jianhai Xiang
Marine Biotechnology, 2013, Volume 15, Number 1, Page 16
[17]
Timothy Tranbarger, Wanwisa Kluabmongkol, Duangjai Sangsrakru, Fabienne Morcillo, James W Tregear, Somvong Tragoonrung, and Norbert Billotte
BMC Plant Biology, 2012, Volume 12, Number 1, Page 1
[18]
Estelle Jaligot, Sophie Adler, Émilie Debladis, Thierry Beulé, Frédérique Richaud, Pascal Ilbert, E. Jean Finnegan, and Alain Rival
Annals of Botany, 2011, Volume 108, Number 8, Page 1453
[19]
Jernej Jakse, Natasa Stajner, Zlata Luthar, Jean-Marc Jeltsch, and Branka Javornik
Molecular Breeding, 2011, Volume 28, Number 2, Page 227
[20]
Ngoot-Chin Ting, Noorhariza Mohd Zaki, Rozana Rosli, Eng-Ti Leslie Low, Maizura Ithnin, Suan-Choo Cheah, Soon-Guan Tan, and Rajinder Singh
Journal of Genetics, 2010, Volume 89, Number 2, Page 135

Comments (0)

Please log in or register to comment.
Log in