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Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.)

Chai-Ling Ho1*, Yen-Yen Kwan19, Mei-Chooi Choi17, Sue-Sean Tee1, Wai-Har Ng111, Kok-Ang Lim1, Yang-Ping Lee110, Siew-Eng Ooi2, Weng-Wah Lee13, Jin-Ming Tee18, Siang-Hee Tan14, Harikrishna Kulaveerasingam15, Sharifah Shahrul Rabiah Syed Alwee26 and Meilina Ong Abdullah2

Author Affiliations

1 Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia

2 Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), 6 Persiaran Institusi, Bandar Baru Bangi, Selangor, Malaysia

3 KOOPrime Technologies (M) Sdn Bhd, 729, Block B, Jalan PJS 8/5, Mentari Business Park, Dataran Mentari, 46150 Petaling Jaya, Selangor, Malaysia

4 Sime Plantations Sdn. Bhd., Wisma CONSPLANT 1, 2, Jalan SS 16/4, 47500 Subang Jaya, Selangor, Malaysia

5 Sime Darby Technology Centre Sdn. Bhd., 2, Jalan Tandang, 46050 Petaling Jaya, Selangor, Malaysia

6 Felda Agricultural Services Sdn Bhd., 7th Floor, Balai Felda, Jalan Gurney 1, 54000 Kuala Lumpur, Malaysia

7 Interscience Sdn Bhd. 26 & 28, Jalan 25/34 Taman Mayang, 47301 Petaling Jaya, Selangor, Malaysia

8 Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

9 Institut fur Genetics, University zu Koln, Zulpicherstr. 47, 50674 Koln, Germany

10 Friedrich Miescher Institute, Maulbeerstrasse 66, CH 4058, Basel, Switzerland

11 Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre of Singapore, 11, Hospital Drive, 169610, Singapore

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BMC Genomics 2007, 8:381  doi:10.1186/1471-2164-8-381

Published: 22 October 2007



Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST) analysis on oil palm.


In this study, six cDNA libraries from oil palm zygotic embryos, suspension cells, shoot apical meristems, young flowers, mature flowers and roots, were constructed. We have generated a total of 14537 expressed sequence tags (ESTs) from these libraries, from which 6464 tentative unique contigs (TUCs) and 2129 singletons were obtained. Approximately 6008 of these tentative unique genes (TUGs) have significant matches to the non-redundant protein database, from which 2361 were assigned to one or more Gene Ontology categories. Predominant transcripts and differentially expressed genes were identified in multiple oil palm tissues. Homologues of genes involved in many aspects of flower development were also identified among the EST collection, such as CONSTANS-like, AGAMOUS-like (AGL)2, AGL20, LFY-like, SQUAMOSA, SQUAMOSA binding protein (SBP) etc. Majority of them are the first representatives in oil palm, providing opportunities to explore the cause of epigenetic homeotic flowering abnormality in oil palm, given the importance of flowering in fruit production. The transcript levels of two flowering-related genes, EgSBP and EgSEP were analysed in the flower tissues of various developmental stages. Gene homologues for enzymes involved in oil biosynthesis, utilization of nitrogen sources, and scavenging of oxygen radicals, were also uncovered among the oil palm ESTs.


The EST sequences generated will allow comparative genomic studies between oil palm and other monocotyledonous and dicotyledonous plants, development of gene-targeted markers for the reference genetic map, design and fabrication of DNA array for future studies of oil palm. The outcomes of such studies will contribute to oil palm improvements through the establishment of breeding program using marker-assisted selection, development of diagnostic assays using gene targeted markers, and discovery of candidate genes related to important agronomic traits of oil palm.