title: Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.).
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia. clho@biotech.upm.edu.my
authors.forename: Chai-Ling
authors.initials: CL
authors.lastname: Ho
authors.forename: Yen-Yen
authors.initials: YY
authors.lastname: Kwan
authors.forename: Mei-Chooi
authors.initials: MC
authors.lastname: Choi
authors.forename: Sue-Sean
authors.initials: SS
authors.lastname: Tee
authors.forename: Wai-Har
authors.initials: WH
authors.lastname: Ng
authors.forename: Kok-Ang
authors.initials: KA
authors.lastname: Lim
authors.forename: Yang-Ping
authors.initials: YP
authors.lastname: Lee
authors.forename: Siew-Eng
authors.initials: SE
authors.lastname: Ooi
authors.forename: Weng-Wah
authors.initials: WW
authors.lastname: Lee
authors.forename: Jin-Ming
authors.initials: JM
authors.lastname: Tee
authors.forename: Siang-Hee
authors.initials: SH
authors.lastname: Tan
authors.forename: Harikrishna
authors.initials: H
authors.lastname: Kulaveerasingam
authors.forename: Sharifah Shahrul Rabiah Syed
authors.initials: SS
authors.lastname: Alwee
authors.forename: Meilina Ong
authors.initials: MO
authors.lastname: Abdullah
mesh_terms: D028023:Arecaceae / Q000235:genetics*; D002874:Chromosome Mapping; D030541:Databases, Genetic; D020224:Expressed Sequence Tags / Q000737:chemistry; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis; D018514:Plant Structures / Q000737:chemistry; D012639:Seeds / Q000235:genetics; D017422:Sequence Analysis, DNA