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Malaysian Oil Palm Genome Programme (MyOPGP)
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Introduction

The goal of the Malaysian Oil Palm Genome Programme (MyOPGP) is to produce a draft sequence of the oil palm genome. The sequence will provide a deeper understanding of the genome architecture and become a resource for biomarker discovery and development of diagnostic tools. The programme was first initiated in 2004 to selectively sequence the hypomethylated regions of the genome, and was subsequently expanded to the whole genome, facilitated by advancements in sequencing technologies and bioinformatics.

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Three oil palm genomes, the dura and pisifera fruit forms of E. guineensis, and E. oleifera were sequenced, assembled and annotated. The E. guineensis (pisifera) and E. oleifera genomes were de novo assembled and represent reference sequences. About 93-fold coverage of the genomes was achieved using a combination of new sequencing technologies, namely Roche 454 and Illumina. The transcriptome and epigenome of oil palm were also deciphered.

MyOPGP data has facilitated the development of important genomic platforms, such as single nucleotide polymorphism (SNP), oligo and methylation arrays. These platforms are being leveraged on to improve efficiency of oil palm breeding and tissue culture.

Objectives

The objectives of the programme are:
1 To obtain a gold standard reference of the oil palm (E. guineensis and
E. oleifera) genome
2 To identify markers and genes/promoters of interest associated with important agronomic traits
3 To use the genome information to develop disease resistant palms with enhanced productivity
4 To develop value-added products

Highlights

Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data
Kuang-Lim Chan, Rozana Rosli, Tatiana V. Tatarinova, Michael Hogan, Mohd Firdaus-Raih and Eng-Ti Leslie Low
Published online: 27 January 2017 Read this ..

Non-tenera contamination and the economic impact of SHELL genetic testing in the Malaysian independent oil palm industry
Leslie C.-L. Ooi, Eng-Ti L. Low, Meilina O. Abdullah, Rajanaidu Nookiah, Ngoot C. Ting, Jayanthi Nagappan, Mohamad A. A. Manaf, Kuang-Lim Chan, Mohd A. Halim, Norazah Azizi, Wahid Omar, Abdul J. Murad, Nathan Lakey, Jared M. Ordway, Anthony Favello, Muhammad A. Budiman, Andrew Van Brunt, Melissa Beil, Michael T. Leininger, Nan Jiang, Steven W. Smith, Clyde R. Brown, Alex C. S. Kuek, Shabani Bahrain, Allison Hoynes-Oânnor, Amelia Y. Nguyen, Hemangi G. Chaudhari, Shivam A. Shah, Yuen-May Choo, Ravigadevi Sambanthamurthi & Rajinder Singh
Published online: 21 June 2016 Read this ..

Fine-mapping and cross-validation of QTLs linked to fatty acid composition in multiple independent interspecific crosses of oil palm
Ngoot-Chin Ting, Zulkifli Yaakub, Katialisa Kamaruddin, Sean Mayes, Festo Massawe, Ravigadevi Sambanthamurthi, Johannes Jansen, Leslie Eng Ti Low, Maizura Ithnin, Ahmad Kushairi, Xaviar Arulandoo, Rozana Rosli, Kuang-Lim Chan, Nadzirah Amiruddin, Kandha Sritharan, Chin Ching Lim, Rajanaidu Nookiah, Mohd Din Amiruddin & Rajinder Singh
Published online: 14 April 2016 Read this ..