Analyses of hypomethylated oil palm gene space.
Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.
Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia.
Eng-Ti L
ET
Low
Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia.
Rozana
R
Rosli
Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia.
Nagappan
N
Jayanthi
Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia.
Ab Halim
AH
Mohd-Amin
Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia.
Norazah
N
Azizi
Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia.
Kuang-Lim
KL
Chan
AgResearch Ruakura Research Centre, Hamilton, New Zealand.
Nauman J
NJ
Maqbool
AgResearch Ruakura Research Centre, Hamilton, New Zealand.
Paul
P
Maclean
AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand.
Rudi
R
Brauning
AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand.
Alan
A
McCulloch
AgResearch Grasslands Research Centre, Palmerston North, New Zealand.
Roger
R
Moraga
Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia.
Meilina
M
Ong-Abdullah
Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia.
Rajinder
R
Singh
D028023:Arecaceae / Q000235:genetics*; D019175:DNA Methylation; D060467:Disease Resistance / Q000235:genetics; D020224:Expressed Sequence Tags; D063990:Gene Ontology; D017343:Genes, Plant; D035683:MicroRNAs / Q000235:genetics; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D018749:RNA, Plant / Q000235:genetics; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant; D014157:Transcription Factors