Analyses of Hypomethylated Oil Palm Gene Space

Abstract

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.

Oil palm natural diversity and the potential for yield improvement

“…De novo assembly from RNA-seq data resulted in 51,452 oil palm unigenes (Lei et al, 2014). To characterize the genic regions in a greater detail, the methylation filtered libraries of the African and American oil palm species were sequenced (Low et al, 2014). Sequence analysis revealed single nucleotide polymorphisms (SNP) at densities 2.30 and 2.83 per 100 bp for E. guineensis and E. oleifera , respectively.…”

“…Molecular breeding uses genetic markers linked to the traits of choice for earliest pre-selection of desired phenotypes and has a potential to greatly shorten the breeding cycle, reducing costs. The data of (Low et al, 2014) were used to generate a final set of 4,451 SNPs that were selected for developing a customized oil palm specific SNP array (OPSNP3) printed on the Infinium HD iSelect BeadChips platform (Ting et al, 2014). Genotyping across 199 palms from two separate mapping F1 hybrid populations, e.g., E. oleifera × E. guineensis interspecific cross and a dura × pisifera intraspecific cross took less than 3 months (Ting et al, 2014) and greatly improved marker density and genome coverage in comparison to the first reference maps based on AFLP and SSR markers (Barcelos, 1998a; Barcelos et al, 2002; Singh et al, 2009; Billotte et al, 2010; Ting et al, 2013).…”

Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers

“…Commercial E. guineensis (African oil palm) originated in intertropical Africa (Ting et al, 2014) and was imported into South Asia, where its industrial plantations started approximately 100 years ago. It has become one of the most important crops in Indonesia and Malaysia (Abram et al, 2014;Low et al, 2014). The history of oil palm introduction into China is more than 80-years-old.…”

PEMANFAATAN TEKNOLOGI GENOMIKA DAN TRANSFORMASI GENETIK UNTUK MENINGKATKAN PRODUKTIVITAS KELAPA SAWIT / The Use of Genomic and Genetic Transformation Technologies for Oil Palm Productivity Improvement

“…Untuk mempelajari tingkat metilasi genom kelapa sawit yang terkait dengan studi epigenetika, telah juga disekuen pustaka genom dari E. guineensis yang telah difilter kandungan metilnya (methylated-filter libraries) (Low et al, 2014). Dari data tersebut telah ditemukan mekanisme terjadinya fenomana buah mantel kelapa sawit yang diakibatkan oleh hilangnya senyawa metil pada retrotransposon Karma pada gen DEFICIENS (Ong-Abdullah et al, 2015).…”