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Oil Palm Genomes Provide Resource for Exploring Plants' Biology, Palm Oil Production

NEW YORK (GenomeWeb News) – In a study appearing online today in Nature, researchers from the Malaysian Palm Oil Board, Orion Genomics, and elsewhere reported on findings from a genome and transcriptome sequencing study of two key palm oil-producing species, the African oil palm Elaeis guineensis and the South American oil palm species, E. oleifera.

"The oil palm genomes are a rich resource for palm breeders, geneticists and evolutionary biologists alike," Ravigadevi Sambanthamurthi, director of the Malaysian Palm Oil Board's advanced biotechnology and breeding center, said in a statement, "and will facilitate future identification of genes responsible for important yield and quality traits such as fruit color, disease resistance and height."

Sambanthamurthi was co-corresponding author on the study, along with the Cold Spring Harbor Laboratory's Robert Martienssen, a scientific co-founder at Orion Genomics.

With genome and transcriptome sequences for both species in hand, the team has been able to look at oil palm's gene coding capabilities as well as its divergence in the Old and New Worlds and relationships with other plants.

The sequences are also expected to serve as a resource for tracking down genetic contributors to important oil palm traits and finding improved strategies for growing oil palm crops in tropical locales without negatively affecting nearby rainforests.

Plants from the West African E. guineensis species and from E. oleifera, from Central and South American, are the two main sources of palm oil, researchers noted, producing almost half of the edible vegetable oil used around the world.

Despite the high productivity of oil palm plants, though, demand for its oil product has led to expansions in oil palm crops that sometimes stretch into rainforest areas, prompting interest in finding ways to further up the oil yield of oil palm plants.

In an effort to generate the first oil palm genome, researchers started with genomic DNA from a form of E. guineensis called AVROS, using a combination of Sanger and Roche 454 GS FLX Titanium sequencing to tackle the plant's 1.8 billion-base genome.

From that sequence data, the team successfully assembled more than 1.5 billion bases of the E. guineensis genome, before going on to resequence the draft genome of the E. oleifera species and transcriptome libraries representing various oil palm plant tissues.

Among the 34,802 predicted protein-coding genes found on E. guineensis' 16 chromosomes, the researchers saw several genes resembling those implicated in oil production, sugar metabolism, or transcriptional regulation in other plants.

They also identified a slew of duplicated sequences and a range of transposable elements, including retroelements from the copia and gypsy groups and long terminal repeat retrotransposons.

By folding in transcriptional data, the group got a glimpse at when and where genes are expressed as oil accumulates in plants, while comparisons between the African oil palm genome and sequences from plants such as date palm and Arabidopsis thaliana offered a look oil palm's place in the plant tree.

Using sequence data from both oil palm species, meanwhile, investigators estimated that the E. guineensis and E. oleifera species — which can still cross with one another to form viable hybrids — split from one another some 51 million years ago, roughly 14 million years after the divergence between the date and oil palm lineages.

In an accompanying paper also published online early in Nature, Sambanthamurthi, Martienssen, and colleagues also described alterations in a single gene that influence oil palm's palm oil yield.

Through an analysis that hinged on linkage mapping, genome resequencing, and homozygosity mapping by sequencing, the team uncovered a gene called Shell gene — and two mutations in it — that apparently mediate the relationship between the oil palm plant's shell type, the size of its fruit, and the amount of oil it produces.

Plants from the African oil palm species can be classified into three different groups depending on the type of shell separating oil palm's fruit from its seed, or kernel, authors of that study said.

These results made it possible to peek at the Shell alleles associated with thick-shelled oil palm plants, shell-free plants, and a third, thin-shelled hybrid form of the plant that is linked with optimal palm oil production. That, in turn, is expected to help in identifying the thin-shelled plants much earlier, at the seed or seedling stage.

"Accurate genotyping for enhanced oil yields will optimize and help stabilize the acreage devoted to oil palm plantations, providing an opportunity for the conservation of rain forests," Martienssen said in a statement.

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