Nature Paper Reveals Epigenetic Cause for Mantling - a Devastating Epi-mutation Occurring in Cloned Elite Oil Palms

Discovery Made Possible with Orion Genomics' MethylScope® Technology, Paves Way for a Simple DNA Test that Selects High Performers, Allowing for a More Sustainable Oil Palm Industry

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Orion Genomics

Sep 09, 2015, 01:02 ET

ST. LOUIS and KUALA LUMPUR, Malaysia, Sept. 9, 2015 /PRNewswire/ -- A multinational team from the Malaysian Palm Oil Board (MPOB), Orion Genomics, and Cold Spring Harbor Laboratory today announced the publication of a paper in Nature detailing the epigenetic cause of mantling – a catastrophic phenotype which results in low-yielding oil palm in a significant but unpredictable portion of plants that are propagated by cloning. The study showed that while palms with mantled fruit are genetically identical to their high performing parents, the loss of DNA methylation in a specific region of an oil palm genome containing a transposable element called 'Karma' is responsible for the low-yielding mantled fruit. The discovery was enabled by the combination of MPOB's and the oil palm industry's vast collection of highly characterized clonal palms with a solid knowledge of oil palm and tissue culture and Orion's MethylScope® technology, a tool used to precisely map DNA methylation across entire genomes.

Healthy (top) versus mantled (bottom) oil palm fruit. Mantled fruit have commercially unviable yields of oil and occur in an unpredictable number of oil palms propagated through cloning.

Somaclonal variation among otherwise identical oil palm clones raises sustainability concerns.

"Mantling has severely curtailed the ability of oil palm growers to take advantage of the significantly increased yield that cloned palms can have over palms produced from seed," stated Datuk Dr. Choo Yuen May, Director General of MPOB. "Because oil palm producers have had no way of knowing at the time of planting which clonal palms will be productive and which will carry the low-yielding mantled phenotype, many were unable to take the risk that they may plant completely unproductive palms. With this discovery, it will now be possible to test palms at the nursery stage with a simple DNA test, and to select only high performing clonal palms for cultivation. Removing this risk is significant, because clonal palms have the potential to produce 20 to 30 percent more oil on the same planted area as palms grown from seedlings, and this will decrease pressure on natural rain forests."

Although the crop is planted on 5 percent of global land dedicated to producing vegetable oil, the African and South American oil palms, Elaeis guineensis and E. oleifera, respectively, together account for 45 percent of the edible oil production worldwide. The crop is also the most efficient producer of oil, yielding ten times more edible oil per unit of land than soybean. However, oil palm grows in the tropics, and its expanded cultivation can threaten sensitive habitats. Advancements that enable increased yields on existing planted area can help increase the sustainability of oil palm cultivation.

Researchers from MPOB and the oil palm industry, Orion Genomics and Cold Spring Harbor Labs discovered that an epigenetic state they called Bad Karma resulted from the loss of DNA methylation of the oil palm Karma transposon embedded within an important flowering transcription factor gene. Low methylation of Karma disrupts the normal splicing of the gene, causing the low oil yielding mantled phenotype. However, when dense methylation of the transposon was present, an epigenetic state the research team called Good Karma, oil palm clones thrived in production fields. The discovery has led to the development of a simple, leaf-based test that can predict the mantling phenotype at a stage before clonal palms are planted in the field, years before the mantling phenotype would normally appear. The new approach will enable the exclusive cultivation of high-performing plants, further optimizing the use of environmentally sensitive land resources. The precision DNA test is being marketed by Orion Biosains, the Southeast Asian affiliate of Orion Genomics.

"We have had a long-standing collaboration with the MPOB that has successfully combined Orion's strengths in genomics and precision agriculture with MPOB's expertise in oil palm breeding, tissue culture and biology, and this combination has allowed us to discover together several important genetic characteristics of the oil palm that can help the industry increase yields without increasing planted area," said Nathan Lakey, President and CEO of Orion Genomics, and co-founder and Chairman of Orion Biosains. "It is especially gratifying that Orion's MethylScope technology, licensed from Cold Spring Harbor Laboratory, was instrumental in making this important discovery."

About the Malaysian Palm Oil Board

The Malaysian Palm Oil Board (MPOB) is a Malaysian government agency dedicated to serving the country's palm oil industry. The agency envisions the development of a highly diversified, globally competitive and sustainable oil palm industry. MPOB is focused on improving production efficiency and the quality of palm oil-derived products, optimizing land use in oil palm areas and finding new uses for palm oil derivatives. The Malaysian government halted the conversion of new forest land for agriculture, including oil palm, in the 1990s. It has also committed to preserve 50 percent of its total land area as forest. To meet increased demand for the palm oil, the Malaysian government converted colonial rubber and cocoa plantations to oil palm plantations.

About Orion Genomics

Orion Genomics LLC is a St. Louis-based biotechnology company that develops epigenetic and genomic research tools and molecular diagnostics to help fulfill the promise of personalized medicine and precision agriculture. The company's lead diagnostic product is a simple epigenetic blood test, in late-stage clinical trials, that identifies people at elevated risk of developing colorectal cancer in the future. Orion's proprietary precision agricultural tests are being marketed to the tropical plantation agricultural sector world-wide through its subsidiary companies. Through the company's services division, Orion offers genomics research and assay development services to the medical, agricultural and bio-fuels research communities.

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