DNA Methylation and ‘Bad Karma’ To Blame for Oil Palm Trees’ Useless Fruit

Bisulfite conversion and microarrays pinpoint the epigenetic cause of “mantled” plants

DNA methylation and bisulfite conversion affect oil palm fruit production

“Bad karma” and epigenetics are to blame for the spoiling of tens of thousands of young oil palms grown at large plantations in Southeast Asia, particularly Malaysia, according to a group of researchers at the Cold Spring Harbor Laboratory. Not only have millions of dollars been wasted on these plants, also known as African oil palm or Elaeis guineensis, but the tropical environment has suffered as a result of some faulty epigenetic machinery. Researchers utilized bisulfite conversion and microarrays to analyze the methylation of the plant DNA and published their results in Nature.

Six years after planting young oil palm plants that were created by cloning the highest-yielding specimens, palm growers have found that their fruits are worthless. When they matured, these barren mutated palm plants produced useless “mantled” fruit, despite being cloned from only the finest hybrids.

The fruits and seeds gathered from oil palms contribute to nearly a half of the world’s supply of edible vegetable oil and are also heavily used for biofuel. Because it takes around 6 years for these plants to mature, their value is not fully realized until their fruits are produced, well after valuable time and money have been invested. As demand continues to grow for palm oil worldwide, it is in the industry’s interest to improve yield. Plant geneticists, including Professor Robert A. Martienssen, FRS, from Cold Spring Harbor Laboratory (CSHL), have been involved in promoting the oil palms’ fruit production.

“Our work in this area has been driven in part by environmental concerns,” Martienssen explained. “As we devise ways to reliably boost yields, we thereby lessen the economic motivation to spread oil palm holdings into sensitive rainforest areas that are important to preserve.” In past work, Martienssen has identified a gene that controls how much fruit is produced by the plant, known as the SHELL gene.

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Mantled oil palm fruit
Oil palm plants bearing normal fruit (left) and worthless ‘mantled’ fruit (right). Credit: Cold Spring Harbor Laboratory.

In their study, the team investigated the issue of “mantled” oil palms and a way to prevent it from happening. The cause of the mantled oil palms can be attributed to karma, according to the paper’s lead author, Meilina Ong Abdullah, her coworkers at the organization that oversees Malaysia’s oil palm industry called the Malaysian Palm Oil Board (MPOB), Martienssen, and researchers from a private firm in the United States known as Orion Genomics, which was created out of CSHL.

Highly valued palm oil plant hybrids, grown in culture dishes, are at the root of the problem of these mantled organisms. Stem cells are harvested from tissue samples taken from the tip of the plant, what is known as the “heart of palm.” The optimal, highly desirable oil palms are then cloned, since natural seed cultivation does not adequately produce fruits.

Martienssen, specializing in epigenetics, suspected that the problem of these mantled oil palms, despite being cloned from prized plants, could be attributed to an epigenetic mechanism. Ultimately, they found that the very common epigenetic mechanism known as DNA methylation was to blame.

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The team assessed the genome of numerous commercially important cloned varieties of oil palm using bisulfite conversion and then microarrays to analyze the methyl tags. Bisulfite conversion converts cytosine to thymine without affecting methylated cytosine, which the researchers can then analyze to determine amount of DNA methylation. They found that at one location on the genome these methyl tags were absent and this location actually corresponded to a version of a gene that was formerly connected to mantled plants.

The DEFICIENS gene, first found in the snapdragon plant, is the equivalent oil palm gene assessed in the study and was aptly renamed MANTLED by the research team. This gene plays a role in sexual organ fate which, when mutated, can lead to male organs developing in the place of female organs. A retrotransposon, one of many genomic invaders that are normally dormant inside the genes of all organisms, is lodged within the MANTLED gene in these plants. One genomic invader similar to this, called karma, was first noticed in rice plants.

The researchers ultimately found that the mantled plants were missing a methyl mark that normal plants had at an area called the “splice spot”, located in the karma retrotransposon. Karma rests within an intron in the MANTLED gene. This DNA hypomethylation is associated with alternative splicing and premature termination. When the splice spot is unmethylated, this gene will use karma as opposed to a normal exon to splice the intron. Then, a mutant protein is encoded by the gene which results in plants bearing useless fruit. The researchers used the term “bad karma” to describe this faulty gene message. At the karma splice site, the methyl tag is always present in healthy oil palms that produce desirable fruit and the team aptly referred to this normal gene message as “good karma.”

The reason for “bad karma” that arises in plants cloned and grown in culture is not entirely understood. Martienssen believes it could be caused by the separation of oil palm tissue from the meristem, which contains stem cells. Small RNAs are also contained in the meristems which guide methyl marks and various epigenetic signals to specific positions on the DNA.

Luckily, farmers can easily identify which plants they should cull and discard by using an epigenetic test similar to those that detect diseases in human fetuses during pregnancy. This will increase oil palm fruit yield, according to Martienssen, and will save millions of dollars. The healthy hybrids will propagate and reduce the need for farmers to expand their land to increase their chances of getting more valuable fruit.

 

Source: Robert A. Martienssen et al. (2015). Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature. Advance online publication. doi: 10.1038/nature15365.

Reference: Cold Spring Harbor Laboratory. What’s behind million-dollar crop failures in oil palm? Would you believe bad karma? News & Features. 17 Sep 2015. Web.

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Bailey Kirkpatrick
About Bailey Kirkpatrick 164 Articles
Bailey Kirkpatrick is a science writer with a background in epigenetics and psychology with a passion for conveying scientific concepts to the wider community. She enjoys speculating about the implications of epigenetics and how it might impact our perception of wellbeing and the development of novel preventative strategies. When she’s not combing through research articles, she also enjoys discovering new foods, taking nighttime strolls, and discussing current events over a barrel-aged sour beer or cold-brewed coffee.

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