Thousands of miles away, in Southeast Asia, an oil industry is booming,
gobbling up giant tracts of rainforest in the process.
A St. Louis genomics company believes it has come up with a solution that could prevent further damage to the region's sensitive -- and ecologically valuable -- environment.
In the past three decades, global palm oil production has quintupled, turning the humble tropical tree into a $44 billion industry.
The oil -- virtually absent from products decades ago -- can be found in everything now, from toothpaste to sauces, having gained traction among manufacturers because it's cheap and shelf-stable. It is now the world's most widely produced food oil, at about 60 million tons a year.
But the boom, like most, has come at a cost. As demand has shot up, so has the consumption of vast swaths of Southeast Asian tropical rainforest, which have been plowed under to make space for palm oil plantations. The deforestation has pushed certain species of orangutan, elephant and tiger to the brink of extinction, while slash-and-burn practices have led to smog and huge releases of climate-warming carbon.
Enter Orion Genomics.
The company and its partner, the government-funded Malaysian Palm Oil Board, just announced they have sequenced the massive palm oil genome, and have identified the gene mutations that lead to higher-yielding palm oil trees. That identification could mean fewer palm trees are needed on fewer acres, placing less pressure on rainforests while still satisfying surging global demand.
"We believe the technology is the answer," said Nathan Lakey, president and CEO of the company, which is based in St. Louis' Central West End. "If we can make palm trees more and more productive, that will enable us to provide enough food and biofuels on the existing planted area."
Malaysia is the world's second-largest producer of palm oil. It and neighboring Indonesia grow roughly 90 percent of the world's palm oil.
The oil is often referred to as the "backbone" of the Malaysian economy, so the quasi-governmental palm oil board, which regulates the industry, also funds research to make it more efficient and profitable.
About a decade ago, the board became interested in biotechnology and sequencing, so it approached James Watson, the Nobel laureate who co-discovered the structure of DNA, and asked for his counsel. He referred them to Orion.
"We definitely could not afford a whole genome sequencing, so we realized the company offered a unique technology, where you didn't have to sequence the entire genome," said Ravigadevi Sambanthamurthi, director of the board's Advanced Biotechnology and Breeding Centre. "They had a proprietary technology where the nonfunctional part of the genome is filtered out, and we could zoom in on the expressed gene."
The palm oil tree, like a coconut tree, has a fleshy interior, a hard shell, and then a softer, fleshy exterior. It, uniquely, yields three types of fruit: one with a thick shell, one with no shell, and one with a thin shell -- the latter, a hybrid of the first two, being the most productive and the one grown commercially. This hybrid produces 30 percent more oil.
While growers purchase the hybrid seeds that produce the thin-shelled variety, they end up with a dud -- one of the two undesirable types -- about 10 percent of the time. Because the trees are slow to produce fruit, that 10 percent ends up being quite costly and takes up valuable land.
"There's a certain amount of contamination, and you get wild trees in the mix," Lakey said. "It takes them six years to realize they have a low-yielding type, but by then you can't chop the tree down because they're too tall."
So the researchers at the board and Orion set out to determine first of all, which gene was responsible for the shell thickness, and then how mutations in that gene are responsible for differences in shell thickness, and therefore, oil yield. That was the prize target.
"When I met with the leadership," Lakey said, recounting frequent meetings, "the first questions were, 'Where are we on this project? Have you found the shell gene?'"
In late 2011 the team did, indeed, find the gene. And by 2012 it was certain of its discovery.
"We wanted to do lots of validation," Lakey said. "I didn't want to say, 'We have it' -- and not have it."
The Malaysian government, according to Sambanthamurthi, has put limits on the rainforest acreage that can be developed for agriculture. That's why, she said, the finding was critical. In theory, it means no more rogue trees -- only highly productive ones -- and that could translate to hundreds of million of dollars for the Malaysian economy, without exploiting new lands.
The board hasn't settled on how the discovery will be utilized -- how it will get into the hands of producers. But it will likely be in the form of a diagnostic test that the board will license, and for which it will receive some royalties. The board spent the last year filing patents on the gene applications and various diagnostic approaches.
The larger genome, too, could enable further research toward identifying genes that control other traits, such as tree height or drought tolerance. "Having the sequence now opens a whole new avenue of looking at other genes," Sambanthamurthi said. "The shell is just the start."
ST. LOUIS ASSETS
On the world's scientific stage, the team was not the only one scrambling to find the "shell" gene.
"Clearly the Orion and MPOD (board) team felt pressure," Lakey said. "There were other teams around the world looking, and with more money. We were outspent, and had to be very diligent and work very fast."
So, in other words, Orion and the board beat some formidable researchers to the target, and its findings, published last week in the prestigious science journal, Nature, cement their discovery. At the same time, Lakey says, it helps solidify its own reputation -- and its hometown's.
"As a company this was another validation of our leadership in this space -- to have such high-profile papers come out," he said. "It will help us secure additional contracts."
In doing the work, Orion subcontracted with several St. Louis biosciences companies, so being here was critical, Lakey said. "The St. Louis community -- the broader technology community -- has tremendous assets."
Lakey would not discuss the financial terms of company's contract with the board. But, he said, typically providers, such as Orion, are paid lucrative service fees. Often they have "milestone" or "success" fees if there are breakthrough discoveries. Sometimes the discoverer gets royalties.
"We have a deal that's one of those combinations," Lakey said.
Some critics have expressed concern that this discovery, or genetic manipulations in the future, could lead to more deforestation.
"Yes, increased oil production could mean fewer acres would be needed to yield the same amount of oil," said Hank Stelzer, associate professor of forestry at the University of Missouri. "But, land ownership patterns (are) what generally drives land use. If anything, if such a palm tree was developed it could lead to speculation by others to clear more land in order to plant a commercially valuable tree."
But for now, the board, at least, is satisfied.
"At a minimum," Lakey said. "Our customers, they're really happy."
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