That vegetable oil in your kitchen cabinet comes at a price. Demand for the oil—used in everything from food to biofuel—is so high that oil palm plants have taken over large swaths of the world’s rainforests. About 40 years ago, researchers hoped to reduce rainforest destruction by cloning the highest yielding oil palm trees (Elaeis guineensis), thus boosting oil production. But when the supposedly identical trees matured, many failed to produce oil-filled fruit. Now, researchers think they know why.

The discovery should help growers weed out bad seedlings, making cloning a viable option again, says Jerzy Paszkowski, a plant geneticist at the University of Cambridge in the United Kingdom, who was not involved with the work. “They can avoid growing the worthless palms for years before they fruit.”

Palm oil accounts for about 65% of all vegetable oil traded internationally, and demand for this resource continues to rise. Efforts are underway to try to curb the resulting rainforest destruction. One effort, begun in 1974, involved cloning the palm oil plant. Researchers took cells from leaves of the most productive trees and grew them in a lab dish to produce cloned seedlings. They expected to increase yields per hectare by 30%. But today less than 1% of the area devoted to oil palms uses clones because some of the cloned trees produced fruit that developed abnormally, appearing jagged and forming a thick outer coating. This “mantled” fruit failed to produce much oil, creating a vexing problem. Because the abnormality shows up in genetically identical clones, “it’s impossible to attack genetically,” an approach often taken when a crop has a bad trait that can be bred out of that variety, says study co-author Robert Martienssen, a plant geneticist at the Cold Spring Harbor Laboratory in New York.

Plant geneticist Ravigadevi Sambanthamurthi and her colleagues at the Malaysian Palm Oil Board in Selangor have been trying to understand why supposedly identical trees don’t all produce equally good fruit for 30 years. More than a decade ago, they began collaborating with Martienssen and other scientists to sequence the oil palm genome, which was completed 2 years ago. With the genome in hand they were in a better position to start evaluating the “epigenome,” chemical modifications to DNA that also affect how and when genes work.

Already Martienssen’s team had developed a way to assess one such modification, called methylation, of the genome of Arabidopsis, a fast-grower that scientists often study in the lab to learn basic plant biology. His group and Sambanthamurthi’s team applied that technique to five strains of oil palm, sampling the parent, a normal clone, and a mantled clone in each strain. Although they found many differences in the epigenomes between the samples from each strain, there was just one spot in the genome where all abnormal clones had the same change: They all lost methylation in the noncoding region of a gene important for flower growth and development, Sambanthamurthi and Martienssen report online today in Nature.

Further study showed that when that spot lost its methylation, the coding regions of the gene were not translated correctly and the resulting protein was abnormal. “Finding that one single element within a gene that worked for all the clones was an absolute high,” Sambanthamurthi says. “It was more incredible than finding a needle in a haystack.”

Already, the team has developed a simple test that seems to be completely capable of weeding out the bad clones very early, perhaps even at the tissue culture stage. “This discovery will greatly increase confidence in clones,” Sambanthamurthi says.

And other plant researchers are very pleased: “This is a great paper … with great importance to agriculture,” says Steven Jacobsen, a plant geneticist at the University of California, Los Angeles, who was not involved with the work.