GMO the old fashioned way

Monsanto gives up on GMO but uses phenotype-genotype modeling to crossbreed vegetables.

WIRED: ... Furthermore, genetically modifying consumer crops proved to be inefficient and expensive. Stark estimates that adding a new gene takes roughly 10 years and $100 million to go from a product concept to regulatory approval. And inserting genes one at a time doesn’t necessarily produce the kinds of traits that rely on the inter­actions of several genes. Well before their veggie business went kaput, Monsanto knew it couldn’t just genetically modify its way to better produce; it had to breed great vegetables to begin with. As Stark phrases a company mantra: “The best gene in the world doesn’t fix dogshit germplasm.”

What does? Crossbreeding. Stark had an advantage here: In the process of learning how to engineer chemical and pest resistance into corn, researchers at Monsanto had learned to read and understand plant genomes—to tell the difference between the dogshit germplasm and the gold. And they had some nifty technology that allowed them to predict whether a given cross would yield the traits they wanted.

The key was a technique called genetic marking. It maps the parts of a genome that might be associated with a given trait, even if that trait arises from multiple genes working in concert. Researchers identify and cross plants with traits they like and then run millions of samples from the hybrid—just bits of leaf, really—through a machine that can read more than 200,000 samples per week and map all the genes in a particular region of the plant’s chromosomes.

They had more toys too. In 2006, Monsanto developed a machine called a seed chipper that quickly sorts and shaves off widely varying samples of soybean germplasm from seeds. The seed chipper lets researchers scan tiny genetic variations, just a single nucleotide, to figure out if they’ll result in plants with the traits they want—without having to take the time to let a seed grow into a plant. Monsanto computer models can actually predict inheritance patterns, meaning they can tell which desired traits will successfully be passed on. It’s breeding without breeding, plant sex in silico. In the real world, the odds of stacking 20 different characteristics into a single plant are one in 2 trillion. In nature, it can take a millennium. Monsanto can do it in just a few years.

And this all happens without any genetic engineering. Nobody inserts a single gene into a single genome. (They could, and in fact sometimes do, look at their crosses by engineering a plant as a kind of beta test. But those aren’t intended to leave the lab.) Stark and his colleagues realized that they could use these technologies to identify a cross that would have highly desirable traits and grow the way they wanted.  ...