Massive gene sequencing of thousands of strains of each type of crop are guiding rapid cross breeding programs

– Massive gene sequencing enables millions of varieties of thousands of varieties of crops to be completely understood to guide rapid cross breeding
– Big data analysis enables understanding how to optimally combine desired traits
– Robotic cross breeding enables dozens of desired traits to be successfully combined

The result is a constant stream of successful supercrops without resorting to genetic engineering and cross-species engineering.

BGI has already begun to apply the lessons learned from that project to a much larger endeavor. In cooperation with the International Rice Research Institute (IRRI), based in the Philippines, the company has embarked on an ambitious effort to sequence the genomes of 10 000 strains of rice. The researchers have already produced the first 3000 genomes and are now working to link that genetic information to the specific traits of each strain, a process known as genotyping. Researchers and breeders can then create crops that are customized to produce high yields while meeting specific local challenges, like saltwater flooding, drought, or particular pests.

Researchers can dive deep into the diverse gene pool of rice—there are 24 species and up to 500 000 varieties within those species—to find plenty of useful traits. Until recently “this research would have been impossible,” Nissilä says, “but with today’s technology it’s not even that expensive.”

1.5 years to complete gene sequencing and use that info to guide cross breeding and then grow higher yield crops

A foxtail-millet project was intended to demonstrate the potential of BGI’s sequencing technology to revolutionize agriculture. Zhang’s team spent about four and a half months and US $1.5 million to sequence the plant’s genome and published the results in Nature Biotechnology. The BGI team took another two months to complete genetic maps showing which stretches of sequence controlled which traits in the plant, then crossbred plants to create seeds with the exact mix of traits they sought. One and a half years after they began sequencing the millet genome, BGI researchers were admiring their hearty, high-yield crops in that research field in Guangdong province.

Archaeologists believe that people began cultivating foxtail millet in China as early as 6500 B.C.E., but the plant looked considerably different in those Neolithic days—the foxes’ tails were thin and scrawny. Nevertheless, this early cereal crop had many things going for it, and researchers believe the hardy, quick-growing millet was more common than rice in China’s arid north for millennia.

“It’s [foxtail millet] very drought tolerant,” explains Zhang Gengyun, general manager of BGI’s life-science division. “So I think that this plant could be valuable in the future, especially with conditions of global climate change.

Robotic Breeding: Robot-assisted genetic analysis helps plant breeders combine several genetic traits into one plant breed.

“Twenty years ago, if I was to try to put 20 traits together in the same plant, they would have laughed,” says Robert Fraley, chief technology officer at the world’s biggest biotech seed company, Monsanto. “The odds of that working would be one in a trillion.”

Switzerland’s Syngenta discovered varieties of 13 genes that enhance maize’s ability to withstand drought and, using its proprietary cycle of breeding and genotyping, inserted combinations of them into high-yield breeds that were put through their paces during a drought that parched much of the United States in 2012.

Industrial scale genotyping and robotic plant breeding

A new $40 miillion lab is an information factory whose primary purpose is to answer a single question more than a 100 million times per year: Does this seed contain variants of genes that are associated with these traits? The difference is that the database is, quite literally, the DNA of various crop strains and the search is executed using biochemistry. Armed with the answers to their queries, breeders can know whether it’s worth growing that seed and which of thousands of other seeds to cross it with.

The basic procedure is this: First, DNA is extracted from a bit of a plant and unzipped down the middle, so that a complementary sequence can bind to it. (In the search engine analogy, that DNA is the database.) Then short sequences of DNA, called genetic markers, are added. (These are analogous to the search terms.) Usually not the complete genes themselves, these markers code for distinct patches of DNA in the plant’s genome that are of interest to breeders. For instance, a particular sequence might be found in all maize that can survive in near-desert conditions but not in any that can’t. The marker, which is chemically labeled so it can be identified later, will stick to the plant’s unzipped DNA if it’s a match or wash away if it isn’t.

What was decades ago months of work that would earn you an advanced degree is done tens of thousands of times each day. At Pioneer’s lab, robotic arms swing to a hypnotic beat, moving cassettes of plant material from one step to another, adding just the right amount of just the right chemicals and markers to each of thousands of DNA samples. All the while technicians and scientists keep track of the results on giant screens.

On the economic side, the technology can be used to improve the yield of crops for markets that were heretofore too small to catch the attention of the big seed firms. It makes “the technology more accessible to the crops and regions that in the past haven’t been able to afford it,” says Arbuckle.

More benign and accurate genetic engineering

A side effect of the new, more-precise genome-editing technology is that it’s raising questions about how genetically modified crops should be regulated by governments. For instance, tolerance to the herbicide glyphosate has so far been engineered into commercial crops by transferring in a gene from a bacterium. But some plants, as a growing glyphosate-tolerance problem shows, already carry a much less potent variant of that gene, explains Jennifer Kuzma, an associate professor in the Center for Science, Technology, and Public Policy at the University of Minnesota, Twin Cities. If scientists were to edit the plant’s own gene using the new molecular methods so that it functioned more like the bacterium’s gene, would the resulting resistant plant really be GM?

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