The world's most widely planted cereal has also proved to be among the hardest to improve. Plant breeders vastly increased wheat yields during the Green Revolution of the 1960s, but since then efforts to improve the crop through traditional breeding or genetic technology have been painstakingly slow because of the fiendish complexity of its genome. Thanks to a decadelong effort, the wheat genome has finally come into sharp focus, speeding the search for genes that could boost harvests and even make wheat less likely to trigger allergies.
The data, described this week in Science, represent the long-awaited culmination of the International Wheat Genome Sequencing Consortium, a massive collaboration of academic and industry researchers from 20 countries. Wheat geneticists say the newly finished genome, which pinpoints 107,000 genes on the 21 chromosomes of bread wheat, has transformed their research as they and others gained early access to it. "What took us years in the past now takes us one night," says Jorge Dubcovsky of the University of California, Davis, who recently found a new gene for wheat height. "It's like walking with a Google map."
Already the new genome has helped plant geneticists from the John Innes Centre (JIC) in Norwich, U.K., to boost grain size by 20% in lab-grown wheat. In a preprint posted on the bioRxiv server in May, they report identifying multiple copies of a gene for grain size originally found in rice, then bulking up wheat grains by mutating the genes using CRISPR gene-editing technology. Many more traits beckon. The new sequence "ushers in a new era in wheat genetics," says James Anderson, a plant breeder at the University of Minnesota in St. Paul who was not part of the effort.
For him and thousands of other wheat researchers, bread wheat's DNA has been an impenetrable thicket. Natural breeding between two grasses many thousands of years ago gave rise to the durum wheat now used in pasta. That hybrid was mated with yet another grass to yield the grain that makes everything from bread to beer all over the world. But this interspecies mingling produced a genome more than five times the size of the human one, harboring three sets of very similar chromosomes, 21 pairs in all, with six copies of most genes. Lacking a map of this complex landscape, wheat breeders had trouble tracking genes from generation to generation to see whether a crossing had worked, and genetic engineers trying to alter a specific DNA sequence often did not know where to find it.
The consortium—born in 2005 as an initiative by Kansas farmers—has finally mapped the thicket by breaking out and sequencing each chromosome separately. In contrast, a genome published last year by a group of academics had some longer stretches of contiguous sequence but did not describe genes or order and orient them on the chromosomes. The new genome "represents a major step forward," says JIC's Michael Bevan, whose group also produced a rival draft wheat genome last year, before working with the consortium.
JIC researchers including Cristobal Uauy, Ricardo Ramírez-González, and Philippa Borrill have now built on the consortium's data to document gene activity in different tissues and at various points of the plant's life cycle. They took 850 snapshots of messenger RNA levels to gauge which genes are active under conditions including drought, pest attack, and other kinds of stress, aiming to trace networks of genes underlying yield and other traits. With these surveys, "we can see which of the copies are most useful to target," Borrill says.
So far, consortium members and others have drawn on the genome for more than 100 published papers, says the consortium's executive director, Kellye Eversole, who is based in Bethesda, Maryland. Their finds are already being put to use. For example, commonly planted varieties won't sprout unless the seeds have overwintered in the ground. Last year, plant geneticist Antje Rohde, now at BASF in Ghent, Belgium, reported her team had pinned down a key gene responsible for the sprouting delay. By disabling that gene using CRISPR, the team hopes to shorten the wheat breeding cycle.
The genome could also help bolster wheat's resistance to disease. Drawing on the consortium data, Curtis Pozniak and Kirby Nilsen at the University of Saskatchewan in Saskatoon, Canada, found a gene that makes wheat stems stiffer, and hence more resistant to stem-boring insect pests called sawflies. Stiffer wheat has more copies of the gene, Nilsen found, which points to ways to protect other wheat varieties.
The genome could even aid human health, says consortium co-leader Rudi Appels, a molecular geneticist at Murdoch University in Perth, Australia. In Science Advances this week, he, fellow Murdoch University researcher Angéla Juhász, and Odd-Arne Olsen from the Norwegian University of Life Sciences near Oslo report identifying 365 genes coding for wheat proteins that stimulate an immune or allergic response. The data could help breeders aim for less problematic wheat—what Appels calls "my personal dream."
"For the first time, people working in wheat have the quality of resources that people have in other crops," says consortium co-founder Catherine Feuillet, chief scientific officer at Inari Agriculture, a new ag-biotech startup in Cambridge, Massachusetts. "We now have the tools to do [breeding] in a knowledge-based way."