The green revolution was launched, in large part, with rather squat plants. In the 1960s, farmers began using semidwarf varieties of wheat and rice that produced many grain-bearing branches known as tillers. When farmers added nitrogen fertilizer, the plants gained tillers, not height. “Farmers could use large amounts of nitrogen and that got translated into yield,” says plant geneticist Nicholas Harberd of the University of Oxford in the United Kingdom.
But nitrogen fertilizer also translates into environmental harm—from polluted waterways to greenhouse gases. Now, Harberd and a team of colleagues from the Chinese Academy of Sciences have identified a gene that’s integral to dwarf rice’s ability to add more branches as farmers add more nitrogen. Their findings, reported in Science, could help rice breeders develop new rice varieties that boost the expression of this gene without the high nitrogen input.
Researchers didn’t entirely understand how nitrogen fertilizer worked despite its widespread use, says Harberd. “Everybody knows that if you give plants fertilizer, they get more bushy,” he says. “But nobody knew why.” So Harberd and his colleagues sought to understand how nitrogen promotes outward branching. They screened over 100,000 mutagenized semidwarf rice plants, hoping to find a mutant that had lost its ability to increase branch number in response to nitrogen. One mutant in particular had the low branch number they were after. When the researchers added nitrogen, it had no effect.
The team then used a series of molecular techniques to identify the mutant gene responsible for this lack of response. Using map-based cloning, for example, they examined which known molecular markers along the rice genome passed from one generation to the next along with the mutant trait. Markers that consistently appeared with the mutant trait were likely located close to the mutant gene.
The researchers ultimately homed in on a gene they labeled NGR5. When they gave the normal semidwarf rice plants more nitrogen, the plants’ cells increased the levels of the protein that NGR5 encodes. Giving the mutant plant more nitrogen, however, had no effect on NGR5 protein levels.
Harberd and his colleagues then probed the pathway that enables the NGR5 protein to trigger branching in the presence of nitrogen. NGR5, they found, is a transcription factor, a type of protein that influences the expression of other genes. In this case, it switches off genes that would otherwise halt branching. NGR5 turns these branch-inhibiting genes off by changing the structure of histones—proteins that wrap around the genes and control their activity.
The team then wondered if it was possible to increase NGR5 levels directly, without relying on nitrogen fertilizer. They surveyed publicly available genome sequence data for rice varieties in search of natural variation in the NGR5 gene, and uncovered a handful of different versions. One in particular, they discovered, could produce high levels of NGR5 and many branches even under low nitrogen conditions.
“These variants do exist in the rice gene pool,” says Harberd. The researchers are now using traditional plant breeding techniques to breed the beneficial version of the NGR5 gene into new varieties. Their initial field trials show that the varieties under development increase grain yield by up to 25% at low fertilizer levels. They aim to make these new varieties available to farmers within the next few years.
This research is “a great example of how basic science can pay off in real-world agriculture,” says plant geneticist and Howard Hughes Medical Institute investigator Rob Martienssen of Cold Spring Harbor Laboratory in NY, who was not involved in the research.
“I am very excited about the fact that they can uncouple the nitrogen input from the tillering process,” adds plant geneticist Shannon Pinson from the US Department of Agriculture Dale Bumpers National Rice Research Center in Stuttgart, AR, who also wasn’t involved in the study. Pinson hopes this breakthrough could lead to similar discoveries in other cereal crops. “The genetics of tillering [are] very shared between wheat and barley and rice,” she says.
Indeed, Harberd and his colleagues are now turning their attention to varieties of semidwarf wheat, another key player in the green revolution. They expect wheat may use nitrogen to encourage branching via a similar mechanism.