Scientists have pinpointed a master gene in rice that keeps plants growing strongly even when fertilizer is scarce. The discovery could help farmers cut costs and pollution while protecting harvests in a warming world.
A newly identified “master regulator” gene in rice could help farmers grow more grain with less fertilizer, easing pressure on both wallets and the environment.
An international team of researchers from the University of Oxford, Nanjing Agricultural University and the Institute of Genetics and Developmental Biology (Chinese Academy of Sciences) has discovered how a single gene helps rice balance root and shoot growth when nitrogen, a key plant nutrient, is in short supply. By harnessing a naturally stronger version of this gene, the team boosted rice yields by up to nearly 24% in field trials, even under reduced fertilizer use.
The findings, published in the journal Science, point to a powerful new way to improve global food security while cutting reliance on synthetic nitrogen fertilizers, which are expensive to produce and a major source of greenhouse gas emissions and water pollution.
Modern agriculture depends heavily on nitrogen fertilizer to drive high yields. But when nitrogen levels in soil drop, crops typically respond by channeling more energy into roots to search for nutrients, sacrificing shoot growth and grain production. That survival strategy works in the wild, but it limits harvests on farms.
Until now, scientists did not know what molecular switch controlled this trade-off. The new study identifies a gene in rice, called WRINKLED1a, as the central regulator that coordinates how the plant grows above and below ground in response to nitrogen availability.
In greenhouse and field experiments, the researchers tested what happens when WRINKLED1a is turned up or shut down. Rice plants lacking a functional version of the gene lost their ability to ramp up root growth under low-nitrogen conditions and also showed weaker shoot growth when nitrogen was plentiful. In contrast, plants engineered to overexpress WRINKLED1a grew more vigorously in both roots and shoots and kept a more stable balance between the two as nitrogen levels changed.
To move beyond the lab and toward real-world farming, the team then looked for natural variation in the gene across rice varieties. By screening more than 3,000 cultivars, they found a version of WRINKLED1a that is expressed more strongly. They bred this “improved” allele into rice plants that originally carried a weaker form of the gene.
In three field trials in Hainan and Anhui provinces in China, the upgraded plants held a steadier root-to-shoot ratio across different nitrogen conditions and produced more grain. Under relatively low nitrogen fertilizer application, they delivered a 23.7% yield increase. Even under high fertilizer use, yields still rose by 19.9%.
The results highlight the gene’s potential as a tool for more sustainable farming, according to corresponding author Zhe Ji, a postdoctoral researcher in the Department of Biology and affiliated with the Calleva Research Centre at Magdalen College of the University of Oxford.
“Our study clearly shows that this regulator is a promising target for sustainable crop improvement. It was extraordinary to see the difference that the improved version of the gene had on rice yields during our field trials,” Ji said in a news release.
Digging deeper into how WRINKLED1a works, the team showed that the gene plays different roles in different parts of the plant.
In shoots, WRINKLED1a acts as an activator, turning on another regulatory gene known as NGR5 that promotes branching. More branches can mean more sites for grain production. In roots, WRINKLED1a switches on genes involved in nitrogen uptake, helping plants pull more of the nutrient from the soil.
The gene also interferes with a protein complex in roots that normally prevents the buildup of auxin, a plant hormone that stimulates root growth. By disrupting this complex only in roots and not in shoots, WRINKLED1a helps rice adjust its root system without triggering the usual penalty in above-ground growth. That tissue-specific behavior appears to be key to avoiding the classic “more roots, less shoot” trade-off.
Rice is the staple food for more than half of the world’s population, and demand is rising as global population grows. At the same time, climate change is putting rice harvests at risk. Studies suggest that every 1 degree Celsius increase in temperature during the rice-growing season can cut yields by more than 8%.
Nitrogen fertilizer is also one of the biggest costs for rice farmers, sometimes making up about a third of total production expenses. Producing and applying that fertilizer releases greenhouse gases and can contaminate waterways when excess nitrogen runs off fields.
By enabling plants to maintain high yields with less nitrogen, the WRINKLED1a strategy could help farmers in both wealthy and low-income regions. For smallholder farmers who cannot afford large amounts of fertilizer, varieties with a stronger version of the gene could mean more reliable harvests from the same land. For large-scale producers, it could lower input costs and environmental impacts.
Lead author Shan Li of Nanjing Agricultural University noted the gene offers a way to redesign how crops respond to nutrient stress.
“WRINKLED1a helps rice avoid the usual ‘more roots, less shoot’ trade-off under nitrogen limitation, supporting stable yields with lower nitrogen inputs. The next step is to investigate whether homologous genes in other crops, such as wheat and maize, can be leveraged to achieve similar outcomes,” Li said in the news release.
That next step could be transformative. If similar genes in other major cereals can be tuned in the same way, the approach might be extended across much of the global grain supply. Researchers could use conventional breeding to introduce stronger natural alleles, or apply gene-editing tools to fine-tune gene activity without adding foreign DNA.
Any widespread rollout will require more testing across different environments, soil types and farming systems, as well as careful assessment of long-term effects on soil health and ecosystems. But the study offers a clear proof of concept: by understanding and adjusting the genetic circuitry that governs how plants allocate their resources, it may be possible to grow more food with fewer inputs.
As climate pressures mount and fertilizer prices fluctuate, that kind of efficiency gain could be crucial. The discovery of WRINKLED1a’s central role in rice growth gives plant scientists and breeders a new, precise handle on one of agriculture’s oldest balancing acts: how to feed the world without overwhelming the planet.
Source: University of Oxford