Left: control. Right: SUSIBA2.Click to enlarge.

Atmospheric methane is the second most important greenhouse gas after carbon dioxide, and is responsible for about 20% of the global warming effect since pre-industrial times. Rice paddies are the largest anthropogenic methane source and produce 7–17% of atmospheric methane. Warm waterlogged soil and exuded nutrients from rice roots provide ideal conditions for methanogenesis in paddies with annual methane emissions of 25–100-million tonnes. This scenario will be exacerbated by an expansion in rice cultivation needed to meet the escalating demand for food in the coming decades.

There is an urgent need to establish sustainable technologies for increasing rice production while reducing methane fluxes from rice paddies. However, ongoing efforts for methane mitigation in rice paddies are mainly based on farming practices and measures that are difficult to implement. Despite proposed strategies to increase rice productivity and reduce methane emissions, no high-starch low-methane-emission rice has been developed.

Here we show that the addition of a single transcription factor gene, barley SUSIBA2, conferred a shift of carbon flux to SUSIBA2 rice, favouring the allocation of photosynthates to aboveground biomass over allocation to roots. The altered allocation resulted in an increased biomass and starch content in the seeds and stems, and suppressed methanogenesis, possibly through a reduction in root exudates.

Three-year field trials in China demonstrated that the cultivation of SUSIBA2 rice was associated with a significant reduction in methane emissions and a decrease in rhizospheric methanogen levels. SUSIBA2 rice offers a sustainable means of providing increased starch content for food production while reducing greenhouse gas emissions from rice cultivation. Approaches to increase rice productivity and reduce methane emissions as seen in SUSIBA2 rice may be particularly beneficial in a future climate with rising temperatures resulting in increased methane emissions from paddies.

—Su et al.

The results represent a culmination of more than a decade of work by the researchers, including Christer Jansson, director of plant sciences at the Department of Energy’s Pacific Northwest National Laboratory and EMSL, DOE’s Environmental Molecular Sciences Laboratory. Jansson and colleagues hypothesized the concept while at the Swedish University of Agricultural Sciences and carried out ongoing studies at the university and with colleagues at China’s Fujian Academy of Agricultural Sciences and Hunan Agricultural University.

The need to increase starch content and lower methane emissions from rice production is widely recognized, but the ability to do both simultaneously has eluded researchers. As the world’s population grows, so will rice production. And as the Earth warms, so will rice paddies, resulting in even more methane emissions. It’s an issue that must be addressed.

—Christer Jansson

Channeling carbon. During photosynthesis, plants absorb carbon dioxide and convert it to sugars to feed or to be stored in various parts of the plant. Researchers have long sought to better understand and control this process to coax out desired characteristics. Funneling more carbon to the seeds in rice results in a plumper, starchier grain. Similarly, carbon and resulting sugars channeled to stems and leaves increases their mass and creates more plant biomass, a bioenergy feedstock.

In early work in Sweden, Jansson and his team investigated how distribution of sugars in plants could be controlled by a special protein called a transcription factor, which binds to certain genes and turns them on or off.

By controlling where the transcription factor is produced, scientists can then dictate where in a plant the carbon—and the resulting sugars—accumulate, Jansson said.

To narrow down the mass of gene contenders, the team started with grains of barley that were high in starch, then identified genes within that were highly active. The activity of each gene then was analyzed in an attempt to find the specific transcription factor responsible for regulating the conversion of sugar to starch in the above-ground portions of the plant, primarily the grains.

The master regulator. Upon discovery of the transcription factor SUSIBA2 (SUgar SIgnaling in BArley 2) further investigation revealed it was a type known as a master regulator. Master regulators control several genes and processes in metabolic or regulatory pathways. As such, SUSIBA2 had the ability to direct the majority of carbon to the grains and leaves, and essentially cut off the supply to the roots and soil where certain microbes consume and convert it to methane.

Researchers introduced SUSIBA2 into a common variety of rice and tested its performance against a non-modified version of the same strain. Over three years of field studies in China, researchers consistently demonstrated that SUSIBA2 delivered increased crop yields and a near elimination of methane emissions.

Next steps. Jansson will continue his work with SUSIBA2 this fall to further investigate the mechanisms involved with the allocation of carbon using mass spectrometry and imaging capabilities at EMSL. Jansson and collaborators also want to analyze how roots and microbial communities interact to gain a more holistic understanding of any impacts a decrease in methane-producing bacteria may have.

Funding for this research was provided by The Swedish University of Agricultural Sciences, the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, the National Natural Science Foundation of China and the Carl Tryggers Foundation.

Resources

• J. Su, C. Hu, X. Yan, Y. Jin, Z. Chen, Q. Guan, Y. Wang, D. Zhong, C. Jansson, F. Wang, A. Schnurer, C. Sun (2015) “Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice,” Nature doi: 10.1038/nature14673