Biotechnology could make agriculture climate-resilient

Studies of food crops such as corn, sugarcane, rice, wheat, soybeans and cocoa, as well as rubber trees, were presented at an event organized by FAPESP and the Japanese agency JST to foster collaboration between researchers from São Paulo State and Japan.

By Bruno de Pierro  |  Agência FAPESP – Microorganisms found in sugarcane could be one of the keys to the enhancement of crop yields and mitigation of the effects of climate change such as severe droughts that damage several crops used for food and the production of bioenergy.

In a project conducted at the Genomics for Climate Change Research Center (GCCRC) in Brazil, researchers identified fungi and bacteria that boost sugarcane growth and later inoculated these microorganisms into corn plants. Experiments resulted in plants that were more resistant to water scarcity, as well as a threefold increase in biomass.

The GCCRC is an Engineering Research Center (ERC) established by FAPESP and the Brazilian Agricultural Research Corporation (EMBRAPA). It is hosted by the University of Campinas (UNICAMP) in São Paulo State.

“Corn grown with microorganisms that inhabit sugarcane took longer to suffer from drought and recovered faster after suffering water stress,” said geneticist Paulo Arruda, GCCRC’s principal investigator, during a workshop on Biotechnologies for Efficient and Improved Production of Food Crops and Bioenergy, held in late 2019 at FAPESP in São Paulo City.

According to Arruda, the experiments showed that fungi and bacteria can change plant physiology. For example, they can lower leaf temperature by as much as 4 °C, helping plants to control water consumption. In an experiment conducted in Bahia, the researchers observed that the microorganisms also acted against corn stunt, a disease that reduces cob ear yield. Bahia is a state in Northeast Brazil, where long droughts are a frequent occurrence.

Researchers at GCCRC are currently sequencing the genomes of this group of microorganisms, comprising 25,000 bacteria and 10,000 fungi, to determine how they act in plants. Artificial intelligence is used to help analyze the large amount of data. “Algorithms do the work of mapping the genetic patterns associated with the microorganisms’ metabolic functions,” Arruda said, emphasizing the importance of microorganism banks to genetic research and the development of inoculants that can serve as an alternative to chemical fertilizer.

New collaborations

Organized jointly by FAPESP and the Japan Science and Technology Agency (JST) to foster new collaborations, the workshop was attended by scientists from São Paulo State and Japan who research plant biotechnology. “We’ve begun a dialogue with Japanese researchers interested in inoculating microorganisms into rice crops,” said Arruda, who has partnerships with groups in the United States and Europe.

For biologist Marie-Anne Van Sluys, a professor at the University of São Paulo’s Bioscience Institute (IB-USP) and one of the organizers of the event, the meeting was an opportunity for Japanese scientists to engage with colleagues in São Paulo.

Van Sluys said FAPESP and JST want to promote new research partnerships by issuing a joint call for proposals, for example. This would be possible under the aegis of JST’s Strategic International Collaborative Research Program (SICORP).

“Support from SICORP enables two institutions to choose a common research interest and allocate funding for projects selected by both parties,” said JST Program Officer Makie Kokubun.

Tsukasa Nagamine, JST Research Supervisor, presented on projects funded by the agency that resulted in the improvement of crops, especially rice, wheat and soybeans, in countries such as Afghanistan, Madagascar, Kenya and Sudan, stressing the importance of germplasm banks such as that of Japan’s National Agriculture and Food Research Organization (NARO). “One of the research projects that have benefited from NARO’s collection succeeded in developing varieties of plants resistant to striga [or witchweed], a genus of seriously harmful crop pests,” Nagamine said.

Carlos Américo Pacheco, Executive Director of FAPESP, recalled the cooperation agreement with JST signed in 2014. “The dialogue between FAPESP and JST began five years ago to promote scientific and technological collaboration in priority areas, one of which is biotechnology,” he said.

More mature collaborations

Brazilian expertise in genomics applied to agriculture and Japan’s technological prowess can join forces in more mature collaborations that produce cutting-edge knowledge and innovation, according to biologist Anete Pereira de Souza, who is affiliated with the University of Campinas’s Center for Molecular Biology and Genetic Engineering (CBMEG-UNICAMP).

“Novel genetic sequencing techniques have been developed in Japan and this certainly interests us,” Pereira de Souza said. “We’re ready and able to enter into high-level partnerships with competitive Japanese laboratories such as the Riken institute.” Brazil should be considered a strategic scientific partner, she added, and no longer a mere supplier of germplasm [seeds, cells and other genetic material] to other countries.

In recent years, Pereira de Souza has focused on sequencing the genomes of different crops, such as cocoa and rubber, to test a technique called genomic selection, long used in cattle breeding, for example, and now gaining momentum in agriculture.

“It’s an alternative to conventional genetic improvement,” said Pereira de Souza, referring to the standard method of plant breeding that consists of combining progenies from different parental plants to obtain a variety with superior characteristics after several generations.

The problem is that this process is expensive and time consuming, she noted. Conventional genetic improvement takes into consideration only the plant’s observable (phenotypic) traits, whereas genomic selection associates phenotype and genome sequences. “This can be used to predict complex phenotypes based on an analysis of molecular markers, which are pieces of DNA,” she said, stressing that new varieties can be developed with less time and money using this technique.

Pereira de Souza and her team are currently studying genetic data from the rubber tree Hevea brasiliensis with the aim of applying genomic selection to develop more productive and resilient varieties. H. brasiliensis is the main source of latex used to produce natural rubber.

“We urgently need to develop a variety of the natural rubber plant that’s adapted to colder, drier climates as a solution to prevent the action of the fungus that causes South American leaf blight, which affects the plant in warm, humid places. Asian countries such as China and Thailand are particularly interested, as their rubber plantations are infested with the fungus,” she said.

Sugarcane breeding

The much-awaited publication of the complete sugarcane genome will give a massive boost to genomic selection in Brazil, according to Glaucia Mendes Souza, a biochemist at the University of São Paulo’s Chemistry Institute (IQ-USP) and a member of the steering committee for the FAPESP Bioenergy Research Program (BIOEN). The study took ten years and was recently published in GigaScience (read more at: agencia.fapesp.br/32089).

“This means that sugarcane breeding programs won’t have to work in the dark any longer,” Mendes Souza said. BIOEN participated in the Brazilian project that sequenced 99.1% of the sugarcane genome, decoding 373,000 genes and evidencing the plant’s complexity – the human genome has 22,000 genes, for example.

Mendes Souza recently attended a public hearing convened by the Brazilian Senate’s Science and Technology Committee, where she spoke about the possible contributions of science to the new national biofuels policy (RenovaBio) due to enter into force in 2020.

“By 2045, Brazilian ethanol can replace 13% of the petroleum consumed worldwide, as well as contributing to a 5.6% reduction in world carbon emissions in the same period. However, our nation has yet to establish a bioenergy governance framework. RenovaBio fills this gap,” Mendes Souza said.

The workshop held at FAPESP also featured a presentation by Tsai Siu Mui, an agronomic engineer affiliated with the University of São Paulo’s Center for Nuclear Energy in Agriculture (CENA-USP). She has been studying the microbiome of anthropogenic dark earth, a soil type found in the Amazon. This soil was created by prehistoric Amerindians, and its oldest presence has been detected in the Upper Madeira region. It was formed through the deposition of organic material from human activities during long periods of occupation. “It’s extremely fertile and rich in phosphorus and can be recreated with the aim of rehabilitating degraded areas,” she explained.