A “genetic gold mine” discovered for the survival of plants in one of the most difficult environments on the planet

The evolutionary genomics approach identifies genes that enable plants to live in the Atacama Desert, offering clues to designing more resilient crops to cope with climate change.

An international team of researchers has identified genes associated with the survival of plants in one of the harshest environments on earth: the Atacama Desert in Chile. Their findings, published in Proceedings of the National Academy of Sciences (PNAS), can help scientists create resilient crops that can thrive in increasingly drier climates.

“In an era of accelerated climate change, discovering the genetic basis for improving crop production and resilience in dry, nutrient-poor conditions is critical,” said Gloria Coruzzi, Professor Carroll & Milton Petrie at the New York University (NYU) Department of Biology and Center for Genomics and Systems Biology, who co-led the study with Rodrigo Gutiérrez.

The Chilean research team has established an unprecedented “natural laboratory” in the Atacama Desert in northern Chile, one of the driest and harshest environments on earth. Credit: Melissa Aguilar

The study was an international collaboration between botanists, microbiologists, ecologists, evolutionary and genomic scientists. This unique combination of expertise allowed the team to identify the plants, associated microbes, and genes that allow Atacama plants to adapt and thrive in extreme desert conditions, which could ultimately contribute to improve crop growth and reduce food insecurity.

“Our study of plants in the Atacama Desert is directly relevant to areas of the world that are becoming increasingly arid, with factors such as drought, extreme temperatures and salt in the water and soil constituting a significant threat to global food production, ”Gutiérrez said. , professor in the Department of Molecular Genetics and Microbiology of the Pontificia Universidad Católica de Chile.

Establish a “natural laboratory” in one of the driest places on Earth

The Atacama Desert in northern Chile, sandwiched between the Pacific Ocean and the Andes Mountains, is the driest place on the planet (excluding the poles). Yet dozens of plants grow there, including grasses, annuals and perennial shrubs. In addition to a lack of water, Atacama plants have to cope with high altitude, low availability of nutrients in the soil, and extremely high solar radiation.

Gabriela Carrasco, an undergraduate researcher at the time, identifies, labels, collects and freezes plant samples in the Atacama Desert. These samples then traveled 1,000 miles, kept under dry ice to be processed for RNA extractions in Rodrigo Gutiérrez’s laboratory in Santiago, Chile. The species Carrasco collects here are Jarava frigida and Lupinus oreophilus. Credit: Melissa Aguilar

The Chilean research team established an unprecedented “natural laboratory” in the Atacama Desert over a period of 10 years, in which they collected and characterized the climate, soil and plants at 22 sites in different areas of vegetation and altitudes (every 100 meters of altitude) along the Talabre-Lejía transect. Measuring a variety of factors, they recorded temperatures that fluctuated over 50 degrees from day to night, very high radiation levels, largely sandy and nutrient-deprived soil, and minimal rains, most of the time. annual rains falling over a few days.

Using genomics to explore the evolution of resilient plants

Chilean researchers took the plant and soil samples, stored in liquid nitrogen, 1,000 kilometers to the lab to sequence the genes expressed in the 32 dominant plant species of Atacama and assess soil microbes associated with them. plants based on DNA sequences. They found that some plant species developed growth-promoting bacteria near their roots, an adaptive strategy to optimize nitrogen supply – a nutrient essential for plant growth – in the nitrogen-poor soils of the Atacama.

To identify genes whose protein sequences have been adapted in the Atacama species, researchers at NYU then conducted an analysis using an approach called phylogenomics, which aims to reconstruct the history of evolution using data. genomics. In consultation with colleagues at the New York Botanical Garden, they compared the genomes of 32 Atacama plants with 32 unadapted but genetically similar “sister” species, as well as several model species.

“The objective was to use this evolutionary tree based on genomic sequences to identify changes in the acid sequences encoded in genes that support the evolution of Atacama plant’s adaptation to desert conditions, ”said Coruzzi.

“This computationally intensive genomic analysis involved comparing 1,686,950 protein sequences across more than 70 species. We used the resulting super-matrix of 8,599,764 amino acids for the phylogenomic reconstruction of the evolutionary history of the Atacama species, ”said Gil Eshel, who conducted this analysis using NYU’s High Performance Computing Cluster.

The study identified 265 candidate genes whose protein sequence changes were selected by evolutionary forces across several Atacama species. These adaptive mutations have occurred in genes that may underlie the adaptation of plants to desert conditions, including genes involved in the response to light and photosynthesis, which may allow plants to adapt to desert conditions. extremely bright radiance of the Atacama. Likewise, the researchers discovered genes involved in the regulation of the stress response, salt, detoxification and metal ions, which could be linked to the adaptation of these Atacama plants to their stressful and poor environment. in nutrients.

What we can learn from this “genetic gold mine”

The majority of scientific knowledge on stress responses and plant tolerance has been generated by traditional laboratory studies using a few model species. While beneficial, such molecular studies likely ignore the ecological context in which plants evolved.

“By studying an ecosystem in its natural environment, we were able to identify adaptive genes and molecular processes among species facing a difficult common environment,” said Viviana Araus of the Pontificia Universidad Católica de Chile in the laboratory of Gutierrez and former postdoctoral associate at New York University. Center for Genomics and Systems Biology.

“Most of the plant species that we characterized in this research have never been studied before. As some Atacama plants are closely related to staple crops including grains, legumes and potatoes, the candidate genes we have identified represent a genetic gold mine for designing more resilient crops, a necessity counts. given the increasing desertification of our planet, ”said Gutiérrez.

In addition to Gutiérrez and Araus, their collaborators in Chile included Claudio Latorre from the Pontificia Universidad Católica de Chile and Mauricio González from the Universidad de Chile. Coruzzi and Eshel at NYU worked on the phylogenomic pipeline and analysis with collaborators in the United States including Kranthi Varala from Purdue University, Dennis Stevenson from the New York Botanical Garden, Rob DeSalle from the American Museum of Natural History. , as well as members of their research teams.

Reference: “Plant ecological genomics at the limits of life in the Atacama desert” November 1, 2021, Proceedings of the National Academy of Sciencess.
DOI: 10.1073 / pnas.2101177118

This work was supported by the Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007) in Chile, and in the United States by the Zegar Family Foundation (A160051), and by a grant from the Department of Energy Biological and Environmental Research (DE -SC0014377).