A new study has identified the genetic underpinnings of adaptive strategies adopted by major plant lineages in a naturally harsh environment. These strategies that include the enrichment of growth-promoting bacteria at the roots and the positive selection of genes necessary for survival, can potentially direct the breeding of crops that are more resilient to climate change.

“In an era of accelerated climate change, it is critical to uncover the genetic basis to improve crop production and resilience under dry and nutrient-poor conditions,” says Gloria Coruzzi, professor at the New York University (NYU) Department of Biology and Center for Genomics and Systems Biology, who co-led the study with Rodrigo Gutiérrez, PhD, professor at the Department of Molecular Genetics and Microbiology at Pontificia Universidad Católica de Chile.

The study, an international collaboration among botanists, microbiologists, ecologists, evolutionary and genomic scientists, is published in an article in the journal Proceedings of the National Academy of Sciences (PNAS), titled, “Plant ecological genomics at the limits of life in the Atacama Desert.”

Gabriela Carrasco, an undergraduate researcher at the time, is identifying, labeling, collecting, and freezing 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 lab in Santiago de Chile. The species Carrasco is collecting here are Jarava frigida and Lupinus oreophilus. [Melissa Aguilar]

The Atacama Desert in Chile—one of the harshest environments on Earth—offers a natural laboratory to study plant adaptation to extreme environments. The team identifies plant lineages, associated microbes, and genes that enable the Atacama plants to adapt and flourish in the extreme desert conditions.

Although the Atacama Desert in northern Chile is one of the driest places on the planet, dozens of plants grow here, including grasses, annuals, and perennial shrubs. Plants in the Atacama must cope with limited water, high altitude, low availability of nutrients in the sandy soil, extremely high radiation from the sun and temperatures that fluctuated more than 50 degrees from day to night.

“Our study of plants in the Atacama Desert is directly relevant to regions around the world that are becoming increasingly arid, with factors such as drought, extreme temperatures, and salt in water and soil posing a significant threat to global food production,” says Gutiérrez.

The Chilean research team collected and characterized the climate, soil, and plants at 22 sites in different vegetational areas and elevations (at every 100 meters of altitude) along the Talabre-Lejía Transect, over 10-years. They preserved plant and soil samples in liquid nitrogen and transported them to the lab to sequence the genes expressed in 32 dominant plant species and plant-associated soil microbes. They found some plant species developed growth-promoting bacteria near their roots, an adaptive strategy to optimize the intake of nitrogen—a nutrient critical for plant growth—in the nitrogen-poor soils of the Atacama.

Next, researchers at NYU conducted phylogenomic analysis by comparing the genome sequences of the 32 Atacama plants with 32 non-adapted but genetically similar ‘sister’ species, and several other model species. Based on this comparative analysis they reconstruct the evolutionary history of the resilient Atacama species and identify the genes with altered sequences.

“The goal was to use this evolutionary tree based on genome sequences to identify the changes in amino acid sequences encoded in the genes that support the evolution of the Atacama plant adaptation to desert conditions,” says Coruzzi.

Gil Eshel, who conducted this analysis using the High Performance Computing Cluster at NYU says, “This computationally intense 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 phylogenomic reconstruction of the evolutionary history of the Atacama species.”

The researchers identify 265 genes in multiple Atacama plant species with changes in their protein sequences that favored their evolutionary selection. The team found these resilience-promoting, adaptive changes in genes such as those responsible for photosynthesis, detoxification, regulation of stress response, and response to salt, light and metal ions.  These genetic changes may underlie the successful adaptation of Atacama plants to extreme radiation, heat and nutrient-poor soil.

The molecular mechanisms of plant stress responses have mostly been studied in labs using a few model species. Although informative, such studies may miss the ecological context in which plants evolve.

“By studying an ecosystem in its natural environment, we were able to identify adaptive genes and molecular processes among species facing a common harsh environment,” says Viviana Araus of the Pontificia Universidad Católica de Chile in Gutierrez’ lab, a former postdoctoral associate at NYU’s Center for Genomics and Systems Biology.

“Most of the plant species we characterized in this research have not been studied before. As some Atacama plants are closely related to staple crops, including grains, legumes, and potatoes, the candidate genes we identified represent a genetic goldmine to engineer more resilient crops, a necessity given the increased desertification of our planet,” says Gutiérrez.

Insights obtained from this study could enhance engineered crop growth and reduce food insecurity.

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