Researchers uncover 'genetic goldmine' underlying plant resilience in extreme desert environment

A Chilean research team created an unrivalled natural laboratory in the Atacama Desert, northern Chile. This desert is one of the most extreme and harshest places on Earth. Credit: Melissa Aguilar
A team of international researchers identified genes that are associated with plant survival in the Atacama Desert, Chile. These findings were published in Proceedings of the National Academy of Sciences. They could be used to help scientists develop resilient crops that can thrive even in drier environments.

"In this era of accelerated global warming, it is crucial to discover the genetic basis to increase crop production and resilience in dry and nutrient poor conditions," Gloria Coruzzi, Carroll & Milton Petrie professor at New York University (NYU), Department of Biology and Center for Genomics and Systems Biology. She co-led the study along with Rodrigo Gutirrez.

This study was a collaboration between botanists and microbiologists as well as ecologists, evolutionary, genomic, and genetic scientists. The unique combination of expertise allowed the team to identify the plants and associated microbes and the genes that allow the Atacama plants adapt to extreme desert conditions. This could help increase crop growth and decrease food insecurity.

Gutirrez, professor at the Pontificia Universidad Catlica de Chile's Department of Molecular Genetics and Microbiology, said, "Our study of plants from the Atacama desert is directly relevant to areas around the world which are becoming increasingly arid with factors such as drought and extreme temperatures and salt in soil and water posing a significant threat for global food production."

In one of the driest areas on Earth, establish a "natural laboratory".

The Atacama Desert, located in northern Chile, is sandwiched between the Pacific Ocean, Andes Mountains and the Pacific Ocean. It is also the most dry place on Earth, except for the poles. There are many plants that grow there, including perennial shrubs and annual grasses. The Atacama plant must also be able to withstand high altitudes, low soil nutrients, and intense sunlight.

Over a period of 10 years, a Chilean research team created an unsurpassed "natural laboratory" at the Atacama desert. They collected data and characterized climate, soil and plants at 22 locations in various vegetational areas and elevations along the Talabre–Leja Transect. They measured a wide range of factors including temperatures that varied more than 50° from day to night, high radiation levels, soil that was mostly sandy and lacking nutrients, and little rain.

Genomics to study the evolution of resilient plants

The Chilean researchers took the preserved soil samples and plant samples, which had been stored in liquid nitrogen for over 1,000 miles, back to the lab to sequence genes in 32 dominant species of Atacama plants and to assess plant-associated soil microbes using DNA sequences. The researchers discovered that some plants developed growth-promoting bacteria close to their roots. This is an adaptive strategy to maximize the intake of nitrogen, a vital nutrient for plant growth in the Atacama's nitrogen-poor soils.

Gabriela Carrasco is an undergraduate researcher who is currently identifying, labeling and collecting plant samples from the Atacama desert. The samples were then transported 1,000 miles and kept under dry ice until Rodrigo Gutirrez's laboratory in Santiago de Chile could process them for RNA extractions. Carrasco is currently collecting Jarava frigida, and Lupinus Oreophilus. Credit: Melissa Aguilar

The NYU researchers next used phylogenomics to identify genes whose protein sequences had been adapted in Atacama species. This approach uses genomic data to reconstruct evolutionary history. They compared the genomes from 32 Atacama species with 32 non-adapted, but genetically identical "sister" species as well as several models.

Coruzzi stated that the goal of this evolutionary tree was to identify changes in amino acids encoded in genes supporting the evolution of Atacama plant adaption to desert conditions.

"This computationally intensive genomic analysis involved the comparison of 1,686,950 sequences of protein across more than 70 species. The super-matrix, which included 8,599764 amino acids, was used for phylogenomic reconstructions of the evolutionary history and Atacama species' evolution," stated Gil Eshel of NYU, who performed this analysis with the High Performance Computing Cluster.

The study found 265 candidate genes, whose protein sequences changed by evolutionary forces from multiple Atacama species. These adaptive mutations were found in genes that may underlie plant adaptation to desert conditions. This includes genes involved in light response and photosynthesis. This could allow plants to adapt to high-light radiation levels in the Atacama. Researchers also discovered genes that regulate stress response, salt detoxification, metal ions and detoxification. This could have been related to Atacama's adaptation to their stressful, nutrient-poor environment.

This "genetic goldmine" reveals what we can learn.

Most of the scientific knowledge about plant tolerance and stress has been derived from traditional laboratory-based studies with a small number of model species. Although these molecular studies are beneficial, they miss the ecological context within which plants evolved.

"By studying an ecosystem within its natural environment, it was possible to identify adaptive genes and molecular mechanisms among species faced with a common harsh environmental," stated Viviana Araus, a former postdoctoral associate of NYU's Center for Genomics and Systems Biology.

"Most of these plant species that we identified in this research were not previously studied." Gutirrez stated that some Atacama plants are closely related with staple crops like potatoes and legumes. The candidate genes we discovered represent a genetic goldmine for engineering more resilient crops, which is a necessity due to increasing desertification on our planet.

Gutirrez, Araus and Mauricio Gonzlez were their Chilean collaborators. Coruzzi at NYU and Eshel worked together on the analysis and phylogenomic pipeline with collaborators in the U.S. including Dennis Stevenson of New York Botanical Garden and Kranthi Varala of Purdue University. Rob DeSalle of American Museum of Natural History was also part of their research teams.

Further exploration of Atacama Desert microbes could reveal clues to life on Mars

Additional information: Plant ecological genomes at the limits of the Atacama desert, Proceedings of the National Academy of Sciences (2021). Information from Proceedings of the National Academy of Sciences, Plant ecological genomics at The Limits of Life in the Atacama Desert (2021). DOI: 10.1073/pnas.2101177118