Plant genome research to find genes that adapt to harsh climates

Published Nov 24, 2021 

A new study identifies the genetic basis behind the adaptation strategies used by plants to cope with the harsh natural environment. These adaptation strategies include enriching the growth-promoting bacteria in the roots and actively selecting genes necessary for survival, which may be used to guide the cultivation of crops to make them more adaptable to climate change.

"In an era of accelerating climate change, it is vital to reveal the genetic basis for increasing crop yield and resilience under drought and malnutrition conditions," said Gloria Coruzzi, a professor in the Department of Biology and the Center for Genomics and Systems Biology at New York University. She co-led the research with Dr. Rodrigo Gutiérrez, a professor in the Department of Molecular Genetics and Microbiology at the University of Ponticia, Chile. The team identified the plant lineages, related microbes, and genes that allowed Atacama plants to adapt and grow under extreme desert conditions. This research is an international collaboration between botanists, microbiologists, ecologists, evolutionists, and genomicists. It was published in the PNAS.

The Atacama Desert in northern Chile is one of the harshest environments on earth-although it is one of the driest places on earth, dozens of plants still grow here, including grasses, annual plants and perennial shrubs. Atacama's plants must adapt to limited water, high altitude, lack of nutrients in sandy soil, extremely high solar radiation, and temperatures that fluctuate more than 50 degrees from day to night. This provides a natural laboratory for studying the adaptation of plants to extreme environments. Gutiérrez said: "Our research on plants in the Atacama Desert is directly related to increasingly arid regions around the world. Drought, extreme temperatures, and salt in water and soil pose a major threat to global food production."

The Chilean research team collected climate, soil, and plant characteristics at 22 locations in different vegetation zones and altitudes (every 100 meters) in the Talabre-Lejía transect over a period of more than 10 years. They preserved plant and soil samples in liquid nitrogen and transported them to the laboratory to sequence the genes expressed by 32 dominant plants and soil microorganisms related to the plants. They found that some plant species grow growth-promoting bacteria near the roots. This is an adaptive strategy to optimize nitrogen intake in the poor soil of Atacama, which is a key nutrient for plant growth.

Next, researchers at New York University used high-performance computing clusters to conduct systematic genome analysis, comparing the genome sequences of 32 Atacama plants with 32 unsuitable but genetically similar "sister" species and several other model species for comparison. Based on this comparative analysis, they reconstructed the evolutionary history of the highly adaptable Atacama species and identified the genes with altered sequences. "This computationally intensive genome analysis involves comparing 1,686,950 protein sequences of more than 70 species. We use the 8,599,764 amino acid supermatrix generated to reconstruct the systematic genome of the evolutionary history of the Atacama species." "Our goal is to use it. This evolutionary tree based on the genome sequence determines the changes in the amino acid sequence encoded in the genes that support the evolution of the Atacama plant to adapt to the desert environment."

Researchers found 265 genes with altered protein sequences in multiple Atacama plant species. These genes include genes responsible for photosynthesis, detoxification, stress response regulation, and response to salt, light, and metal ions. Genetic changes are conducive to their evolutionary selection-such as the promotion of resilience and adaptability, which may be the basis for the success of Atacama plants in adapting to extreme radiation, high temperature, and malnutrition soil.

The molecular mechanism of plant stress response is usually studied in the laboratory using a few model species. Although these studies provide a wealth of information, they may miss the ecological environment of plant evolution. "By studying the ecosystems in the natural environment, we can identify the genetic and molecular processes that each species adapts to in the face of a common harsh environment," said Viviana Araus of the University of Ponticia, Católica de Chile, a former professor of genomics at New York University. And a postdoctoral assistant at the Center for Systems Biology. "Most of the plant species described in this study have not been studied before. Since some Atacama plants are closely related to major crops (including grains, beans, and potatoes), the candidate genes we identified represent a genetic gold mine that can transform more plastic crops, necessary given the increasing desertification of our planet, "Gutiérrez said.

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