According to a new study led by plant scientists Pennsylvania State University, a plant’s success may depend on how well the three sets of genetic instructions it carries in its cells cooperate.
In an analysis of the hybrids of two crossbred tree species, the researchers found that two sets of those genes inherited from different species may not work well together, disrupting the plant’s ability to harvest light for photosynthesis and take up key nutrients. However, when the combination of inherited genes better matches up, those plants may be better able to adapt to changing environments.
According to the researchers, who published their findings in Proceedings of the Royal Society B, the work could help inform plant breeding to help produce plants that are more resilient to the changing climate.
How plant genomes interact in hybrids
They focused on two of the three sets of genetic instructions, or genomes: One resides in the cell’s nucleus, or control center, while the other genome is contained in the chloroplast, the structure essential for photosynthesis. The third genome is in the mitochondria, which is crucial for cellular respiration, but the team did not include it in their analysis because the study focused on photosynthetic activity.
“Different components of a plant’s genome—its genetic material—work together to keep it functioning well, and when two different species or populations interbreed, or hybridize, this coordination can break down,” said study first author Michelle Zavala-Paez, doctoral candidate in Penn State’s Intercollege Graduate Degree Program in Ecology.
She explained that when the nuclear and chloroplast—the specialized organelle in plant cells converting light energy into chemical energy, or sugars, using sunlight, water and carbon dioxide, releasing oxygen as a byproduct—genomes have evolved separately in different species, their “teamwork” might not work smoothly in hybrids and result in what is called “cytonuclear mismatch.”
Focused on two closely related tree species in the Pacific Northwest, black cottonwood and balsam poplar, the team was led by study senior author Jill Hamilton, associate professor in Penn State’s College of Agricultural Sciences, director of the Schatz Center for Tree Molecular Genetics and Zavala-Paez’s adviser.
Research methods and genetic analysis
The researchers collected vegetative cuttings—branches that can regrow roots and shoots—from 574 different trees within the natural hybrid zone between black cottonwood and balsam poplar in a geographic swath stretching from Alaska to the southeast through Canada’s Yukon Territory, British Columbia and Alberta and through the U.S. states of Washington, Idaho, Montana and Wyoming. Within this region, the researchers identified six different east-west contact zones where the two species naturally hybridize.
The cuttings were sent to Blacksburg, Virginia, where collaborators at Virginia Tech propagated them under controlled greenhouse conditions. The researchers extracted the DNA and analyzed the genomes of the propagated vegetation, capturing both the whole nuclear and chloroplast genomes.
Sequencing the genomes of so many hybrid trees and analyzing the huge amount of genetic data collected in this research would not have been possible, Hamilton noted, without the immense computing power of the Roar Collab Cluster, the high-performance computing facility managed by the Institute for Computational and Data Sciences at Penn State.
The team also sent the propagated material to field locations in Virginia and Vermont, where seedlings were used to establish common garden experiments. Growing genetically identical trees with mixed genetic ancestry across different environments allowed the team to assess how different nuclear and chloroplast interactions influence plant health, including photosynthetic traits and nutrient use critical to plant fitness.
The researchers said they wanted to determine, when hybridization occurs, whether genes in the nucleus and chloroplast genome that evolved together tend to stay together. Additionally, they aimed to understand if mismatches between nuclear and chloroplast ancestry influence plant performance in different environments.
Overall, the researchers found that the chloroplast genome and the nuclear genes that interact with it did not consistently stay together across hybrid zones. However, in certain locations where steep environmental gradients were observed—including the transition from warmer, more humid maritime conditions associated with coastal environments to cooler boreal environments, like in the Rockies Mountains of northwestern Canada—local environmental conditions appeared to select for genes that had evolved together. In other words, the environment can select for genes that work well together, to stay together.
The researchers also discovered that when a tree’s chloroplast ancestry did not match its nuclear ancestry, its physiological performance could change—sometimes for better, sometimes for worse—depending on the environment in which it grew. For example, trees whose chloroplast and nuclear genomes did not match generally showed lower photosynthetic efficiency—meaning they were less effective at turning sunlight into usable energy. This effect was observed across environments but was exacerbated in the warmer Virginia environment.
Implications for plant evolution and breeding
The study offers new insight into how plants evolve and how scientists might help them face the challenges of a warming world, according to Hamilton, who is currently a Leadership Fellow with Penn State’s Huck Institute of the Life Sciences.
“Understanding which genome combinations perform best could guide breeding programs to develop more resilient plants and help preserve biodiversity in a rapidly changing climate,” Hamilton said. “The study shows that the interaction between nuclear and chloroplast genomes affects how well hybrid plants function, and that the environmental context of these interactions can strengthen, weaken or even reverse the effects of these genetic mismatches.”
Provided by Pennsylvania State University
