More genome copies in switchgrass leads to increased climate flexibility

by: Sarah Sharman, PhD, Science writer

Most mammals, including humans, have two copies of each gene, one from mom and one from dad. Mammals that inherit more than two copies (a phenomenon known as polyploidy) rarely survive to birth. One known exception is the tetraploid red viscacha-rat which lives comfortably with double the usual number of chromosomes as its ancestors.

Plants, on the other hand, have embraced surviving (and thriving) with many copies of their genome. Many plants have a history of polyploidy, in fact, a quarter of all plants on earth have more than two copies of each chromosome. While the exact benefit of polyploidy has not been fully realized, in plants it is thought to be a major driver of climate and environmental adaptation. Higher numbers of copies of each chromosome could drive shifts in habitat preference, adaptability, and fitness.

Researchers from the HudsonAlpha Genome Sequencing Center (GSC) were investigators in a recent study that looked at the impact of polyploidy on climate adaptation in an important prairie grass called switchgrass (Panicum virgatum). Results from the study were recently published in The Proceedings of the National Academy of Sciences (PNAS).

Using switchgrass to study polyploidy effects on climate adaptation 

Switchgrass is a native North American grass with a widespread distribution across the eastern United States, ranging from Canada to southern Mexico. There has been growing interest in switchgrass since the Department of Energy (DOE) designated it as a promising candidate for biofuel, a renewable fuel source that is produced from the biomass of plants. It can also be used for livestock grazing, habitat restoration, erosion control, flood management, and reduction of nutrient loading of waterways.

Switchgrass plants typically have either four (“tetraploid”, 4X) or eight (“octoploid”, 8X)  copies of each chromosome. Previous work by this team revealed that tetraploid switchgrass populations grow best in their local climate but produce much less biomass when grown in climates that are different from home. This strong pattern of “local” adaptation means that a single cultivar is typically productive only in a narrow geographic range, limiting the efficacy of large-scale breeding efforts.

“Our group, along with many collaborators, has studied switchgrass for over a decade with the goal of harnessing natural variation in switchgrass to create plants that can survive across a range of environments while still growing big and tall for use as biofuel or habitat restoration,” says Jeremy Schmutz, HudsonAlpha faculty investigator and co-director of the HudsonAlpha GSC.

While tetraploid switchgrass has been studied extensively, octoploid switchgrass has not been the subject of such research. In their new study, the collaborative team led by researchers at the HudsonAlpha Institute for Biotechnology and the University of Texas at Austin set out to investigate the effects of variation in polyploidy level on switchgrass climate adaptation by comparing the genetic diversity, environmental niche, and fitness responses across climate gradients between tetraploid and octoploid switchgrass.

Octoploid switchgrass thrives in habitats unsuitable for tetraploid switchgrass 

(A) Differences in habitat suitability for all 4× and 8×. More intense blue coloration indicates higher 8× habitat suitability, while more intense red coloration indicates higher 4× habitat suitability. (From Napier JD, Grabowski PP, et al. PNAS 2022)

The team again relied on more than ten different switchgrass research gardens where a diverse set of switchgrass plants, collected from across its natural range, are grown. When tetraploid switchgrass was grown in gardens outside of their climates of origin, their biomass yield steeply decreased. In contrast, biomass production of octoploid switchgrass decreased far less dramatically when grown outside their climate of origin, and octoploid switchgrass maintained appreciable productivity even in climates far different from where they originated.

Mapping out the collection location of the samples in the diversity panels also revealed large areas where the distributions of tetraploid and octoploid switchgrass do not overlap, suggesting that they have adapted to different niches.

The common garden results point to an intriguing explanation for why tetraploid and octoploid switchgrass occupy these different niches: a generalist-specialist trade-off. Tetraploid switchgrass is a specialist that has consistently high productivity in its ‘home’ climate but is much less successful in different climates. In contrast, octoploid is a generalist with more tolerance to climate variations and is able to maintain high productivity and fitness in a wider variety of climates.

“If you plot tetraploid switchgrass on a map of the switchgrass growing region, there are distinct bare spots where we know switchgrass grows,” says Paul Grabowski, PhD, a GSC computational biologist and co-first author of the study. “The results from the common garden support the idea that octoploid switchgrass has adapted to ‘fill in the gaps’ in climates where tetraploid switchgrass is unable to thrive. It is a fascinating example of how plants have dealt with stress and climate change over time.”

Genetic diversity from ancestral switchgrass gives octoploid switchgrass its generalist properties   

Octoploid switchgrass has the ability to thrive in climates where tetraploid switchgrass cannot, but what is responsible for this difference? Digging into the switchgrass genomes uncovered some interesting information about octoploid switchgrass that may help explain its generalist nature. By comparing the tetraploid specialist to the octoploid generalist, researchers found unique combinations of genetic variation in octoploid switchgrass that likely allowed for the expansion of switchgrass’ ecological niche, representing a valuable breeding resource.

The octoploid genomes contained genetic diversity that came from distant switchgrass lineages, likely resulting from historical gene flow between genetically diverged switchgrass populations. For example, in Midwest switchgrass, octoploids exhibit higher levels of Southern switchgrass ancestry than the tetraploids. The genetic variation from the distant switchgrass lineages promoted the evolution of the switchgrass range into previously unsuitable habitats for tetraploid switchgrass.

The valuable information gleaned from this study will help with the successful breeding of high-yielding switchgrass even amidst the current acceleration of climate change. It may be possible to combine the agricultural benefits of the generalist strategy of octoploids with strong locally adapted trade-offs of tetraploids to buffer the increased variability and unpredictable nature of future climates. Optimizing switchgrass to grow efficiently in many diverse environments is a key component of ensuring its success as a biofuel feedstock.

“On a broader level, the results from our study suggest that careful examination of the genomic divergence present in systems with different ploidy levels could hold answers for capitalizing on natural diversity to mitigate the effects of ongoing environmental shifts,” says Joseph Napier, PhD, a postdoctoral fellow at the University of Texas at Austin and first author of the article. “Other economically valuable crops with histories of polyploidy might benefit from similar analysis to identify the fittest and most adaptable variety to grow in different environments.”

Researchers from Michigan State University, South Dakota State University, USDA Agricultural Research Service Grassland, Soil, and Water Research Laboratory, University of Michigan, Argonne National Laboratory, USDA Natural Resources Conservation Service, USDA Agricultural Research Service Wheat, Sorghum, and Forage Research Unit, Texas A&M University, Oklahoma State University, and the Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory also contributed to the project.