It’s no secret that the world’s petroleum-based resources are finite.

At some point, our reliance on fossil fuel as an energy source will need to be replaced by something more viable.

In response to this ever-growing dilemma, the scientists at HudsonAlpha Institute for Biotechnology have been looking into plant genomes – particularly switchgrass, as an important biofuel source.

Since the Human Genome Project, the researchers at HudsonAlpha have become adept at sequencing some of the most complicated genomes. Although the completion of the first human genome was a monumental accomplishment, plant genomes are far more complex.

Humans have two copies of every chromosome, whereas plants possess anywhere from 4 to 10 copies – or even more – of each chromosome. Plants have more variants per chromosome pair and those variants are very repetitive.

The HudsonAlpha Genome Sequencing Center, led by HudsonAlpha Faculty Investigators Dr. Jane Grimwood and Jeremy Schmutz, are experts at generating complex plant genomes. As of this year, they have sequenced reference genomes for more than 175 plants.

Using next-generation and third-generation sequencing technologies, Grimwood and Schmutz’s team is part of a multinational cohort of researchers that have been studying the switchgrass genome for over ten years.

Results from their research were published in the January 2021 issue of Nature. The article describes findings that would not have otherwise been possible without the presence of a high-quality genome assembly.

What exactly is switchgrass?

Switchgrass is a native North American plant that spans from the East Coast to the Rocky Mountains, to Canada, and down into southern Mexico.

The Department of Energy has designated switchgrass a promising candidate for biofuel, a renewable fuel that is produced from the biomass of plants. As a perennial, switchgrass can be harvested for biomass for years after it’s been planted. Switchgrass also can grow on suboptimal land, requiring very little resource input.

Plants observed from the northern region are generally smaller. Despite their size, the northern species can better withstand the cold. The southern variety are large and produce significant biomass, however, they lack the resilience to survive the northern winter climate.

By utilizing the best of both traits, scientists hope to develop a hardier variety that produces large amounts of biomass and can also withstand the cold.

Schmutz and senior scientist Dr. John Lovell worked on the switchgrass genome at HudsonAlpha while collaborators from the University of Texas lab set out on a cross-country mission, collecting switchgrass from all over the region.

The team then planted diversity sets at more than 10 research gardens – spanning eight states and roughly 1,100 miles.

The research team analyzed the genomes of 732 diverse switchgrass plants from the research gardens to map out switchgrass adaptations, linking the traits to underlying genetics.

Along with the new reference genome, the knowledge allows for researchers to map regions of the switchgrass genome that are associated with climate adaptation and fitness.

“The complexity of plant genomes has been a major barrier to developing genetic resources to accelerate effective molecular breeding,” said Lovell. “Genetic models are useful for gaining a foundational understanding of biology. However, to accelerate breeding, we need to find genetic variants that are associated with yield in crop species.

“Now we can develop genome resources for nearly any species, allowing us to study them directly without the need for a less complex model.”