The genetic roadmap of whitebark pine trees, a threatened species, has been sequenced/Quinn Lowrey

A potential breakthrough in the fight to save whitebark pines has been reached through the sequencing of the tree's genome, a milestone scientists say could help the high-altitude tree endure environmental challenges.

“Sequencing the whitebark pine reference genome is an important scientific contribution,” said project lead David Neale, professor emeritus in the Plant Sciences department at the University of California, Davis. “It is the first step in creating genomic tools that can rapidly screen trees for disease resistance and climate adaptation. With this information, researchers can expedite the supply of resistant seedlings for cost-effective restoration.”

The sequence is now accessible at TreeGenes, a Forest Tree Genome Database. A pre-print version of the scientific paper is available on bioRxiv, and it is undergoing the peer-review process.

Keystone Whitebark Pine in Decline

In January 2023, the U.S. Fish & Wildlife Service listed whitebark pine as threatened under the Endangered Species Act after more than 325 million whitebark pine died due to a variety of factors. These threats include the introduced fungal pathogen white pine blister rust, mountain pine beetle outbreaks, wildfire and climate change.

The decline of whitebark pine is of concern given its role as a keystone species across its 80.6 million-acre range in the Western U.S. and Canada. Found up to the tree lines of Western mountains, whitebark pine is particularly imperiled in the Rocky Mountains, Pacific Northwest, and northern Sierra Nevada.

These trees protect snowpack that helps prolong streamflow, supply critical food resources for grizzly bears and red squirrels, and provide cultural value to Indigenous communities through its spiritual significance as a resilient tree species. Whitebark pine also shares a special mutualistic relationship with the Clark’s nutcracker, the primary distributor of whitebark pine seeds.

Whitebark Pines: A Threatened Species

It was a year ago when the U.S. Fish and Wildlife Service agreed to list the tree specis as threatened under the ESA, saying that Whitebark pines, that grow across Western national parks and feed birds and bears and serve as living snow fences, are at risk of disappearing due to disease, beetle attacks, and climate change.

Roughly 70 percent of the species' range lies within the United States, according to Fish and Wildlife staff, with the remaining 30 percent in Canada, where the trees can be found in all of that country's mountain national parks — Waterton Lakes, Banff, Kootenay, Yoho, Mount Revelstoke, Glacier, and Jasper.

More than a decade ago the agency was sued to consider listing the species, a "stone" pine that grows in the very highest reaches of Yellowstone, Glacier, Grand Teton, Olympic, Lassen Volcanic, Rocky Mountain, Yosemite, Sequoia, and Kings Canyon national parks.

Whitebark pine health is designated by the National Park Service as a "vital sign" of the subalpine ecosystems where it grows because it is a keystone species. This means that it is critical to the ecosystems' ecological function, supporting many other plants and animals that live there and influencing ecological processes like snow retention and spring run-off.

Declines in whitebark pine populations have been attributed to an interacting set of factors including blister rust disease, mountain pine beetle infestations, and climate change.

 25,000 Genes Isolated From Oregon Tree

Sequencing conifer genomes can be challenging because they are three to 10 times larger than the human genome. To date, the genomes of loblolly pine, Douglas fir, sugar pine, coastal redwood, giant sequoia, and now, whitebark pine, have all been sequenced, according to the Whitebark Pine Ecosystem Foundation. The Whitebark Pine Genome Project used genetic material from a 150-year-old tree from the Deschutes National Forest near Bend, Oregon, to isolate and sequence the DNA.

Researchers identified 25,362 genes and mapped 87 percent of the genetic material within the whitebark pine’s 12 pair chromosomes. These genomic findings can enhance scientists’ understanding of natural genetic resilience to blister rust, bark beetle outbreaks, drought and other climate extremes.  

New Restoration Opportunities

With the whitebark pine genome sequencing completed, forest managers are now one step closer to developing cost-effective genomic screening tools that identify genetic traits important for whitebark pine survival.

Previous methods involved identifying rust-resistant trees, collecting their cones, growing seedlings in a greenhouse for two years, conducting rust-resistance screenings on the seedlings for three years, and monitoring seedlings for up to an additional five to 10 years before planting in the field. This process costs about $1,200-$1,800 per tree.

Genome sequencing offers a faster, more efficient approach that could reduce costs to as little as $100 per tree and time to a matter of weeks, the foundation said. That is because only small amounts of needle tissue are needed to identify genes responsible for resistance to environmental threats.

The next steps include securing funding to investigate how different environmental conditions are linked to genetic variations within whitebark pine populations.

“Sequencing just one tree, as we did for the reference genome, is not enough,” Neale said. “We need to understand the genetic variation of whitebark pine to develop future genomic tools for rapid screenings and inform restoration efforts of this iconic species. We’d like to test many trees with varying resistance levels and relate this genetic diversity with the genes responsible for resistance.”

The research was done in collaboration with UC Davis, the Whitebark Pine Ecosystem Foundation, Johns Hopkins University and University of Connecticut.

Funding was provided by the USDA Forest Service Forest Health Protection, American Forests, and the Krieger Charitable Trust.