A collaboration among UBC, the B.C. Ministry of Forests and industry uses targeted genome sequencing to produce resilient western redcedar seedlings

By Geoff Gilliard, UBC Faculty of Science

There is a legend that in the 1860s the huge 500-year-old oak beams holding up the dining hall ceiling at Oxford’s New College become infested with beetles and would have to be replaced. But where were trees of sufficient size to be found?

The college forester was called in. He explained that centuries before, an oak grove had been planted for the inevitable day when the 14-metre-long beams needed replacing. Generations of Oxford foresters had passed down the word that those oaks were earmarked for the dining hall.

The traditional approach to breeding involves phenotypic selection — collecting seeds or cuttings from plants whose progeny appear most likely to grow tall and healthy, growing their offspring, and then using prediction models to select the best performing families. These families and their very best trees are then used to produce the next generation, by mating them together in a process that can be repeated for several generations

However, phenotypic selection is slow work where trees are involved. Unlike crop and animal breeders who need to wait only a short time for cows or wheat to mature, foresters may have to wait 60 to 80 years to find out if they’ve selected the best seeds.

But University of British Columbia geneticists — partnered with British Columbia’s Ministry of Forests — have decoded a quicker method of breeding western redcedar, perhaps B.C.’s most iconic tree. The Cedar Enhanced Durability and Resistance (CEDaR) project, funded by Genome British Columbia and Genome Canada, could deliver elite seedlings for reforestation — giving the Ministry of Forests and industry a new tool in breeding climate change-hardy trees.

“CEDaR is a classic example of a symbiotic partnership among government, industry and academia, where none of the individual partners could have done this work on their own,” said Dr. Joerg Bohlmann, a professor with the Michael Smith Laboratories and the departments of Botany and Forest and Conservation Sciences at UBC. “Western redcedar aren’t model organisms, as you’d find in genetic studies on fruit flies or yeast where you can quickly grow a culture. Our partners have decades of data from their tree breeding programs which we would never have had access to without this collaboration.”

The breeding program in B.C. was established in 2010 by project co-leader Dr. John Russell, who died in 2018. Dr. Russell, a research scientist for the B.C. Ministry of Forests, was the world’s leading expert on western redcedar.

Genomic selection speeds up the breeding cycle from 30 years to just five because breeders can select the best parent trees faster. This isn’t genetic modification but rather identifying regions of the western redcedar genome associated with desired traits and using that data to select the best seedlings for the province’s second- and third-growth forests.

Tree of life

Indigenous people of the Pacific Northwest call western redcedar (WRC) the “tree of life.” Archeological digs in Metro Vancouver and on Vancouver Island have revealed baskets, ropes and tools made of WRC estimated to be 5,000 to 8,000 years old. The tree’s wood is used for ceremonies and medicines, clothing and canoes, bentwood boxes and longhouses, as well as the iconic totem poles lining village shores. Cedar continues to be a material of choice for much of contemporary West Coast Indigenous art and culture.

B.C. has the world’s largest stock of standing WRC and is the largest producer of redcedar products in the world — primarily lumber, shakes and shingles, and secondary products such as furniture, doors, leaf oil and log homes. In all, WRC is worth more than $1.3 billion to the province’s economy annually.

Forestry licensees in B.C. are required to replant forests they’ve harvested on Crown land with high-quality seedlings. Companies and other licensees send seed lots to the Ministry of Forests Tree Seed Centre for testing, registration and long-term storage. When it’s time to replant, they order seed back from the Centre to grow seedlings in their nurseries. About ten million WRC seedlings are planted in the province every year.

“Each species has its ecological niche, and how much we’re harvesting in that western redcedar niche will determine how much we plant,” said Annette van Niejenhuis, tree improvement forester at Western Forest Products’ seed orchard and nursery at the Saanich Forestry Centre. She also serves as chair of the Forest Genetics Council of B.C.’s coastal technical advisory committee. “Where western redcedar is ecologically suitable it’s our number one species for regeneration.”

Genomic selection for a changing climate

A faster breeding cycle for second growth forests has become imperative because of B.C.’s changing climate. WRC thrive in moist soil and shady forests at low to middle elevations. After a few years of very dry, hot conditions, a substantial number of WRC are slowly losing their colour and dying in a process called cedar dieback — largely driven by loss of water through the leaves due to heat stress. While precipitation has increased in B.C., more is falling as rain rather than snow. Snowpacks are melting earlier and faster in the spring, and fire seasons are getting longer.

WRC is particularly susceptible to drought. When it becomes extremely hot, WRC trees tend to transpire more and lose more water from leaves than most other conifer tree species. Survival comes down to whether a tree is able to draw in more water than it’s losing.

B.C. has become the only jurisdiction in the world that has implemented climate-based rules to determine where new trees will be planted.

“Trees by a riverbed, for example, should draw enough water from the roots, but if they’re tall enough to be above the canopy they’re exposed to the sun and dying because they’re losing water,” said Dr. Tal Shalev, an expert on forest tree genomics and climate-based seed transfer in Dr. Bohlmann’s research group. “Trees may need to be planted in less exposed areas, such as shaded slopes. Then there are other things like forest fires to consider, so we need to factor in a lot of elements when we’re deciding where to plant.”

The prevailing wisdom in the mid 20th century was that planting local seed was best because local seeds are adapted to their environment. But with the effects of climate change accelerating, locally selected trees may no longer survive 30 or 40 years. In response, B.C. has become the only jurisdiction in the world that has implemented climate-based rules to determine where new trees will be planted.

“Twenty years ago, climate change models and field trials prompted the Ministry of Forests to make plans to replant the most trees used in reforestation higher in elevation and farther north,” said Dr. Alvin Yanchuk, team lead in forest genetics research at B.C. Ministry of Forests and CEDaR’s co-leader. “We established more experiments to plant trees in ‘off-site’ places just to tie down the responses at very drought- or frost-prone sites. As of 2020, we’re moving the trees where we think they’ll be well-adapted in 30 years.”

“Biotic issues such as tree-destroying herbivores, disease and pathogens are also a concern,” said Dr. Bohlmann. “Imagine if western redcedar were affected by forest disease issues related to climate change in the same way as we have seen with hemlock trees in Vancouver’s Stanley Park and the local Northshore Mountains from an infestation by looper moths due to a few years of mild winters. Chances are that we might see something similar with western redcedar as the range of another pathogen or disease expands northward.”

WRC also have a high incidence of heartwood rot, which doesn’t necessarily kill the tree, but does reduce its economic value. Although mature WRC trees produce a natural fungicide which makes them resistant to rotting, saplings don’t produce the chemical. Research scientists have to wait about 20 years for the rot to appear in core samples from trees. This type of long timeframe is where genomic selection can be cost-effective for improving this trait.

All in the family

When glaciers covered much of North America 20,000 years ago, WRC were likely reduced to a population of about 300 trees in northern California. As the ice receded, WRC’s range expanded northward, reaching B.C.’s southern coast, then inland to the Rockies, the eastern slope of the Coast Mountains and finally to Haida Gwaii about 2,200 years ago. All of those trees descended from a small population of ice age survivors, leaving a small gene pool.

Generally, when organisms that are closely related breed, genetic disorders that reduce the biological fitness of a population can occur. WRC, however, are amenable to ‘selfing’ — self-fertilizing themselves by producing both pollen, the male part of the tree, and cones, the female part which contain seeds. Douglas-fir and various spruce and pine trees can self-fertilize as well, but typically don’t produce viable offspring.

“Self-fertilized WRC seedlings aren’t clones — they’re 100 per cent related to themselves because these trees have male and female structures, so it’s possible for them to pollinate their own cones,” Dr. Shalev explains. “You’re going to get the exact same stretches of base pairs because the DNA is coming from the same individual — both chromosomes are exactly the same. We’ve gone as far as five generations of repeated selfing and I think it would have been possible to do even more.”

A genome is the complete set of genes in an organism. Genes are made from deoxyribonucleic acid (DNA) which serves as a blueprint for how an organism grows. Different segments of the DNA chain account for different genetic traits. By determining the exact order of base pairs, and their expression on traits of interest, researchers can identify genetic markers for those traits. Comparing sequences of base pairs across populations of the same species reveals variations in genomes that account for the differences between individuals.

CEDaR’s statistical model for genomic selection began by phenotyping redcedar trees by measuring the key traits on each tree to establish breeding values— a statistical description of how well a tree or family of trees perform in terms of desirable traits above or below the average of the population. The CEDaR team measured a training population of 1,520 18-year-old WRC for eight traits related to growth, wood and leaf chemistry, as well as resistance to pests and pathogens. Selecting for multiple traits meant compromises on ideal values, for example, between height and resilience to heartwood rot.

DNA was extracted from the training trees and they were genotyped (a form of reduced-coverage sequencing) for a range of targeted genome regions. Dr. Shalev, postdoctoral fellow Dr. Omnia Gamal El-Dien, and CEDaR project manager Dr. Carol Ritland used those results to identify 45,378 single nucleotide polymorphisms (SNPs) — a one-letter place where one genome sequence varies from another — that could be associated with WRC’s desirable traits.

The 26 mother trees of the training population were known but the pollen came from a mixed bag of fathers. To determine the relationship between the parents and the 1,520 offspring, the team coded the SNP marker information using zeroes, ones and twos based on which genetic material an offspring inherited. The researchers used that relationship information to predict which trees will have the best breeding values when they mature.

Another tool in the (cedar) toolbox

Five years ago, 119 genomically selected seedlings from the “target” population of 3,000 trees were planted at the Cowichan Lake Research Station. Over the next few years, some of these selections will be given to partners Western Forest Products, Mosaic Forest Management and Ministry seed orchards for seed production.

“The forest industry is curious and supportive about genomic selection but they want to see the result,” said Dr. Yanchuk. “If we decide to use those nursery trees, sales of their seeds would begin 10 years after.”

The results of that genomic selection will be measured in terms of genetic gain, a factor of how much improvement in desirable traits is achieved from an individual tree or group of trees, and the amount of time saved in the selection process.

“Quantitative genetics theory predicts the height growth in CEDaR seed orchard trees will be 25 per cent—better than wild trees, with substantial improvements in a few other of the traits we selected for,” Dr. Yanchuk said. “We’ve planted row plot trials to demonstrate that they’re actually growing as we predicted. The next generation of breeders will measure the trees and analyze the results to show how much genetic gain we actually made as the trees approach commercial ages, but we do that regularly with all of our species.”

In addition to a new generation of resilient, healthy trees, CEDaR is also driving other vital economic benefits.

“We’ve also trained the next generation of forest geneticists and retained that know-how in B.C.,” said Dr. Bohlmann. “That’s something that I’m very proud of having contributed to because genomic selection is a very transferable technology. The people who have trained with us in these projects could apply their knowledge to other tree and crop systems.”

Genomic selection isn’t expected to replace phenotyping entirely, but rather will serve as one of the tools in foresters’ predictive toolbox.

“Although the technology is mature it’s still not totally cost effective yet — for most forest trees,” Dr. Yanchuk said. “The price for genotyping a tree is about $50 and we’ve got to genotype 10,000 to 20,000 trees a year in our program.”

However, the cost of genotyping is dropping as research and development in the health and biotech sectors drive advances in the field. On the other hand, the cost of old-school phenotyping will only increase because people must be paid to go into the forest, measure progeny trials, and select the parent trees.

“Forest genetics in B.C. is very collaborative,” said van Niejenhuis with Western Forest Products. “The industry is invested heavily in this process, as well as Genome BC and Genome Canada. I’ve been looking at this from the outside since they came to the table 20 years ago and CEDaR forms the building blocks. We might not see all of the benefit of it today, but these investments are going to help us find the genetic markers that we’ll be able to use in the future.”