Funding period: 2024-2028
Leads: Nicolas Feau, Isabel Leal, Jun-Jun Liu
Total GRDI funding: $253,500
The project objective aims to uncover the molecular mechanisms underlying Douglas-fir tolerance to drought and Swiss Needle Cast disease (SNC). Douglas-fir is a dominant conifer of high ecological and economic value in the Pacific Northwest. Climate change is intensifying stress in this species through increased drought and more frequent, and severe SNC outbreaks.
Building on previous work that identified drought-related phenotypic and genetic variation in BC-Ministry of Forests breeding population, we are refining this approach by targeting extreme phenotypes through cross-population genome-wide association studies (XP-GWAS). In parallel, controlled-condition experiments will integrate transcriptomics, proteomics, and metabolomics to identify molecular bases of SNC tolerance or resistance.
The knowledge generated will reduce the risk of mismatches between trees and future environments. As part of a broader effort by Pacific Forestry Centre and academic (University of British Columbia & University of Victoria) researchers, this project will translate foundational insights into operational breeding tools that benefit tree improvement programs and the forest industry.
Research tools/processes
- Bioinformatics pipeline for analysis of sequencing reads obtained by target enrichment (XP-GWAS) (R. Perry). Pipeline combining bioinformatic softwares (GATK & mpileup) for the generation of high-quality SNP sets from target enrichment resequencing. Used at PFC for analysis of target enrichment dataset generated for our XP-GWAS analysis of 159 Douglas-fir individuals x probes for 4,200 gene targets.
- DNA extraction optimized for real-time PCR assays used for identification and quantification of SNC on inoculated Douglas-fir needles. DNA isolation was improved by using a cellulose dipstick (Whatman paper) that bind DNA and deliver it directly into the PCR mix. This method reduces the cost and time required for DNA extraction. Tool used at PFC for SNC detection & quantification after inoculation (N. Feau) and at UBC (Hamelin's lab.) for SNC surveillance project on SNC lineages under BC-MoF contract.
- Inoculation protocol of Douglas-fir seedlings with SNC. Protocol optimized in previous project (Feau, Tanney and Leal, “GenSTRESS”) and improved in fy 2024-25. Used at PFC in Tanney's GRDI project. Transferred and used in LeBoldus lab at Oregon State University for operational testing of Douglas-fir breeding population (N. Feau invited in Dec. 2024 at OSU for protocol transfer & SNC cooperative meeting).
- New in-house RNA extraction protocol optimized (C. Woods, D. Wiggins) at PFC for Douglas-fir needles. Improved the quantity and quality of the RNA extracted, and reduces costs, comparatively to previous protocol that used the Spectrum™ Plant Total RNA Kit, Sigma. Will be used at PFC during fy 2024-25 for Act. 2.
Publications
- Hessenauer, P., Feau, N., Heinzelmann, R. and Hamelin, R.C., 2025. Genomic exploration of climate-driven evolution and evolutionary convergence in forest pathogens. Genome Biology and Evolution, 17(5), p.evaf069. https://doi.org/10.1093/gbe/evaf069
- Singh, P., St Clair, J.B., Lind, B.M., Cronn, R., Wilhelmi, N.P., Feau, N., Lu, M., Vidakovic, D.O., Hamelin, R.C., Shaw, D.C. and Aitken, S.N., 2024. Genetic architecture of disease resistance and tolerance in Douglas‐fir trees. New Phytologist, 243(2), pp.705-719. https://doi.org/10.1111/nph.19797
Contact us
For additional information, please contact:
Genomics R&D Initiative
Email: info@grdi-irdg.collaboration.gc.ca