Selective breeding of lodgepole pine and interior spruce generates growth gains but maintains phenotypic and genomic adaptation to climate

Climate change is disrupting local adaptation in temperate and boreal tree species. As climates shift, tree breeding zones are becoming dissociated from their historical climatic optima and no longer represent optimal seed deployment zones. Assisted gene flow (AGF) policies that match reforestation seedlots with future climates require accurate knowledge of genetic variation in climatically adaptive traits in breeding populations. In this thesis I evaluate the effects of selective breeding on climatic adaptation in the two most planted species in western Canada, lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, P. engelmanii and their hybrids), to inform provincial AGF prescriptions. I compared natural stand seedlots (n = 105 pine, 154 spruce) with selectively bred seedlots (n = 20 pine, 18 spruce) from across Alberta and British Columbia in common garden experiments. Phenotypic variation among breeding zones was assessed for growth, phenology and cold hardiness in relation to climate. For both species, phenotypic differences between natural and selected seedlings in growth traits were substantial. Height gains resulted from increased growth rate and delayed growth cessation, but autumn cold hardiness was not substantially reduced. Seedlings were also genotyped for ~30,000 candidate single nucleotide polymorphisms for growth and adaptive traits. Selection for growth has shifted interior spruce hybrid ancestry in some breeding populations, but these effects are not consistent across zones. A genome-wide association study of pine identified many trait-associated SNPs. Positive effect allele frequencies among pine breeding zones were strongly associated with climatic variation. Selection has resulted in small increases in the frequency of positive effect alleles in breeding populations. Associations among cold hardiness phenotypes, genotypes and climate dominated signals of local adaptation were preserved in breeding populations. Selection, breeding and progeny testing combined have produced taller pine and spruce seedlings without compromising climatic adaptation. Strong phenotype-genotype-climate associations suggest AGF will be necessary to match breeding populations with future climates, but selectively bred and natural seedlots can be safely redeployed using the same AGF prescriptions. Multi-locus genomic profiles of adaptive traits associated with climate provide an accurate, rapid method to assess climatic adaptation that is independent from long-term provenance trials.Forestry, Faculty ofForest and Conservation Sciences, Department ofGraduat