Using genomic tools to understand and manage adaptation to climate - PowerPoint PPT Presentation

Using genomic tools to understand and manage adaptation to climate Sally Aitken Department of Forest and Conservation Sciences University of British Columbia

Climate change is already affecting forests globally Extreme events Heat and drought Insects (mountain pine beetle) Diseases (Swiss needle cast)

Natural cold population responses Climatic niche Natural migration distribution from leading edge with warming Adaptation over generations using Climatic gradient standing variation and gene flow Historical range Lagging edge and climate population extirpation warm

Conservation and Management Options cold Long-distance introduction of Assisted species Climatic niche exotics migration distribution with warming Types of assisted migration Climatic gradient Assisted gene flow: Assisted Intentional gene flow translocation of individuals within a species range to Historical range facilitate adaptation to Ex situ and climate anticipated local conservation conditions ( Aitken&Whitlock Monitoring 2013) warm

Seed zones based on local populations no longer match genotypes with climates 2050s Current Mean BC BC Alberta Alberta annual temperature (MAT) Assisted gene flow (AGF) prescriptions needed for natural seedlots, selectively bred material and novel plants.

Risks of actions cold • Altered ecosystems • Maladaptation if predictions Climatic niche are wrong distribution • with warming Lack of public acceptance Climatic gradient Risks of inaction • Low productivity • Dropping timber Historical range supply and climate • Increased pests warm

Focal biological scale varies with discipline Genotypes Populations Species Ecosystems • • • • Insects Clonal forestry Reforestation and Species selection • • • Diseases Plantation restoration Natural or • • Mutualists forestry Breeding assisted range • • • Species diversity Short rotation Local adaptation shifts • • • Habitat crops Adaptive capacity Climatic niche • • • Forest Breeding Genetic diversity projections • • • management Genetic Variable Endangered modification environments species • Homogeneous conservation environments My focus: Populations of long lived, widespread temperate and boreal species

Outline • Genetics of climate adaptation • Genomic approaches for guiding reforestation in a changing climate • Potential of biotech approaches for climate adaptation, insect and pest resistance • Diversity as a tool to mitigate uncertainty of effects of climate change

Moderate to strong local adaptation to climate in temperate & boreal trees; less evidence of other environmental drivers California Sitka spruce planted in 12 o C Oregon ----British Columbia---- Vancouver provenance trial 10 o C 11 o C --------Alaska------------- 8 o C 7 o C 4 o C 5 o C 4 o C 3 o C Aitken and Bemmels. 2016. Evol. Appl.

Seasonal growth and dormancy cycle influenced by $ Environmental$effect$of$ climate$change$ $ GeneAc$effect$of$AGF$from$ both genetics and warmer$provenance$ Growth$ environment Bud$flush$ Summer' Winter' Bud$$$$$$$set$ Bud$flush$ Dormancy$ $ Stresses Stresses& Frost injury Frost$injury$ Drought Drought$ Insects Insects$ Diseases Diseases$ $ Aitken and Bemmels 2016 Evol. Appl.

AdapTree Project: Analyzed phenotypes and genomes for >250 populations of two species Lodgepole pine ‘Interior’ spruce complex Picea glauca Pinus contorta ssp. latifolia hybrid P. engelmannii

Genomics can rapidly assess climate adaptation Genomic data GEA and GWAS Genotype-phenotype (GWAS) Genotype-environment (GEA) identify climate- associated genetic P OPULATION GENOMICS markers (SNPs) L ANDSCAPE E S C C O G I L M E O O N G O N I C M E A G I C L S E COLOGICAL S PATIAL Q UANTITATIVE GENETICS ANALYSIS GENETICS Environmental Phenotypic Phenotype-environment (PEA) data data

Seedlings phenotyped for growth, phenology, cold hardiness, heat and drought stress response in growth chambers or outdoor common gardens Interior spruce H OT H OT DRY M ILD C OLD H OT WET H OT DRY H EAT STRESS HEAT STRESS PiaSmets

Strong associations between cold hardiness and phenology phenotypes and low temperatures 30-year extreme Fall cold injury – lodgepole pine minimum temp. Liepe et al. 2016. 281 populations sampled Evolutionary Applications

Pine and spruce show very similar phenotypic patterns of adaptation to low temperatures Fall cold injury – lodgepole pine Fall cold injury – interior spruce Liepe et al. 2016. Evolutionary Applications

Exome capture and SNP arrays used for genotyping due to large genome size (Suren et al. 2016. Mol Ecol Res) 1) Exon-oriented sequence capture (Nimblegen 40-50Mb capture) • ~23,000 genes per species • >1 million single nucleotide polymorphisms (SNPs) per species Lodgepole pine • ~700 trees/species 2) ~50K SNP Affymetrix array with adaptation candidates • ~19,700 genes • ~32,000 high-quality SNPs • 2,500-4,000 trees/species Interior spruce

Environment- Genotype- environment environment associations associations Genotype- environment associations show complex Genotype- patterns of genotype climate associations adaptation 3 contigs 28 contigs 21 contigs 28 contigs 801 SNPs in 117 “top candidate” genes of lodgepole pine Lotterhos et al. Biorxiv

We risk oversimplifying climate adaptation by focusing on a few genes or climatic factors e.g., patterns of variation for individual SNPs (lodgepole pine) A) “Multi” cluster (SNP from contig #1) A) “Aridity” cluster (SNP from contig #8) Mean Annual Annual Heat:Moisture Temperature Index K. Lotterhos et al. Biorxiv

Yeaman et al. 2016 Science Genetic complexity of adaptation to low temperatures in pine and spruce: A comparative approach 260 pine “top 450 spruce “top candidate” genes candidate” genes 47 “top candidate” genes for adaptation to low temperatures shared by pine and spruce

Genomic analyses identify the same climatic drivers of local adaptation as provenance trials Pine Provenance Trial at 54°N MCMT TD DD_0 R 2 for GEA prediction MAT 0.6 0.6 eFFP FFP CMD 0.4 Eref 0.4 DD5 MSP EMT MWMT AHM SHM 0.2 bFFP PAS MAP 0.2 EXT NFFD 0.0 0.0 0.1 0.2 0.3 0.4 0.5 R 2 from provenance trial data 2 (Unpublished data)

Genomic data recapitulates climatic clines for phenotypic traits Measured cold Freq. of cold injury Lodgepole pine breeding zones injury associated alleles Cold Injury SNPs Freq. of cold injury alleles 0.55 Natural r 2 = 0.76 Frequency of Positive Effect Alleles Selected r 2 = 0.87 Cold injury (%) 0.50 0.45 0.40 0.40 − 1 0 1 2 3 4 5 − 1 0 1 2 3 4 5 MAT MAT 0.55 0.55 MacLachlan et al. 2017. Tree Genetics and Genomes; MacLachlan 2017 PhD dissertation

Selection and breeding for faster growth results in small changes in allele frequency at hundreds of genes 0.020 Height Natural Selected Wilcoxon rank sum 0.015 Lodgepole pine breeding zones p < 0.0001 0.010 0.005 0.000 100 120 140 160 180 200 220 240 0.020 Cold Injury Natural Selected 0.015 0.010 0.005 0.000 MacLachlan et al. 2017. Tree Genetics and Genomes; 120 140 160 180 200 220 240 260 Number of Positive Effect Alleles MacLachlan 2017 PhD dissertation

CoAdapTree project targets adaptation to climate and pathogens in four conifers (S. Aitken, S. Yeaman, R. Hamelin, co-project leaders) Douglas-fir and western larch Lodgepole pine and jack pine Climate Climate adaptation Dothistroma needle Climate adaptation & Swiss needle cast blight resistance & adaptation tolerance tolerance

Pathogen resistance/tolerance: CoAdapTree studying genetics of fungi causing Swiss needle cast and Dothistroma needle blight as well as hosts Risk Risk 1996- 2050s 2006 Identify candidate genes and population Define pathogenicity zones and predict variation for disease resistance or tolerance. disease response to climate change

One source of uncertainty: Climate novelty Mahony et al. 2017. Global Change Biology

Longer rotations…greater uncertainty • Species with long rotations will experience more climate change and more uncertainty • Species diversity and genetic diversity provide insurance • Little opportunity for biotech solutions for resistance to insects or diseases attacking later in life as testing would take decades • Opportunities for biotech applications will be greatest for short-rotation fiber farms

Understanding values and perceptions of stakeholders key to implementing new technologies Acceptance of forest management interventions (N=1,544 households) Completely reject 100.0 Tentativeley reject 90.0 Tentatively Accept Proportion on respondents 80.0 Completely Accept 70.0 Total Accept 60.0 50.0 40.0 30.0 20.0 10.0 0.0 Sc. 1 Sc.2 Sc. 3 Sc. 4 Sc. 5 Sc. 6 Sc. 1 Sc. 2 Sc. 3 Sc. 4 Sc. 5 Sc. 6 Do nothing, Local seeds, no Local seeds, Assisted gene Assisted species GMOs natural regen. breeding with breeding flow migration Hajjar et al. 2014. Can. J. For. Res.