Laying the Groundwork for Assisted Gene Flow: Genomic Basis of Local Adaptation to Climate in Conifers

Climate change is creating a mismatch between conifer populations and the climates they inhabit. Assisted gene flow between populations has the potential to mitigate this maladaptation.  To better plan reforestation for new climates, the AdapTree project is characterizing the extent of local adaptation in two widespread conifers in western Canada, lodgepole pine (Pinus contorta) and the interior spruce species complex (Picea engelmannii, P. glauca, and their hybrids). Seedlings from over 250 populations per species have been phenotyped for climate-related traits including growth, bud phenology, cold hardiness, and heat and drought stress responses under a range of simulated climatic conditions. Whole transcriptome sequencing yielded 348 Gb of sequence data from 97 individuals. From these data, sequence capture probes were designed for exons in >28K genes in lodgepole pine, and for >35K genes in interior spruce. Over 600 seedlings per species have been re-sequenced for >90% of these exons as well as for control, non-coding regions using targeted sequence capture. Relationships between provenance climate and both phenotypes and SNP genotypes are being used to characterize the extent of local adaptation and the importance of various climate drivers in both species. Results will be used to design climate-based seed transfer policies for future climates, and to evaluate the capacity of natural populations to rapidly adapt to new climatic conditions.