Ecogenomics of transcontinental black spruce: identification of climate adaptation genes across the Canadian boreal landscape

Black spruce (Picea mariana [Mill.] B.S.P.) is an emblematic and ubiquitous species of the North America's boreal forest. While conifer breeding programs have traditionally focused on growth and wood property traits, the study of climate adaptation traits is becoming increasingly prevalent, given the predicted impact of climate change on North America's boreal zone. Through this study, we aimed to identify genes associated with climate adaptation in black spruce across Canada. A total of 254 black spruce trees from 30 populations, covering most of the species' distribution range, were sampled and genotyped for SNPs located in ∼5000 gene loci. Uni- and multivariate Genotype-Environment Association (GEA) approaches, namely LFMM and RDA, as well as an outlier method based on population differentiation (FST) were used to identify genes significantly associated with climatic factors. As such, a total of 77 genes carrying significant candidate SNPs were identified, among which 14 candidates were corroborated by at least two methods. Many of these gene SNPs were also confirmed at a smaller geographic scale, across west - east partitions corresponding to the two main black spruce historical lineages. Notably, significant gene SNPs were more frequently associated to moisture/aridity factors in the western part of the range, and more to temperature factors in the eastern part. The genes carrying these SNPs were also frequently associated to abiotic and biotic stress response. In the context of rapid climate change in the Canadian boreal forest, the results obtained within the framework of this study should support implementing gene conservation efforts while assisting prediction in black spruce breeding programs, which are instrumental to producing adapted planting stock for the large-scale reforestation efforts conducted annually across the Canadian boreal forest.