Gene copy number variation (gCNV) contributes to adaptation along environmental gradient

Gene copy number variations (gCNVs) are structural variations that represent a significant source of genetic polymorphism. While single nucleotide polymorphisms (SNPs) have been the primary focus of population and quantitative genomics, recent studies indicated that gCNVs could also play an important role in adaptation notably because of their multiallelic and quantitative nature. In this study, we investigate the role of gCNVs in local adaptation along environmental gradients using extensive genomic datasets in Norway spruce (Picea abies) and Siberian spruce (P. obovata). We used a robust pipeline for the detection and quantification of gCNVs from short-read exome capture data and used haploid samples for validation. We showed that gCNVs are pervasive, representing approximately 11% of the protein coding genes and are notably enriched in genes involved in response to environmental stress, such as temperature tolerance, immune response, and metal ion regulation. Population genetic structure at gCNV was similar to that observed at SNPs. However, some gCNVs also display distinctive adaptive signatures not captured by SNPs. Finally, we conducted gCNV-based genotype-environment association (GEA) and genome-wide association studies (GWAS) to further evidence that gCNVs contribute to local adaptation patterns and to the control of quantitative traits.