Salmonid genomics to advance our understanding of genome evolution, adaptation and the genetic architecture of complex traits

Salmonid genomics to advance our understanding of genome evolution, adaptation and the genetic architecture of complex traits

Sigbjørn Lien, Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Norway.

The release of high-quality genome sequences for rainbow trout and Atlantic salmon bring these species into the post-genomic era and allow researchers to engage full arsenal of omics technologies to transform our understanding of evolution and complex biological processes, while simultaneously enhancing aquaculture sustainability. These genome projects have delivered key insights into mechanisms for rediploidization and functional specialisation of gene duplicates evolving from the ancient autotetraploid ancestor of salmonids. Salmonids are also well suited for revealing the genetic basis for adaptive divergence in wild populations that are widely distributed across continents and latitudinal clines. Furthermore, independent domestication of several salmonid species facilitates investigations into the genetic basis of contemporary adaptation to aquaculture environments. The existence of ancestral wild populations provides a rare opportunity to detect emerging signatures of selection, experimentally test effects of these adaptations at the phenotypic level, and utilize systems biology approaches that integrate genes, pathways and networks to understand genotype-phenotype links. As a first step towards researching the genetic architecture of adaptation and complex traits we have initiated the ‘1000 salmon genomes project’ which seeks to build a comprehensive catalog of genetic variation for Atlantic salmon. The project has generated whole genome or exome sequence data from 1056 salmon, encompassing both Aquacultural stocks and wild populations from both North America and Europe. Another important initiative is the 'Functional Analysis of All Salmonid Genomes' (FAASG) project that aims to coordinating efforts for comprehensive mapping of the functional elements in the salmonid genomes.