Refining the genetic architecture of Atlantic salmon (Salmo salar) maturation using genomics-enabled approaches

• Main Author: Sinclair-Waters, Marion
• Other Authors: Peichel, Catherine, University of Helsinki, Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology, Doctoral Programme in Wildlife Biology, Institute of Biotechnology, Helsingin yliopisto, bio- ja ympäristötieteellinen tiedekunta, Luonnonvaraisten eliöiden tutkimuksen tohtoriohjelma, Helsingfors universitet, bio- och miljövetenskapliga fakulteten, Doktorandprogrammet i forskning om vilda organismer, Primmer, Craig, Barson, Nicola
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: Helsingin yliopisto 2021
• Subjects: evolutionary genomics; Atlantic salmon; Salmo salar
• Online Access: http://hdl.handle.net/10138/335021

Understanding the genetic architecture of adaptive traits is a common goal in evolutionary biology. However, there are relatively few well-characterized genetic architectures for adaptive traits in non-model systems, particularly in wild populations. In this thesis, we further characterize the genetic architecture of age at maturity in Atlantic salmon using a combination of genomic-enabled approaches. First, a large-scale genome-wide association study of ~11000 male Atlantic salmon, with ~500K single nucleotide polymorphisms (SNPs) genotypes, was used to identify loci underlying age at maturity. Significant associations were found on 28 of the 29 Atlantic salmon chromosomes, including two strong signals at the six6 and vgll3 gene regions. Furthermore, 116 candidate loci with varying effect sizes were identified revealing a mixed genetic architecture with a combination of large-effect loci and a polygenic component consisting of multiple smaller-effect loci. A combination of multi-SNP association methods and individual-level sequencing data was then used to resolve the genetic architecture within the 116 candidate loci for Atlantic salmon age at maturity. The genetic architecture within these candidate loci was relatively simple, where the association was driven by a single mutation. Finally, ~6000 male Atlantic salmon with a high frequency of recombinant alleles at a known large-effect locus spanning two linked genes, vgll3 and akap11, were reared to maturation age. Vgll3 SNP variation was strongly associated with maturation timing, however, akap11 SNP variation showed little to no association with maturation timing, suggesting that variation linked to vgll3 is driving the association at this large-effect locus. Together, these findings further refine our understanding of the genetic architecture for Atlantic salmon age at maturity. Additionally, this thesis provides an analytical framework for characterizing the genetic architecture of adaptive traits in non-model systems. Tässä väitöskirjassa hyödynnetään ...