Optimising genomic breeding of farmed salmon

• Main Author: Kokkinias, Panagiotis
• Other Authors: Navarro, Pau, Pong-Wong, Ricardo, Houston, Ross, Hamilton, Alastair, Haley, Chris
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: The University of Edinburgh 2022
• Subjects: Atlantic salmon
• Online Access: https://hdl.handle.net/1842/38810; https://doi.org/10.7488/era/2064

The relatively recent domestication of aquaculture species, such as Atlantic salmon, produces both significant challenges and substantial opportunities for the use of genomic tools in animal breeding which could improve both production and welfare. The recent development of single-nucleotide polymorphism (SNP) genotyping arrays raises the possibility of substantially increasing rates of genetic improvement using genomic selection approaches. Genomic selection utilises computational analysis to combine genome-wide SNP data with trait information to identify individuals carrying the best of the naturally occurring genetic variation for desirable characteristics and hence select the best fish to breed future generations. The project is a collaboration with Landcatch (Hendrix Genetics), a salmon breeding company in Scotland with an extensive experience in genetic breeding programmes, which provide data from several different populations of salmon that have been recorded for traits such as body weight per year, growth and sex. This thesis aimed to investigate the efficiency of genomic prediction within and between populations, by 1) exploring the structure of farmed salmon populations and their genetic diversity, 2) simulating a similar breeding scheme and investigating the impact of various mixing strategies on the accuracy of prediction from genomic evaluation across populations under random and directional selection, 3) estimating the heritability, based on both closely and distantly related individuals, by estimating pedigree-like and SNP-based heritability simultaneously in a single model and 4) investigating the genetic basis of sexual determination and differentiation of farmed Atlantic salmon populations in order to increase the efficiency of breeding programmes. In Atlantic salmon, the broodstock populations follow a breeding programme characterised by discrete generations with a four-year generation interval. This results in the formation of up to four separate parallel lines (‘year groups’) with only ...