Development and application of genomic tools to the genetic improvement of Atlantic salmon and Chilean mussels

Aquaculture is the fastest growing animal food producing sector in the world, providing almost half of the fish consumed worldwide. However, to meet the future large-scale protein demand associated with world population growth, a sustainable increase in production is required. Genetics and genomics techniques have immense potential for enhancing aquaculture production through selective breeding programs, including the incorporation of marker-assisted selection (MAS). These advances are dependent on applying knowledge of the genetic basis of traits of economic importance (i.e. their heritability and genetic architecture) and the availability of genomic resources, particularly DNA markers, genome linkage maps and genotyping techniques. The overall aim of this Master of Philosophy thesis is to investigate the genetic basis of traits of importance to aquaculture, and to develop and characterise genetic markers for potential use in selective breeding. This will be targeted at two aquacultural species of economic importance: the Atlantic salmon (Salmo salar) and the Chilean mussel (Mytilus chilensis). Since these species are at a very different stage of development of genomic research, with salmon selective breeding and genomics more advanced, species-specific aims were proposed as follows: 1. Atlantic salmon: The objective of this study was to assess the possibility of using gene-specific markers in selective breeding programs by discovering new single-nucleotide polymorphisms (SNPs) in a gene known to regulate growth in mammals and perform a large-scale SNP association study. Novel SNP markers were identified on a gene paralogue (myostatin-1b) that negatively regulates skeletal muscle development and growth. The SNPs were tested for association with growth and fillet related traits measured in a commercial population of 4,800 Atlantic salmon at harvest. 2. Chilean mussel: The overall aim was to assess the possibility of selective breeding for growth-related traits by assessing their heritability, and by discovering and characterising the inheritance of genetic markers in mussel families. To achieve this, the heritability of mussel weight and shell length at different ages was estimated. In addition, a powerful new method for SNP discovery and genotyping - restriction-site associated DNA (RAD) sequencing - was used to identify markers across the mussel genome, with the specific aims of (i) creating a novel genomic resource, (ii) studying aspects of the genomic architecture, and (iii) examining the inheritance of the markers from parents to offspring, given the unusual inheritance patterns of other marker types described in the bivalve genetics literature. In the Atlantic salmon population, three novel SNPs were identified on the myostatin- 1b gene. One of the SNPs, which was located within the 5’ flanking region (g.1086C>T), showed a significant association with several harvest weight traits (P<0.05), suggesting an overall effect on fish growth. The SNP acted in an additive matter, with a change from allele C->T associated with an increase in 30 to 50 g in weight depending on the trait. In the Chilean mussel families, the heritability estimate of body weight was low to moderate (0.11-0.28) and of shell length was not significantly different from zero. These results suggest that selective breeding for body weight is feasible, although environmental factors significantly influence the phenotypic outcome of both the growth-related traits analysed. The analysis of the mussel genome using RAD sequencing with the SbfI enzyme allowed the discovery of 4,537 putative SNPs. Interestingly, a high SNP frequency was detected in the sequenced mussel genome - one of the highest across metazoans - with an average of 1 SNP per 30 base pairs (bp). In addition, significant distortions from expected Mendelian inheritance ratios were observed in the majority (approximately 70 %) of the discovered SNPs. Finally, frequent presence of non-parental alleles in the mussel offspring was detected. Further experiments were designed to explore potential biological and technical explanations for these phenomena using re-sequencing of selected loci by Sanger technology and including a number of additional mussel families for segregation analysis. The results exclude sequence or genotype error as a technical explanation and validate the high frequency of SNPs, Mendelian distortion and non-parental alleles in multiple families. Therefore, the source of these phenomena is likely to be biological but remains unexplained. Selective breeding for growth and fillet related traits is routine in salmon production, and the results of this thesis provide an example of a genetic marker in a myostatin paralogue that could advance this selection via the use of MAS. The results presented from the mussel experiment greatly advance genomic resources for this species and provide evidence for heritability of growth traits, thus suggesting that selective breeding is feasible. However, the significant segregation ratio distortions and presence of non-parental alleles in the offspring demonstrate that the inheritance of genetic markers in mussels has yet to be fully understood before MAS can be applied.