| dc.description.abstract | 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. | en_US |
