An investigation into growth-related genes in the Australasian snapper, Chrysophrys auratus

Growth is a complex quantitative trait that is controlled by a variety of genetic and environmental factors. Due to its significance in animal breeding programmes, growth is a commonly studied trait in agriculture and aquaculture species. The Australasian snapper, Chrysophrys auratus, supports significant commercial and recreational fisheries in New Zealand and has the potential to be developed as a new aquaculture species. However, the relatively slow growth rate of C. auratus is a constraint and little is known of the specific regulation of growth in this species. The overall aim of this thesis research was to use genome sequence data and transcriptomics to investigate the loci that influence growth rate of C. auratus.  In Chapter Two, the C. auratus Growth Hormone (GH) gene was identified in the reference genome and the structure and polymorphisms were characterised using re-sequenced data. The GH gene was approximately 5,577 bp in length and was comprised of six exons and five introns. Large polymorphic repeat regions were found in the first and third introns, and putative transcription factor binding sites were identified. Phylogenetic analysis of the GH genes of Perciform fish showed conserved non-coding regions and highly variable non-coding regions. The amino acid sequences and putative secondary structures were also largely conserved across this order. In Chapter Three, the genetic variation of two large intronic repeat regions were assessed in wild C. auratus populations and shown to be polymorphic. The intron 1 locus was then assessed in slow- and fast-growing C. auratus for associations with growth rate. No significant differences were detected in the variation between groups; however, trends seen in the results corroborated other studies of an association between shorter introns and increased gene expression. Further investigation with a larger sample size is needed. A high level of heterozygosity was detected in all populations used in this study and may be due to negative selection acting on one allele (485). In Chapter Four, gene expression data was compared between C. auratus at high (21 °C) and low (13 °C) temperatures to investigate how the gene regulation of growth is influenced by temperature. The high temperature treatment (HTT) was characterized by a large number of differentially expressed genes associated with biosynthesis, skeletal muscle components, and catalytic activity while the low temperature treatment (LTT) had an upregulation of genes associated with important degradation pathways. The results of this study also suggest the action of negative feedback on growth regulation in the HTT, which may be a result of chronic heat stress.  This thesis research represents one of the first studies to explore the genetic regulation of growth in C. auratus and makes a significant contribution to the field of research into growth, not only in C. auratus, but also other fish species. The findings presented in this thesis may be applied to a selective breeding programme of C. auratus that aimed to increase the growth rate, and consequently, improve its economic viability as a commercial aquaculture species in New Zealand.