Loci associated with variation in gene expression and growth in juvenile salmon are influenced by the presence of a growth hormone transgene

Abstract

Background: Growth regulation is a complex process influenced by genetic and environmental factors. We examined differences between growth hormone (GH) transgenic (T) and non-transgenic (NT) coho salmon to elucidate whether the same loci were involved in controlling body size and gene expression phenotypes, and to assess whether physiological transformations occurring from GH transgenesis were under the influence of alternative pathways. The following genomic techniques were used to explore differences between size classes within and between transgenotypes (T vs. NT): RNA-Seq/Differentially Expressed Gene (DEG) analysis, quantitative PCR (qPCR) and OpenArray analysis, Genotyping-by-Sequencing, and Genome-Wide Association Study (GWAS). Results: DEGs identified in comparisons between the large and small tails of the size distributions of T and NT salmon (NT Large , NT Small , T Large and T Small) spanned a broad range of biological processes, indicating widespread influence of the transgene on gene expression. Overexpression of growth hormone led to differences in regulatory loci between transgenotypes and size classes. Expression levels were significantly greater in T fish at 16 of 31 loci and in NT fish for 10 loci. Eleven genes exhibited different mRNA levels when the interaction of size and transgenotype was considered (IGF1, IGFBP1, GH, C3-4, FAS, FAD6, GLUT1, G6PASE1, GOGAT, MID1IP1). In the GWAS, 649 unique SNPs were significantly associated with at least one study trait, with most SNPs associated with one of the following traits: C3_4, ELA1, GLK, IGF1, IGFBP1, IGFII, or LEPTIN. Only 1 phenotype-associated SNP was found in common between T and NT fish, and there were no SNPs in common between transgenotypes when size was considered. Conclusions: Multiple regulatory loci affecting gene expression were shared between fast-growing and slowgrowing fish within T or NT groups, but no such regulatory loci were found to be shared between NT and T groups. These data reveal how GH overexpression affects the regulatory responses of the genome resulting in differences in growth, physiological pathways, and gene expression in T fish compared with the wild type. Understanding the complexity of regulatory gene interactions to generate phenotypes has importance in multiple fields ranging from applications in selective breeding to quantifying influences on evolutionary processes.

Comparing Transcriptomes Reveals Key Metabolic Mechanisms in Superior Growth Performance Nile Tilapia (Oreochromis niloticus)

“…To some extent, these studies have revealed the relationship between growth performance differences and genes in aquatic animals; however, the available research is insufficient to elucidate the mechanisms of transcriptome-level regulation of growth differences in wild-type bony fishes, especially cichliforms. In a study of non-wild type coho salmon ( Oncorhynchus keta ), McClelland et al (2020) found that comparative transcriptome results between GH transgenic (T) and non-transgenic (NT) individuals with different growth performance (T large , T small , NT large , and NT small ) indicated that there are widespread regulatory influences acting to influence body size and gene expression traits, in addition to the effects of GH transgenesis. Those authors also showed that multiple regulatory loci affecting gene expression were shared between fast-growing and slow-growing fish within T or NT groups, but no such regulatory loci were found to be shared between those two groups ( McClelland et al, 2020 ).…”

“…In a study of non-wild type coho salmon ( Oncorhynchus keta ), McClelland et al (2020) found that comparative transcriptome results between GH transgenic (T) and non-transgenic (NT) individuals with different growth performance (T large , T small , NT large , and NT small ) indicated that there are widespread regulatory influences acting to influence body size and gene expression traits, in addition to the effects of GH transgenesis. Those authors also showed that multiple regulatory loci affecting gene expression were shared between fast-growing and slow-growing fish within T or NT groups, but no such regulatory loci were found to be shared between those two groups ( McClelland et al, 2020 ). This demonstrates the complexity and important research potential of gene expression differences among individuals with different growth performance.…”

Sexually Dimorphic Growth Stimulation in a Strain of Growth Hormone Transgenic Coho Salmon (Oncorhynchus kisutch)

“…Genomic and endocrinological analyses revealed that, relative to wild-type, GH transgenesis and domestication affected GH and IGF-1 hormone levels as well as gene expression in similar ways (Devlin et al 2009 ; Devlin et al 2013 ; Fleming et al 2002 ; Tymchuk et al 2009 ). Despite parallel responses, genome-wide association studies (GWAS) have found that loci influencing growth and gene expression levels are highly distinct between GH transgenic and wild-type salmon (Kodama et al 2018b ; Mcclelland et al 2020 ). The degree of growth enhancement is also influenced by environmental conditions and genotype-by-environment interactions.…”

Enhancement of Tiger Shrimp Penaeus monodon Resistance to White Spot Syndrome Virus by Overexpression of Antiviral Gene

“…As a model target species, Yasawa et al (2005) evaluated gene transfer methods for black tiger shrimp using green fluorescence protein (GFP) and chloramphenicol acetyl transferase (CAT) as a marker gene. More recently, growth-enhanced transgenic organisms have been the main research subject in many fish species through the introduction of growth hormone gene constructs (Alzaid et al 2018;McClelland et al 2020). However, transgenic technology provides a great prospect in developing strains that have high resistance to disease-causing pathogens.…”