Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada.
, EKM Consulting 730 Drake St, Nanaimo, BC, V9S 2T1, Canada.
BMC Genomics. 2020 Feb 27;21(1):185. doi: 10.1186/s12864-020-6586-0.
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).
DEGs identified in comparisons between the large and small tails of the size distributions of T and NT salmon (NT, NT, T and T) spanned a broad range of biological processes, indicating wide-spread 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.
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 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.
生长调控是一个受遗传和环境因素影响的复杂过程。我们研究了生长激素（GH）转基因（T）和非转基因（NT）银大麻哈鱼之间的差异，以阐明是否相同的基因座参与控制体型和基因表达表型，并评估 GH 转基因引起的生理变化是否受替代途径的影响。使用以下基因组技术来探索转基因型（T 与 NT）内和之间大小类别之间的差异：RNA-Seq/差异表达基因（DEG）分析、定量 PCR（qPCR）和 OpenArray 分析、测序基因型分析和全基因组关联研究（GWAS）。
在 T 和 NT 大麻哈鱼体型分布的大小尾之间的比较中鉴定的 DEG 涵盖了广泛的生物学过程，表明转基因对基因表达的广泛影响。生长激素的过表达导致了转基因型和大小类别之间调节基因座的差异。在 31 个基因座中的 16 个和 10 个基因座中的 NT 鱼类中，T 鱼类的表达水平显着更高。当考虑大小和转基因型的相互作用时，11 个基因表现出不同的 mRNA 水平（IGF1、IGFBP1、GH、C3-4、FAS、FAD6、GLUT1、G6PASE1、GOGAT、MID1IP1）。在 GWAS 中，649 个独特的 SNP 与至少一个研究性状显着相关，大多数 SNP 与以下性状之一相关：C3_4、ELA1、GLK、IGF1、IGFBP1、IGFII 或 LEPTIN。在 T 和 NT 鱼类之间发现了一个共同的表型相关 SNP，而在考虑大小的情况下，在转基因型之间没有共同的 SNP。
在 T 或 NT 组内，影响基因表达的多个调节基因座在快速生长和缓慢生长的鱼类之间共享，但在 NT 和 T 组之间没有发现共享的调节基因座。这些数据揭示了 GH 过表达如何影响基因组的调节反应，导致 T 鱼与野生型相比在生长、生理途径和基因表达方面存在差异。了解产生表型的调节基因相互作用的复杂性在从选择性繁殖到量化对进化过程的影响的多个领域都具有重要意义。
