Cyprinus carpio Genome sequencing

We have created a new, fast-growing strain of (probably) the most common cultured fish species globally: common carp. To better understand the impacts of gene regulation in intestinal tissue on growth, we conducted a comparative RNA-Seq transcriptome analysis between intestine samples of Selected and Control groups. After eight weeks of cage culture, weight gain of the Selected group was 20.84% higher. As fish meat is an important source of polyunsaturated fatty acids (FAs) in human diet, we have compared the FA composition of muscles: monounsaturated FAs were more abundant in the control group, but polyunsaturated FAs were more abundant in the Selected group. In total, we found 106 differentially expressed genes (DEGs). Only the endocytosis pathway was significantly enriched in DEGs, with two upregulated genes: il2rb and ehd1. The latter is involved in the growth hormone/insulin-like growth factor (Gh/Igf) axis, which plays a key role in the regulation of growth in animals. Two of the upregulated genes are known to be involved in the fatty acid metabolism, several genes are likely to be indicators of heightened transcription levels, several are associated with metabolic and developmental roles, several with neuronal functions (including two with vision), several with the immune system, and two downregulated genes with the development of vasculature. The higher growth rate of the Selected group is likely to be at least partially attributed to increased endocytosis efficiency and genetically-driven behavioural differences (higher aggression levels). However, there are also indications that this new strain might have slightly impaired immune responses, a higher propensity for inherited diseases leading to sight impairment, as well for neurodegenerative diseases in general. The results contribute to the understanding of the genetic basis for growth in fish, as well as vertebrates in general.