Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle

Abstract

We have created a new, fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. To better understand the impacts of gene regulation in intestinal tissue on growth and unsaturated fatty acid content, we conducted a comparative RNA-Seq transcriptome analysis between intestine samples of Selected and Control groups (and corroborated selected results by PCR). After eight weeks of cage culture, weight gain of the Selected group was 20.84% higher. In muscles of the control group, monounsaturated fatty acids (FAs) were more abundant, whereas polyunsaturated FAs were more abundant in muscles of the Selected group. In total, we found 106 differentially expressed genes (DEGs) between the two groups. 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. tll2, which is known to be associated with intestinal regeneration, was extremely highly upregulated in both transcriptomic (infinite) and qPCR (610.70) analyses. Two of the upregulated genes are associated with 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). There are some indications that this new strain might have slightly impaired immune responses, and a higher propensity for inherited diseases leading to sight impairment, as well for neurodegenerative diseases in general, but these indications still need to be confirmed.

Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain

“…As opposed to the above fat deposition-related genes, VPAC2 has lipolytic effects (Karunanithi et al, 2014 ); which suggests that the faster growth of the Xinlong strain is a consequence of a complex bidirectional balance of fat metabolism regulation, rather than unidirectional fat deposition-promoting metabolic control. Finally, ACSF2 is associated with the long-chain fatty acid metabolism (Sano et al, 2015 ), which is in agreement with the higher DHA content observed in the muscles of Xinlong strain (Zhang et al, 2018 ). Finally, some of the identified genes were associated with fat metabolism-related economic traits: TMC7 , neurexin 3 (the same gene family as NRXN1a ) and COL23A1 were associated with milk production of Holstein cows using genome-wide SNPs (Lee et al, 2016b ).…”

Interaction Between the Intestinal Microbial Community and Transcriptome Profile in Common Carp (Cyprinus carpio L.)

“…Similarly, the endocytosis pathway was also significantly differently enriched between control and selection groups in the current study (Supplementary Table 9). The difference between these two studies is that Zhang et al (2018) identified differentially regulated interleukin-2 receptor subunit beta (il2rbeta) in the endocytosis pathway, whereas we identified interleukin-13 receptor subunit alpha-2-like (IL13RA2), transcript variant X2, and interleukin-12 subunit beta-like (IL12B) in the endocytosis pathway were found in this study. Higher expression of IL13RA2 supports the intergenerational transmission of metabolic sequelae (obesity/metabolic diseases) of a high-fat diet (HFD) from father to offspring (Ng et al, 2010).…”

“…Using transcriptome analysis, Zhang et al (2018) found that only the endocytosis pathway was enriched in DEGs in the 2-month-old cage cultured Huanghe carp new strain (selection) compared to the control group. Similarly, the endocytosis pathway was also significantly differently enriched between control and selection groups in the current study ( Supplementary Table 9 ).…”

“…This implies that this gene is involved in the diet-effect intergenerational transmission. Similarly, a high-carbohydrate diet has a positive effect on the growth of and polyunsaturated fatty acid content in the Huanghe carp new strain ( Zhang et al, 2018 ). IL12B and IL12A produce the heterodimer known as interleukin IL-12, which not only elicits intestinal inflammation but also protects the host against microbial invasion ( Danese, 2012 ).…”

Effects of Seasonal Photoperiod on Growth, Lipid Metabolism, and Antioxidant Response in the Huanghe Carp (Cyprinus carpio haematopterus)

“…A carp species called Huanghe carp (Cyprinus carpio haematopterus) is popular among consumers because of its historical and cultural nature. We have utilized selective breeding to develop a new fast-growing Huanghe r carp line based on the traditional Huanghe carp line [19,20]. As temperature, physical activity, and diet may be variable between seasons, the contribution of photoperiod is difficult to isolate.…”