Dataset Information

Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus).

ABSTRACT:

Background

Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic linkage map to arrange scaffolds on chromosomal frameworks. QTL analysis is a powerful tool to detect key locations for quantitative traits, especially in aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture.

Results

In this study, a pair of distantly related parent grass carps and their 100 six-month-old full-sib offspring were used to construct a high-density genetic map with 6429 single nucleotide polymorphisms (SNPs) by 2b-RAD technology. The total length of the consensus map is 5553.43 cM with the average marker interval of 1.92 cM. The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. Additionally, according to the growth-related traits of progenies, 30 quantitative trait loci (QTLs), including 7 for body weight, 9 for body length, 5 for body height and 9 for total length, were identified in 16 locations on 5 linkage groups. The phenotypic variance explained for these QTLs varies from 13.4 to 21.6%. Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents.

Conclusion

A high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. Thirty growth related QTLs were detected. After the cross analysis of Parents resequencing data, 17 candidate genes were obtained for further researches.

SUBMITTER: Huang X

PROVIDER: S-EPMC7168995 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe ultrahigh density intensive farming model of grass carp (Ctenopharyngodon idellus) may elicit growth inhibition, decrease flesh quality, and increase disease susceptibility of fish. The degradation in quality and excessive fat accumulation in cultured C. idellus have long been attributed to possible alterations in the lipid metabolism of fish muscle tissues as a result of overnutrition from artificial diets. To investigate the effects of different diets on fish muscle quality, a large-scale metabolomics study was performed on 250 tails of C. idellus.FindingsThe experimental fish were divided into four groups based on sex and diet-female artificial feed (FAF), female grass feed, male artificial feed (MAF), and male grass feed (MGF). After a 113-day rearing period, the artificial feed (AF) group showed a significantly higher total mass of muscle fat (P < 0.01), with the FAF group being the highest. Metabolomics profiling based on liquid chromatography-mass spectrometry revealed distinctive patterns of clustering according to the four groups. Overall, artificial feeding was associated with higher concentrations of docosapentaenoic acid, dihomo-gamma-linolenic acid, and arachidonic acid, whereas grass feeding was associated with elevated n-3 unsaturated fatty acids (UFAs) such as eicosapentaenoic acid, alpha-linolenic acid, and gamma-linolenic acid. Artificial feeding also resulted in significant increased docosahexaenoic acid in MAF muscle than in MGF fish, whereas there was no significance in the comparison of female samples. Metabolic pathway analyses using both targeted and untargeted approaches consistently revealed that arachidonic acid metabolism and steroid hormone biosynthesis pathways were significantly different between AF and grass fed groups.ConclusionsOur results suggest that grass is a better source of dietary fatty acid and protein when compared to artificial feed. Grass feeding could effectively lower triglycerides in serum, reduce fat accumulation, and alter lipid compositions in fish muscle by increasing the concentrations of n-3 UFAs, leading to better nutrition and health.

Project description:This aim of this study was to investigate the effects of dietary aucubin on the growth, flesh quality, and metabolomics of grass carp (Ctenopharyngodon idella). Five diets were designed with the aucubin inclusion of 0 (control diet), 0.2, 0.4, 0.6, and 0.8 g/kg (Auc-0.2, Auc-0.4, Auc-0.6, Auc-0.8) and were fed to grass carp with an initial body weight of 17.0 ± 0.2 g for 60 d. The results indicated that dietary aucubin did not significantly affect the growth performance of grass carp (P > 0.05). Compared to the control, dietary supplementation with 0.2 to 0.8 g/kg aucubin increased flesh hardness, chewiness, the activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), and the contents of total free amino acids (TFAA) and n-3 polyunsaturated fatty acids (n-3 PUFA) (P < 0.05). The contents of malondialdehyde (MDA) and lactic acid (LD) in the flesh were significantly decreased by the addition of 0.4 to 0.6 g/kg aucubin and by the addition of 0.6 to 0.8 g/kg aucubin (P < 0.05), respectively, while the content of delicious amino acids (DAA) was significantly enhanced by the addition of 0.4 to 0.8 g/kg aucubin (P < 0.05). Moreover, the contents of collagen and C22:6n3 (DHA) in the flesh of the Auc-0.8 group were significantly higher than those of the control (P < 0.05). In the metabolomics profiling of flesh, 133 and 135 named differential metabolites were identified in the Auc-0.4 and Auc-0.8 groups, respectively, compared to the control, and these metabolites were found to be involved in the second-grade pathways of "lipid metabolism" and "amino acid metabolism". Regarding gene expression, the mRNA levels of CuZn-SOD, CAT, COL1A1, COL1A2, Smad4, and FAS in flesh were upregulated in the Auc-0.4 and Auc-0.8 groups, and the expression levels of GPx, Nrf2, and TGF-β1 mRNA were also upregulated in the Auc-0.8 group (P < 0.05). In summary, dietary aucubin did not promote growth, but improved the flesh quality of grass carp, which might be associated with the TGF-β/Smad and Nrf2 pathways. The recommended supplementation level of aucubin in the diet of grass carp was 0.6 to 0.8 g/kg.