Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Oct 9:9:448.
doi: 10.3389/fgene.2018.00448. eCollection 2018.

Genetic Mapping of Head Size Related Traits in Common Carp (Cyprinus carpio)

Lin Chen  1   2 , Wenzhu Peng  1 , Shengnan Kong  1   2 , Fei Pu  1 , Baohua Chen  1 , Zhixiong Zhou  1 , Jianxin Feng  3 , Xuejun Li  2 , Peng Xu  1   4   5
Affiliations

Genetic Mapping of Head Size Related Traits in Common Carp (Cyprinus carpio)

Lin Chen et al. Front Genet. .

Abstract

Head size is important economic trait for many aquaculture fish which is directly linked to their carcass yield. The genetic basis of head size trait remains unclear in many widely cultured fish species. Common carp (Cyprinus carpio) is one of the most widely studied fish due to its importance on both economic and environmental aspects. In this study, we performed genome-wide association study using 433 Yellow River carp individuals from multiple families to identify loci and genes potentially associated with head size related traits including head length (HL), head length/body length ratio (HBR), eye diameter (ED), and eye cross (EC). QTL mapping was utilized to filter the effects of population stratification and improve power for the candidates identification in the largest surveyed family with a published genetic linkage map. Twelve SNPs showed significant for head size traits in GWAS and 18 QTLs were identified in QTL mapping. Our study combining both GWAS and QTL mapping could compensate the deficiency from each other and advance our understanding of head size traits in common carp. To acquire a better understanding of the correlation between head size and body growth, we also performed comparisons between QTLs of head size traits and growth-related traits. Candidate genes underlying head size traits were identified surrounding the significant SNPs, including parvalbumin, srpk2, fsrp5, igf1, igf3, grb10, igf1r, notch2, sfrp2. Many of these genes have been identified with potential functions on bone formation and growth. Igf1 was a putative gene associated with both head size and body growth in Yellow River carp. The teleost-specific igf3 was a candidate head size related gene, related to both HL and HBR. Our study also indicated the importance of Igf signaling pathway for both growth and head size determination in common carp, which could be potentially used in future selective breeding in common carp as well as other species.

Keywords: GWAS; QTL; common carp; head length; head size; linkage mapping.

PubMed Disclaimer

Figures

FIGURE 1
FIGURE 1
Results from genome-wide association study on head size related traits in Yellow River carp. Significance levels are shown by the red line [–log10(1/n) = 5.02] and suggestive the blue line (4.5). HL, head length; HBR, head length/body length ratio; ED, eye diameter; EC, eye cross.
FIGURE 2
FIGURE 2
QTL mapping and GWAS of head length in Yellow River carp. Results are based on mapQTL 6 and SVS using a single full-sib family.
FIGURE 3
FIGURE 3
QTL mapping and GWAS of head length/body length ratio in Yellow River carp. Results are based on mapQTL 6 and SVS using a single full-sib family.
FIGURE 4
FIGURE 4
QTL mapping and GWAS of eye diameter in Yellow River carp. Results are based on mapQTL 6 and SVS using a single full-sib family.
FIGURE 5
FIGURE 5
QTL mapping and GWAS of eye cross in Yellow River carp. Results are based on mapQTL 6 and SVS using a single full-sib family.
FIGURE 6
FIGURE 6
QTL region and candidate genes for head length/body length ratio in Yellow River carp. Genes are extracted in the ± 50 K bp genome regions around the significant SNPs. Black rectangles represent the candidate genes.
See this image and copyright information in PMC

References

    1. Amthor H., Christ B., Rashid-Doubell F., Kemp C. F., Lang E., Patel K. (2002). Follistatin regulates bone morphogenetic protein-7 (BMP-7) activity to stimulate embryonic muscle growth. Dev. Biol. 243 115–127. 10.1006/dbio.2001.0555 - DOI - PubMed
    1. Beyeler M., Trueb B. (2006). Fgfrl1, a fibroblast growth factor receptor-like gene, is found in the cephalochordate Branchiostoma floridae but not in the urochordate Ciona intestinalis. Comp. Biochem. Physiol. Part B 145 43–49. 10.1016/j.cbpb.2006.06.002 - DOI - PubMed
    1. Carmelo F., Paolo F., Viera K., Elmer K. R., Frederico H., Axel M. (2016). Genetic linkage of distinct adaptive traits in sympatrically speciating crater lake cichlid fish. Nat. Commun. 7:12736. 10.1038/ncomms12736 - DOI - PMC - PubMed
    1. Chen J.-J., Gao X.-T., Yang L., Fu W., Liang L., Li J.-C., et al. (2016). Disruption of Notch signaling aggravates irradiation-induced bone marrow injury, which is ameliorated by a soluble Dll1 ligand through Csf2rb2 upregulation. Sci. Rep. 6:26003. 10.1038/srep26003 - DOI - PMC - PubMed
    1. Dey B. R., Frick K., Lopaczynski W., Nissley S. P., Furlanetto R. W. (1996). Evidence for the direct interaction of the insulin-like growth factor I receptor with IRS-1. Shc, and Grb10. Mol. Endocrinol. 10 631–641. - PubMed