The FTO Gene Is Associated with Growth and Omega-3/-6 Ratio in Asian Seabass

  • Fei Sun
  • Rongjian Tu
  • Jun Hong Xia
  • Xiao Jun Liu
  • Gen Hua Yue
Original Article

Abstract

Polymorphisms in the FTO gene are associated with obesity and body mass index in humans and livestock. Little information of whether FTO plays an important role in aquaculture fish species is available. We cloned and characterized the FTO gene in an economically important food fish species: Asian seabass (Lates calcarifer). The full-length cDNA of the gene is 3679 bp, containing an ORF of 1935 bp encoding 644 amino acids, a 216 bp 5′ UTR and a 1538 bp 3′ UTR. The gene consisted of nine exons and eight introns and was 117,679 bp in length. Phylogenetic analysis revealed that the gene in Asian seabass was closely related to those of Japanese flounder and Nile tilapia. Analysis of its expressions using qRT-PCR showed that it was expressed ubiquitously, but was higher in the liver, stomach and intestine. Comparative analysis of the genomic sequences of part of intron 1 of the gene among 10 unrelated individuals identified two SNPs. Analysis of associations between SNPs and traits (i.e. growth, oil content, omega-3 and -6 contents) in an F2 family demonstrated that the two SNPs were significantly associated with growth, oil content, omega-3 content and omega-3/-6 ratio. Altogether, our data suggest that the gene or/and its linked genes play an important role in growth and fatty acid synthesis, and that the SNPs associated with traits may be used as markers for selecting quicker growth and higher omega-3/-6 ratio at the fingerling stage.

Keywords

FTO Polymorphism Trait Breeding Aquaculture 

Notes

Acknowledgements

We thank our colleagues Zi Yi Wan, Hong Yan Pang, Yan Fei Wen and Bing Liang for supplying technical support for this work, and Baoqing Ye for editing the English of this manuscript.

Funding Information

This research was supported by the National Research Foundation, Prime Minister’s Office, Singapore, under its Competitive Research Program (CRP Award No. NRF-CRP7-2010-01) and the internal fund of Temasek Life Sciences Laboratory, Singapore.

Compliance with Ethical Standards

All handling of fish was conducted in accordance with the guidelines on the care and use of animals for scientific purposes set up by the Institutional Animal Care and Use Committee (IACUC) of the Temasek Life Sciences Laboratory, Singapore. The IACUC has specially approved this study within the project “Breeding of Asian seabass” (approval number is TLL (F)-12-004).

Conflict of Interest

The authors declare that they have no competing interests.

Supplementary material

10126_2018_9831_MOESM1_ESM.jpg (770 kb)
Supplementary Figure 1 Genomic organization of FTO and its neighbouring genes (not drawn to scale) in Asian seabass and humans. In Asian seabass, the FTO gene contains nine exons, which are depicted in blue rectangles, and two SNPs (i.e., SNP1 and 2) are located in intron 1 of the gene. In humans, the FTO gene contains nine exons which are depicted in blue rectangles, and the SNP rs9939609 is found in intron 1 of the gene. (JPG 770 kb)
10126_2018_9831_MOESM2_ESM.jpg (6.4 mb)
Supplementary Figure 2 Conserved and variable regions of the FTO gene in 14 species. (JPG 6561 kb)
10126_2018_9831_MOESM3_ESM.jpg (2.9 mb)
Supplementary Figure 3 Two SNPs (SNP1 and SNP2) detected in intron 1 of the FTO gene and their flanking sequences in Asian seabass. (JPG 2984 kb)
10126_2018_9831_MOESM4_ESM.docx (16 kb)
Supplementary Table 1 Primers used for cloning and characterizing the FTO gene in Asian seabass (DOCX 15 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Fei Sun
    • 1
  • Rongjian Tu
    • 1
    • 2
  • Jun Hong Xia
    • 1
    • 3
  • Xiao Jun Liu
    • 1
    • 4
  • Gen Hua Yue
    • 1
    • 5
    • 6
  1. 1.Temasek Life Sciences LaboratoryNational University of SingaporeSingaporeSingapore
  2. 2.Institute of Crop Breeding and CultivationShanghai Academy of Agricultural SciencesShanghaiChina
  3. 3.State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life SciencesSun Yat-Sen UniversityGuangzhouPeople’s Republic of China
  4. 4.Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of EducationShanghai Ocean UniversityShanghaiChina
  5. 5.Department of Biological SciencesNational University of SingaporeSingaporeSingapore
  6. 6.School of Biological SciencesNanyang Technological UniversitySingaporeSingapore

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