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Genomewide association study for economic traits in the large yellow croaker with different numbers of extreme phenotypes

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Abstract

A traditional genomewide association study (GWAS) detects genotype–phenotype associations by the vast number of genotyped individuals. This method requires large-scale samples and considerable sequencing costs. Extreme phenotypic sampling proposes make GWAS more cost-efficient and are applied more widely. With extreme phenotypic sampling, we performed a GWAS for n-3 highly unsaturated fatty acids (HUFA) and eviscerated weight (EW) traits in the large yellow croaker population. Of the 32,249 and 29,748 detected SNPs for the two traits, three candidate regions were found in each trait. Three candidate regions associated with HUFA were known near genes on chromosomes 4 and 11, and three candidate regions were on chromosome 6, and 15 for the EW trait. By combing through our GWAS results and the biological functional analysis of the genes, we suggest that the FABP, DGAT, ATP8B1, FAF2 and CERS2 genes,  as well as the IGF2, BORA, CYP1A1, GRTP1 and HOX genes are promising candidate genes for n-3 HUFA and EW, respectively, in the large yellow croaker. Moreover, compared with the different numbers of the extreme phenotypic sampling, we conclude that 60% of the extreme phenotypic subsample can obtain a similar result as GWAS with whole phenotypes. Thus, extreme phenotypic sampling could save 40% of the cost for genotyping and DNA extraction without loss of the candidate regions and functional genes. Our study may provide a basis for further genomic breeding and a reference for others who want to perform GWAS with extreme phenotypes.

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Acknowledgements

We thank Kun Ye, Shuangbin Xu, Yuxue Gao and other colleagues in the laboratory who participated in fish sampling and measuring the traits. This work was supported by the Key Projects of the Xiamen Southern Ocean Research Centre (14GZY70NF34) and China Agriculture Research System (CARS-47-G04).

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Authors and Affiliations

  1. College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, People’s Republic of China

    Liang Wan & Xiaoqing Wang

  2. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266325, People’s Republic of China

    Liang Wan & Zhiyong Wang

  3. Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, People’s Republic of China

    Liang Wan, Linsong Dong, Shijun Xiao, Zhaofang Han & Zhiyong Wang

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  1. Liang Wan
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  2. Linsong Dong
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  3. Shijun Xiao
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  4. Zhaofang Han
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  5. Xiaoqing Wang
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  6. Zhiyong Wang
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Correspondence to Zhiyong Wang.

Additional information

Corresponding editor: Silvia Garagna

Liang Wan and Linsong Dong contributed equally to this work. XW revised the manuscript. ZW conceived the research and revised the manuscript. LW drafted the manuscript. LD performed the analysis and co-authored the manuscript. SX screened SNP loci. ZH analysed gene function. Two reviewers revised our manuscript and gave very valuable advice. All authors read and approved the final manuscript.

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Wan, L., Dong, L., Xiao, S. et al. Genomewide association study for economic traits in the large yellow croaker with different numbers of extreme phenotypes. J Genet 97, 887–895 (2018). https://doi.org/10.1007/s12041-018-0973-1

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  • DOI: https://doi.org/10.1007/s12041-018-0973-1

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