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A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping

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Abstract

The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms (SNPs) were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including adgrb2, csnkza1, cers5, col22a1, creb5, dnd1, dzank1, dnai1, npy2r, fat3, lrrk2, lrp5, map3k9, and so on. Among these candidate genes, npy2r (neuropeptide Y receptor Y2) was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.

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Acknowledgements

We thank Dr. Yong Zhang, a genetic Professor at Sun Yat-Sen University, for sharing the reference genome sequence of orange-spotted grouper. The work was supported by National Natural Science Foundation of China (31370047), Shenzhen Scientific R&D Grant (GJHS20160331150703934) and Shenzhen Dapeng Special Program for Industrial Development (KY20160102, KY20170205).

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  1. Contributed equally to this work

Authors and Affiliations

  1. BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China

    Hui Yu & Qiong Shi

  2. Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, 518083, China

    Hui Yu, Xinxin You, Jia Li, Xinhui Zhang, Shuai Zhang, Shoujia Jiang, Xueqiang Lin & Qiong Shi

  3. State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, China

    Hao-Ran Lin & Zining Meng

  4. Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China

    Qiong Shi

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  1. Hui Yu
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Correspondence to Xinxin You or Qiong Shi.

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Yu, H., You, X., Li, J. et al. A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping. Sci. China Life Sci. 61, 934–946 (2018). https://doi.org/10.1007/s11427-017-9161-4

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