Science China Life Sciences

, Volume 61, Issue 8, pp 934–946 | Cite as

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

  • Hui Yu
  • Xinxin YouEmail author
  • Jia Li
  • Xinhui Zhang
  • Shuai Zhang
  • Shoujia Jiang
  • Xueqiang Lin
  • Hao-Ran Lin
  • Zining Meng
  • Qiong ShiEmail author
Research Paper


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.


orange-spotted grouper genome-wide association study (GWAS) restriction-site associated DNA sequencing (RAD-seq) growth traits npy2r 


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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).

Supplementary material

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Table S2 Pearson correlation coefficients for body weight and total length


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Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Hui Yu
    • 1
    • 2
  • Xinxin You
    • 2
    Email author
  • Jia Li
    • 2
  • Xinhui Zhang
    • 2
  • Shuai Zhang
    • 2
  • Shoujia Jiang
    • 2
  • Xueqiang Lin
    • 2
  • Hao-Ran Lin
    • 3
  • Zining Meng
    • 3
  • Qiong Shi
    • 1
    • 2
    • 4
    Email author
  1. 1.BGI Education CenterUniversity of Chinese Academy of SciencesShenzhenChina
  2. 2.Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic AnimalsBGI Academy of Marine Sciences, BGI Marine, BGIShenzhenChina
  3. 3.State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic AnimalsSun Yat-Sen UniversityGuangzhouChina
  4. 4.Laboratory of Aquatic Genomics, College of Life Sciences and OceanographyShenzhen UniversityShenzhenChina

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