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

Sci China Life Sci. 2018 Aug;61(8):934-946. doi: 10.1007/s11427-017-9161-4. Epub 2018 Mar 12.


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.

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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bass / genetics*
  • Bass / growth & development*
  • Body Weight / genetics
  • Chromosome Mapping
  • Chromosomes / genetics
  • Fish Proteins / genetics
  • Genome / genetics*
  • Genome-Wide Association Study / methods*
  • Genotype
  • Linkage Disequilibrium
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods*


  • Fish Proteins