GHRH, PRP-PACAP and GHRHR Target Sequencing via an Ion Torrent Personal Genome Machine Reveals an Association with Growth in Orange-Spotted Grouper (Epinephelus coioides)

Int J Mol Sci. 2015 Nov 2;16(11):26137-50. doi: 10.3390/ijms161125940.

Abstract

Growth hormone-releasing hormone (GHRH) and the receptor, GHRHR, constitute important components of the hypothalamus-pituitary growth axis and act on the downstream growth hormone (GH). PACAP-related peptide/pituitary adenylate cyclase activating polypeptide (PRP-PACAP) is a paralog of GHRH. These genes all play key roles in development and growth patterns. To improve the quality of cultured fish strains, natural genetic variation must be examined and understood. A mixed linear model has been widely used in association mapping, taking the population structures and pairwise kinship patterns into consideration. In this study, a mass cross population of orange-spotted grouper (Epinephelus coioides) was examined. These candidate genes were found to harbor low nucleotide diversity (θw from 0.00154 to 0.00388) and linkage disequilibrium levels (delay of 50% within 2 kbp). Association mapping was employed, and two single-nucleotide polymorphisms (KR269823.1:g.475A>C and KR269823.1:g.2143T>C) were found to be associated with growth (false discovery rate Q < 0.05), explaining 9.0%-17.0% of the phenotypic variance. The association of KR269823.1:g.2143T>C was also found via haplotype-based association (p < 0.05). The identified associations offer new insights into gene functions, and the associated single-nucleotide polymorphisms (SNPs) may be used for breeding purposes.

Keywords: GHRH; PGM; association analysis; growth; orange-spotted grouper.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Fishes / genetics*
  • Fishes / growth & development*
  • Genetic Association Studies
  • Genetic Variation
  • Genome*
  • Genomics* / methods
  • Genotype
  • Growth Hormone-Releasing Hormone / genetics*
  • Haplotypes
  • Linkage Disequilibrium
  • Peptide Fragments / genetics*
  • Phenotype
  • Pituitary Adenylate Cyclase-Activating Polypeptide / genetics*
  • Polymorphism, Single Nucleotide
  • Protein Precursors / genetics*
  • Quantitative Trait, Heritable
  • Receptors, Neuropeptide / genetics*
  • Receptors, Pituitary Hormone-Regulating Hormone / genetics*

Substances

  • PACAP-related peptide
  • Peptide Fragments
  • Pituitary Adenylate Cyclase-Activating Polypeptide
  • Protein Precursors
  • Receptors, Neuropeptide
  • Receptors, Pituitary Hormone-Regulating Hormone
  • somatocrinin receptor
  • Growth Hormone-Releasing Hormone