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Open AccessArticle

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)

1
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
2
Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen 518083, China
*
Author to whom correspondence should be addressed.
Academic Editor: Li Lin
Int. J. Mol. Sci. 2015, 16(11), 26137-26150; https://doi.org/10.3390/ijms161125940
Received: 27 August 2015 / Revised: 20 October 2015 / Accepted: 20 October 2015 / Published: 2 November 2015
(This article belongs to the Special Issue Fish Molecular Biology)
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. View Full-Text
Keywords: GHRH; PGM; association analysis; growth; orange-spotted grouper GHRH; PGM; association analysis; growth; orange-spotted grouper
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Guo, L.; Xia, J.; Yang, S.; Li, M.; You, X.; Meng, Z.; Lin, H. 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, 16, 26137-26150.

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