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Int. J. Mol. Sci. 2015, 16(11), 26137-26150; doi:10.3390/ijms161125940

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
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)
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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. View Full-Text
Keywords: GHRH; PGM; association analysis; growth; orange-spotted grouper GHRH; PGM; association analysis; growth; orange-spotted grouper
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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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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