title: 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).
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.
authors.affiliation: 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. zsdxgl@163.com.
authors.forename: Liang
authors.initials: L
authors.lastname: Guo
authors.affiliation: 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. xiajunh3@mail.sysu.edu.cn.
authors.forename: Junhong
authors.initials: J
authors.lastname: Xia
authors.affiliation: 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. yangsen04@163.com.
authors.forename: Sen
authors.initials: S
authors.lastname: Yang
authors.affiliation: 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. yoursliming11@163.com.
authors.forename: Mingming
authors.initials: M
authors.lastname: Li
authors.affiliation: Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen 518083, China. youxinxin@genomics.cn.
authors.forename: Xinxin
authors.initials: X
authors.lastname: You
authors.affiliation: 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. mengzn@mail.sysu.edu.cn.
authors.forename: Zining
authors.initials: Z
authors.lastname: Meng
authors.affiliation: 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. lsslhr@mail.sysu.edu.cn.
authors.forename: Haoran
authors.initials: H
authors.lastname: Lin
mesh_terms: D000818:Animals; D005399:Fishes / Q000235:genetics* / Q000254:growth & development*; D056726:Genetic Association Studies; D014644:Genetic Variation; D016678:Genome; D023281:Genomics / Q000379:methods; D005838:Genotype; D013007:Growth Hormone-Releasing Hormone / Q000235:genetics*; D006239:Haplotypes; D015810:Linkage Disequilibrium; D010446:Peptide Fragments / Q000235:genetics*; D010641:Phenotype; D051219:Pituitary Adenylate Cyclase-Activating Polypeptide / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011498:Protein Precursors / Q000235:genetics*; D019655:Quantitative Trait, Heritable; D018013:Receptors, Neuropeptide / Q000235:genetics*; D018017:Receptors, Pituitary Hormone-Regulating Hormone / Q000235:genetics*
chemical_list: C108999:PACAP-related peptide; D010446:Peptide Fragments; D051219:Pituitary Adenylate Cyclase-Activating Polypeptide; D011498:Protein Precursors; D018013:Receptors, Neuropeptide; D018017:Receptors, Pituitary Hormone-Regulating Hormone; C039542:somatocrinin receptor; D013007:Growth Hormone-Releasing Hormone
keywords: GHRH; PGM; association analysis; growth; orange-spotted grouper