4.7 Article

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)

Journal

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 16, Issue 11, Pages 26137-26150

Publisher

MDPI
DOI: 10.3390/ijms161125940

Keywords

GHRH; PGM; association analysis; growth; orange-spotted grouper

Funding

  1. Special Fund for the National Natural Science Foundation of China [31370047]
  2. Special Fund for Agro-scientific Research in the Public Interest [201403008, 201403011]
  3. Guangdong Provincial Yang Fan Program [201312H10]
  4. Special Project on the Integration of Industry, Education and Research of Guangdong Province [2013B090800017]

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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 ((w) 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.

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