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Mol Biol Rep (2013) 40:50495055 DOI 10.1007/s11033-013-2606-3
Molecular cloning and SNP association analysis of chicken PMCH gene
Guirong Sun Ming Li Hong Li Yadong Tian
Qixin Chen Yichun Bai Xiangtao Kang
Received: 17 August 2012 / Accepted: 29 April 2013 / Published online: 14 May 2013 Springer Science+Business Media Dordrecht 2013
Abstract The pre-melanin-concentrating hormone (PMCH) gene is an important gene functionally concerning the regulations of body fat content, feeding behavior and energy balance. In this study, the full-length cDNA of chicken PMCH gene was amplied by SMART RACE method. The single nucleotide polymorphisms (SNPs) in the PMCH gene were screened by comparative sequence analysis. The obtained non-synonymous coding SNPs (ncSNPs) were designed for genotyping rstly. Its effects on growth, carcass characteristics and meat quality traits were investigated employing the F2 resource population of
Gushi chicken crossed with Anak broiler by AluI CRSPCRRFLP. Our results indicated that the cDNA of chicken PMCH shared 67.25 and 66.47 % homology with that of human and bovine PMCH, respectively. The deduced amino acid sequence of chicken PMCH (163 amino acids) were 52.07 and 50.89 % identical to those of human and bovine PMCH, respectively. The PMCH protein sequence is predicted to have several functional domains, including pro-MCH, CSP, IL7, XPGI and some low complexity sequence. It has 8 phosphorylation sites
and no signal peptide sequence. gga-miR-18a, gga-miR-18b, gga-miR-499 microRNA targeting site was predicted in the 30 untranslated region of chicken PMCH mRNA. In addition, a total of seven SNPs including an ncSNP and a synonymous coding SNP, were identied in the PMCH gene. The ncSNP c.81 A [ T was found to be in moderate polymorphic state (polymorphic index = 0.365), and the frequencies for genotype AA, AB and BB were 0.3648,0.4682 and 0.1670, respectively. Signicant associations between the locus and shear force of breast and leg were observed. This polymorphic site may serve as a useful target for the marker assisted selection of the growth and meat quality traits in chicken.
Keywords Gushi chicken PMCH gene CRS-PCR
RFLP Association analysis Economic traits
Introduction
The hypothalamus plays an important role in the integrated regulation of homeostatic balance and metabolism. The melanin-concentrating hormone (MCH) is a cyclic neuro-peptide isolated initially from salmon pituitary gland, and found to be a...