Single nucleotide polymorphism (SNP) at the GHR gene and its associations with chicken growth and fat deposition traits.

1. The growth hormone receptor (GHR) plays crucial roles on chicken growth and metabolism. 2. The full cDNA of the chicken GHR gene was scanned for single nucleotide polymorphisms (SNP) by means of denaturing high-performance liquid chromatography (DHPLC). Three SNP, C6540334T, C6542011T and G6631778A, were genotyped in a F(2) designed full-sib resource population to analyse their associations with chicken growth and fat deposition traits. 3. Fifty-five SNP and two other variations were identified in the 8908 bp region of the GHR gene. Among the 55 SNP, 10 were located in coding exons (6 resulted in changes of amino acids) and 45 were in non-coding regions (introns, 5'UTR and 3'UTR). The nucleotide diversity (theta), corrected for sample size of chicken GHR gene, is 1.45 x 10(-3). Fourteen PCR-RFLP markers were developed in the chicken GHR gene. 4. The G6631778A was associated with body weight at 63 d (BW63), dressed weight (DW) and subcutaneous fat thickness (SFT), BW35 and BW49 (P < 0.01) as well as hatch weight (HW) and BW42 in the male population. However, G6631778A was only associated with BW28 in the female population. G rather than A was dominant for chicken growth and fat deposition. Haplotypes based on the three SNP were associated with BW21, BW70, BW77 and SFT, BW7, BW35, BW42, BW49 and BW56 in males, and associated with BW7 and BW14 in females. For growth in males, the H2 and H6 haplotypes had positive and negative effects, respectively; meanwhile H6 was predominant for fat deposition.