Single nucleotide polymorphisms in ghrelin gene and the resulting genetic variants at ghrelin locus in different strains of indigenous Tswana chickens

Ghrelin is a growth hormone releasing peptide which also affects feed intake in chickens. Ghrelin is encoded by chicken ghrelin gene (cGHRL) found in chromosome 7. Single nucleotide polymorphisms (SNPs) have been reported in cGHRL in Chinese native chickens, but such studies have not been carried out in chickens native to Africa. The aim of this study was therefore to identify SNPs in cGHRL in three strains of indigenous Tswana chickens. DNA was isolated from the blood of 60 indigenous Tswana chickens and three pairs of primers were used for amplification of cGHRL. The resultant plymerase chain reaction (PCR) products were sent to Inqaba Biotec (Pretoria, South Africa) for DNA sequencing. A total of 25 SNPs were found in cGHRL gene in different strains of Tswana chickens. Fourteen of the SNPs have been previously reported and the rest are novel SNPs, which might be unique to Tswana chickens. Two non-synonymous SNPs (A429G and A2355G) were found in the coding region of cGHRL gene in the normal strain and only the A2355G SNP was found in dwarf and naked neck strains. The SNPs in the coding region resulted in three alleles in the normal strains and two alleles in the dwarf and naked neck strains.Keywords: Single nucleotide polymorphisms (SNPs), ghrelin gene, Tswana chicken

Genetic polymorphisms in the stearoyl-CoA desaturase1 (SCD1) gene and their influence on the conjugated linoleic acid (CLA) and monounsaturated fatty acids (MUFA) content of milk fat of Canadian Holstein and Jersey cows

Stearoyl-CoA desaturase1 (SCD1) catalyzes the synthesis of conjugated linoleic acid (CLA) and mono-unsaturated fatty acids (MUFA) in the mammary gland of ruminant animals. We hypothesized that single nucleotide polymorphisms (SNPs) in the coding region, 5' and 3' untranslted regions (UTRs) of the SCD1 gene would influence the activity of SCD1 enzyme and consequently account for some within-breed variations in milk CLA and MUFA. Sequence analysis of the coding region of the SCD1 gene of Jerseys and Holsteins revealed c.702A→G, c.762T→C and c.878C→T SNPs in exon 5 in both breeds and c.435G→A in exon 3 in Holsteins. The SNPs resulted in: A (G435A702T 762C878), A1 (A435A702T 762C878), B (G435G702C 762T878) and B1 (A435G702C 762T878) coding variants in Holsteins and only variants A and B in Jerseys. Only SNP 878C→T resulted in a non-synonymous codon change resulting in p.293Ala and p.293Val protein variants or alleles at the SCD1 locus. Subsequent association studies found significantly higher C10 index, C12 index and C14 index and consequently higher concentrations of C10:1 and C12:1 in p.293AA cows compared to the p.293VV cows in both breeds. The SCD1 genotype had no influence on concentrations of C141, C16:1, C18:1 and CLA in both breeds.Sequence analysis of the 5' and 3' UTRs revealed no SNPs in the 5'UTR and a total of 14 SNPs in the 3'UTR of both breeds. The SNPs were in complete linkage disequilibrium resulting in 3 haplotypes or regulatory variants: H1 (G1571G1644C1763C2053A2584 A3007C3107G3208 T3290G 3497G3682A4399C4533G4881), H2 (G1571G1644A1763C2053A 2584G3007 C3107G3208T3290G3497G 3682A4399C4533G4881) and H3 (T 1571C1644A1763 T2053G2584G3007T 3107A3208C3290A3497A3682T 4399T4533A4881) in Holsteins and only H1 and H3 variants in Jerseys. A subsequent association study involving 862 Holstein cows, found the H1 regulatory variant to be associated with higher C10 and C12 desaturase indices and consequently with higher concentrations of C10:1 and C12:1 compared with the H3 variant. The effects of the H2 variant were intermediate to those of H1 and H3. 3'UTR genotype had no influence on the concentrations of C14:1, C16:1, C18:1 and CLA. The concentrations of C10:1 and C12:1 in milk fat could therefore be due to effects of SNPs in the open reading frame and the 3'UTR regions of the SCD1 gene. These results indicate that SNPs in the coding and 3'UTR regions of the SCD1 gene could be used as markers for genetic selection for increased C10:1 and C12:1 contents of milk