Molecular characterization and haplotype combination of PrRP gene polymorphism and its association with production traits in Chinese native goats

Two novel InDels within the Promoter of SIRT1 are associated with growth traits in chickens

1. The objectives of the present study were to elucidate the relationship between novel variations of the SIRT1 gene and chicken growth traits. In total, 1,429 chickens, including six breeds and a Gushi ×Anka F2 resource population, were genotyped using PCR-RFLP.

2. Two novel InDels (c.-1552_-1553insCG and c.-450_-451delCG) in the promoter of the chicken SIRT1 gene were identified. An association study showed that c.-1552_-1553insCG was significantly correlated with growth traits and serum lipid indicators.

3. The insertion genotype was most highly associated with body weight at day old, two- and four-week-old chickens, and with shank circumference at four and eight weeks of age. The wild type genotype at this site was most highly associated with serum lipid indicators.

4. In contrast, c.-450_-451delCG was significantly correlated with muscle fibre diameter. The SIRT1 gene expression in chickens with different InDel genotypes was analysed and was significantly higher with heterozygous genotypes at both sites in muscle and fat tissue, relative to expression in chickens with the corresponding homozygous genotypes.

5. The effects of different haplotypes on SIRT1 promoter activity showed that promoter activity depends on haplotype, with haplotype HapII exhibiting the highest activity.

6. It was concluded that the SIRT1 gene is associated with chicken growth traits and that the two InDels influence SIRT1 promoter activity in chickens.

Tetra-primer ARMS-PCR identified four pivotal genetic variations in bovine PNPLA3 gene and its expression patterns

Patatin-like phospholipase domain-containing protein 3 (PNPLA3), a member of the patatin like phospholipase domain-containing (PNPLA) family, plays an important role in energy balance, fat metabolism regulation, glucose metabolism and fatty liver disease. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) is a new method offering fast detection and extreme simplicity at a negligible cost for SNP genotyping. In this paper, we investigated the genetic variations at different ages of 660 Chinese indigenous cattle belonging to three breeds (QC, NY, JX) and applied T-ARMS-PCR and PCR-RFLP methods to genotype four SNPs, SNP1: g.A2980G, SNP2: g.A2996T, SNP3: g.A36718G, SNP4: g.G36850A. The statistical analyses indicated that these 4 SNPs affected growth traits markedly (P<0.05) in QC population, whereas combined haplotypes were not (P>0.05). The qPCR (quantitative PCR) indicated that bovine PNPLA3 gene was exclusively expressed in fat tissues. Besides, the analysis between SNP and mRNA expression revealed that, in SNP1, the expression of AG was much higher than AA and GG (P<0.05), which was in accordance with the results of growth traits association analysis, while the results of SNP4 was not. These results supported high potential that SNPs of bovine PNPLA3 gene might be utilized as genetic markers in marker-assisted selection (MAS) for Chinese cattle breeding programs.

Tetra-primer ARMS-PCR identifies the novel genetic variations of bovine HNF-4α gene associating with growth traits

Hepatocyte nuclear factor-4α (HNF-4α), a member of the hepatocyte nuclear factor family, plays an important role in regulating the expression of genes involved in the development, differentiation and normal function of liver and pancreatic β cells, as well as the maintenance of glucose homeostasis. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) is a new method offering fast detection and extreme simplicity at a negligible cost for SNP genotyping. In this paper, we characterize the polymorphisms of the bovine HNF-4α gene in three Chinese indigenous cattle breeds (n=660). Six novel SNPs were identified including 1 mutation in the coding region and others in introns. The statistical analyses indicated that 4 SNPs (g.T53729C, g.A53861G, g.A65188C and g.T65444C) affected growth traits markedly (P<0.05) in Qinchuan cattle (2 years after birth). Besides, haplotypes involving these 4 SNP sites in the bovine HNF-4α gene were identified and their effects on growth traits were also analyzed. The results showed that haplotypes 2, 7, 9 and 11 were predominant and accounted for 73.2%, 59.6%, and 67.1% in Qinchuan, Nanyang and Jiaxian cattle breeds, respectively. Hap9 (TAAT) was extremely predominant in all test populations, which suggested that individuals with Hap9 were more adapted to the environment. Furthermore, 4 combined haplotypes were constructed to guarantee the reliability of analysis results in Qinchuan cattle. There were also significant differences in body length (P<0.05). These findings will benefit for the application of DNA marker related to the growth traits on marker-assisted selection (MAS), and improve the performance of beef cattle.