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A Candidate Single Nucleotide Polymorphism in the 3' Untranslated Region of Stearoyl-CoA Desaturase Gene for Fatness Quality and the Gene Expression in Berkshire Pigs.

Lim KS, Kim JM, Lee EA, Choe JH, Hong KC - Asian-australas. J. Anim. Sci. (2015)

Bottom Line: The stearoyl-CoA desaturase (SCD) gene plays a crucial role in the conversion of saturated FAs into monounsaturated FAs (MUFAs), and hence, is among the candidate genes responsible for pig fatness traits.Here, we identified a single nucleotide polymorphism (SNP, c.*2041T>C) in the 3' untranslated region by direct sequencing focused on coding and regulatory regions of porcine SCD.In addition, the SNP showed a significant effect on the SCD mRNA expression levels (p = 0.041).

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Korea.

ABSTRACT
Fatness qualities in pigs measured by the amount of fat deposition and composition of fatty acids (FAs) in pork have considerable effect on current breeding goals. The stearoyl-CoA desaturase (SCD) gene plays a crucial role in the conversion of saturated FAs into monounsaturated FAs (MUFAs), and hence, is among the candidate genes responsible for pig fatness traits. Here, we identified a single nucleotide polymorphism (SNP, c.*2041T>C) in the 3' untranslated region by direct sequencing focused on coding and regulatory regions of porcine SCD. According to the association analysis using a hundred of Berkshire pigs, the SNP was significantly associated with FA composition (MUFAs and polyunsaturated FAs [PUFAs]), polyunsaturated to saturated (P:S) FA ratio, n-6:n-3 FA ratio, and extent of fat deposition such as intramuscular fat and marbling (p<0.05). In addition, the SNP showed a significant effect on the SCD mRNA expression levels (p = 0.041). Based on our results, we suggest that the SCD c.*2041T>C SNP plays a role in the gene regulation and affects the fatness qualities in Berkshire pigs.

No MeSH data available.


Genotypes of the c.*2041T>C SNP in the 3′ UTR of the SCD gene. (a) Sequence chromatograms showing c.*2041T>C SNP. (b) The electrophoresis image of PCR-RFLP for c.*2041T>C SNP. Digestion of PCR products (425 bp) by MspI, show genotypes TT, TC, and CC. The arrowheads show and the size of DNA ladder and fragments. SNP, single nucleotide polymorphism; UTR, untranslated region; SCD, stearoyl-CoA desaturase; PCR-RFLP, polymerase chain reaction-restriction fragment length polymorphism.
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f1-ajas-28-2-151: Genotypes of the c.*2041T>C SNP in the 3′ UTR of the SCD gene. (a) Sequence chromatograms showing c.*2041T>C SNP. (b) The electrophoresis image of PCR-RFLP for c.*2041T>C SNP. Digestion of PCR products (425 bp) by MspI, show genotypes TT, TC, and CC. The arrowheads show and the size of DNA ladder and fragments. SNP, single nucleotide polymorphism; UTR, untranslated region; SCD, stearoyl-CoA desaturase; PCR-RFLP, polymerase chain reaction-restriction fragment length polymorphism.

Mentions: Genomic DNA was isolated from LD muscle samples using a DNA isolation kit (Intronbio., Seongnam, Korea). Polymerase chain reaction (PCR) and direct sequencing analysis for the promoter and coding region of SCD were performed using specific primers in Berkshire pigs (Table 3). The individual genomic sequence data were assembled for identification of polymorphism as described previously (Kim et al., 2012) and used for genotyping (Figure 1a). To further validate the genotypes, all pigs were re-genotyped using PCR-restriction fragment length polymorphism method by using specific primer set and MspI restriction enzyme (Figure 1b).


A Candidate Single Nucleotide Polymorphism in the 3' Untranslated Region of Stearoyl-CoA Desaturase Gene for Fatness Quality and the Gene Expression in Berkshire Pigs.

Lim KS, Kim JM, Lee EA, Choe JH, Hong KC - Asian-australas. J. Anim. Sci. (2015)

Genotypes of the c.*2041T>C SNP in the 3′ UTR of the SCD gene. (a) Sequence chromatograms showing c.*2041T>C SNP. (b) The electrophoresis image of PCR-RFLP for c.*2041T>C SNP. Digestion of PCR products (425 bp) by MspI, show genotypes TT, TC, and CC. The arrowheads show and the size of DNA ladder and fragments. SNP, single nucleotide polymorphism; UTR, untranslated region; SCD, stearoyl-CoA desaturase; PCR-RFLP, polymerase chain reaction-restriction fragment length polymorphism.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4283158&req=5

f1-ajas-28-2-151: Genotypes of the c.*2041T>C SNP in the 3′ UTR of the SCD gene. (a) Sequence chromatograms showing c.*2041T>C SNP. (b) The electrophoresis image of PCR-RFLP for c.*2041T>C SNP. Digestion of PCR products (425 bp) by MspI, show genotypes TT, TC, and CC. The arrowheads show and the size of DNA ladder and fragments. SNP, single nucleotide polymorphism; UTR, untranslated region; SCD, stearoyl-CoA desaturase; PCR-RFLP, polymerase chain reaction-restriction fragment length polymorphism.
Mentions: Genomic DNA was isolated from LD muscle samples using a DNA isolation kit (Intronbio., Seongnam, Korea). Polymerase chain reaction (PCR) and direct sequencing analysis for the promoter and coding region of SCD were performed using specific primers in Berkshire pigs (Table 3). The individual genomic sequence data were assembled for identification of polymorphism as described previously (Kim et al., 2012) and used for genotyping (Figure 1a). To further validate the genotypes, all pigs were re-genotyped using PCR-restriction fragment length polymorphism method by using specific primer set and MspI restriction enzyme (Figure 1b).

Bottom Line: The stearoyl-CoA desaturase (SCD) gene plays a crucial role in the conversion of saturated FAs into monounsaturated FAs (MUFAs), and hence, is among the candidate genes responsible for pig fatness traits.Here, we identified a single nucleotide polymorphism (SNP, c.*2041T>C) in the 3' untranslated region by direct sequencing focused on coding and regulatory regions of porcine SCD.In addition, the SNP showed a significant effect on the SCD mRNA expression levels (p = 0.041).

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Korea.

ABSTRACT
Fatness qualities in pigs measured by the amount of fat deposition and composition of fatty acids (FAs) in pork have considerable effect on current breeding goals. The stearoyl-CoA desaturase (SCD) gene plays a crucial role in the conversion of saturated FAs into monounsaturated FAs (MUFAs), and hence, is among the candidate genes responsible for pig fatness traits. Here, we identified a single nucleotide polymorphism (SNP, c.*2041T>C) in the 3' untranslated region by direct sequencing focused on coding and regulatory regions of porcine SCD. According to the association analysis using a hundred of Berkshire pigs, the SNP was significantly associated with FA composition (MUFAs and polyunsaturated FAs [PUFAs]), polyunsaturated to saturated (P:S) FA ratio, n-6:n-3 FA ratio, and extent of fat deposition such as intramuscular fat and marbling (p<0.05). In addition, the SNP showed a significant effect on the SCD mRNA expression levels (p = 0.041). Based on our results, we suggest that the SCD c.*2041T>C SNP plays a role in the gene regulation and affects the fatness qualities in Berkshire pigs.

No MeSH data available.