Investigating SNPs of stearoyl-CoA desaturase (SCD) in Thai Native Cattle (Kho-Isaan)
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Abstract
The stearoyl-CoA desaturase (SCD) gene is involved in fatty acid synthesis and is widely used as a candidate gene for the development of genetic markers in livestock. The SCD gene is related to marbling score and fatty acid composition, which are important economic traits and necessary for the improvement of meat quality in Thai native cattle. The objective of this study was to investigate SNPs of SCD gene and genotype frequencies of SNPs in Thai native cattle (Kho-Isaan) by polymerase chain reaction (PCR) technique, nucleotides sequencing and compared with prototype nucleotide in GenBank by Clustal Omega program, and search for the specific enzyme at mutation site with NEBcutter version 2.0 program. Base variability at the mutation site in 110 cattle samples was analyzed by the Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) technique. At each site, genotype frequencies and allele frequencies of genotype patterns were analysed. The analysis revealed differences in the nucleotide sequences of the Kho-Issan and the prototype nucleotides at 3 sites: g.10329C>T, g.10330G>A and g.10436A>G. This study found that g.10329C>T can change the amino acid, whereas g.10330G>A cannot change the amino acid. Furthermore, the g.10330G>A and g.10436A>G sites were newly discovered mutants in Thai native cattle. When digested by AciI, PstI, and NdeI restriction enzymes, g.10329C>T was digested by AciI enzymes found in three genotype patterns, and genotype frequencies were CC (0.055), CT (0.339), and TT (0.606). The g.10330G>A site was digested by PstI enzymes found in the genotypes AA (0.509), GA (0.355), and GG (0.136), and the g.10436A>G site was digested by the NdeI enzyme, which was found in the genotypes AA (0.879), AG (0.112), and GG (0.009). Therefore, it was concluded that the SNPs g.10329C>T and g.10436A>G might be possible to use as the genetic markers for the association study with meat quality and
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