The single nucleotide polymorphism g.133A>C in the stearoyl CoA desaturase gene (SCD) promoter affects gene expression and quali-quantitative properties of river buffalo milk

The stearoyl-CoA desaturase (SCD) gene has been investigated in depth in ruminants because of its effect on milk fat composition. In river buffalo, the single nucleotide polymorphism (SNP) g.133A>C in the gene promoter has been associated with milk quality and yield. However, the biological reason for such effects remains unexplored. In this study, we combined mRNA profile analysis, an electromobility shift assay, and quantitative PCR to elucidate the role of this SNP on gene transcription and its effects on milk fat traits. A preliminary genotyping of g.133A>C was carried out on a group of 303 river buffaloes to choose individuals for the downstream applications. Analysis of allele frequencies showed an increase in the minor allele C (0.25) compared with previous findings (0.16). Six animals (2 for each genotype) were chosen for cloning and 216 positive cDNA recombinant clones for SCD (72 per genotype) were analyzed by PCR. All clones showed the same length on agarose gel; therefore, random clones were chosen for sequencing. No qualitative differences were found and all gene transcripts assembled correctly. An electrophoretic mobility shift assay was performed to evaluate the binding of the transcription factor Sp1 to DNA sequences including g.133A>C. Genotype CC showed a higher binding affinity (mean ± standard error of the mean) than genotype AA in 2 different conditions [Enzo buffer (EB), Enzo Life Science Inc., Farmingdale, NY: 201.77 ± 4.06 vs. 141.65 ± 3.77 band intensity values and Poletto buffer (PB): 95.90 ± 1.15 vs. 67.30 ± 2.14 band intensity values]. The subsequent quantitative PCR confirmed the upregulation of the CC genotype compared with the AA and AC genotypes. The association study with milk fat traits revealed a favorable effect of allele C. The heterozygous genotype had the highest values for monounsaturated fatty acids, oleic acid (C18:1 cis-9), polyunsaturated fatty acids, and odd- and branched-chain fatty acids, and the lowest values for saturated fatty acids and atherogenic and thrombogenic indices; the heterozygous genotype differed significantly from the AA genotype. The AC genotype has previously been associated with higher milk yield. Therefore, the g.133A>C SNP is a marker with dual effects and is an interesting candidate for assisted selection programs in river buffalo. These data clarified the biological role of the SNP g.133A>C in the SCD promoter and how it affects gene function, providing important knowledge on the genetic background of lipid metabolism, including the future possibility of selecting alleles with quantitatively or qualitatively favorable effects.