Genetic variability of the caprine stearoyl-CoA desaturase 1 (SCD1) gene has been investigated by sequencing a 4.7-kb cDNA in 6 goats from the Murciano-Granadina and Malagueña breeds. Sequence alignment revealed the existence of one synonymous polymorphism at exon 5 (c.732C>T) and one nucleotide substitution (c.*3504G>A) at exon 6 that encodes the 3' untranslated region (UTR). Moreover, the existence of a previously reported 3'UTR polymorphism involving a 3-bp indel (c.*1902_1904delTGT) was confirmed. Single nucleotide polymorphism and haplotype-based association analyses revealed suggestive associations between genetic variability of the SCD1 locus and lactose, stearic, polyunsaturated, and conjugated linoleic fatty acid contents. Associations with milk fatty acid composition might be explained by the global effects that SCD1 exerts on mammary gland lipid metabolism through the down-modulation of key transcription factors. Interestingly, the performance of an in silico analysis revealed that the c.*1902_1904delTGT polymorphism involves a considerable change in the secondary structure of the SCD1 mRNA. Gene reporter assays and quantitative PCR analysis would be needed to assess if this mutation has a causal effect on milk polyunsaturated and conjugated linoleic fatty acid levels by altering the amount of SCD1 transcripts in mammary epithelial cells.
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