association of κ-casein gene (csn3) polymorphism with milk production traits and protein structure changes in iranian mahabadi goat

the κ-casein protein plays a fundamental role in milk production and its composition synthesis in the mammary gland. this protein has an important role in the formation, stabilization, and aggregation of the casein micelles. in this study, we investigated the genetic variability at the exon 4 of the κ-casein gene (also known as csn3) using pcr-sscp analysis and dna sequencing. then a protein sequence and structural analysis were performed in order to predict the possible impact of amino acid substitutions on physicochemical properties and structure of the κ-casein protein. blood samples from 167 iranian mahabadi goats were collected dna extracted and then the then 458bp fragment of the csn3 gene was amplified using pcr-sscp. sequencing analysis showed that there were 8 single nucleotide polymorphisms (snps) in the csn3 exon 4 (g.83c >t, g.85g >a, g.122a>g, g.147a>g, g.222g>a, g.309a>g, g.388t>c and g.429c>t). from the 8 identified polymorphic sites, six sites were non synonymous substitutions and the other two were synonymous substitutions. also, association analysis showed that genotypes of the snps 1, 6, 7 and 8 were significantly associated with fat percentage in the analyzed population (p<0.05), but there were not significant association between genotypes and milk production, the percentage of protein, lactose, solid-not-fat snf, protein and fat yield. in addition, the non-synonymous snps substitutions do not have an affect on the physicochemical properties (hydrophobicity, isoelectric point, and net charge) of κ-casein protein. these results suggest that polymorphism at the csn3 gene could be used as a molecular marker for goat milk’s fat percentage.