Haplotypes of Single Nucleotide Polymorphisms (SNPs) in casein loci of Girgentana goats explain isoelectrofocusing results.

Goat milk, cheese and yoghurt offer an alternative to cow milk products. In Sicily one of the important goat breeds reared is the Girgentana. Traditionally the milk from Girgentana goats was used for nourishment of infants and elderly. Recently, the Girgentana breed has been in decline. This of concern, as the Girgentana may carry unique milk protein genetic variants. If health benefits of Girgentana goat milk is proven, then increasing production from this population will be of great interest. The most abundant proteins in goat milk, as in other milks, are the caseins, αS1-, β-, αS2- and κ-casein, coded by the loci CSN1S1, CSN2, CSN1S2 and CSN3 respectively. In other goat breeds, the casein loci have been found to be highly polymorphic, and a number of genetic variants of the casein genes that affect milk production traits have been described. The aim of this study was to quantify the variation of casein loci within the Girgentana breed, and additionally to determine if there was any agreement between DNA polymorphism and isoelectrofocusing (IEF) protein expression of αS1. Forty individuals including goats and bucks were genotyped for 9 SNPs and one deletion (exon 9) in CSN1S1, 7 SNPs in CSN2, 3 SNPs in CSN1S2 and 13 SNPs in CSN3. Genotypes for the deletion in exon 9 were in very good agreement with the IEF, results; goats that were homozygous for this deletion had no or very low levels of αS1 expression, goats that were heterozygous had intermediate levels of expression, and goats that were homozygous for the non deletion allele had full αS1 expression. For each casein, haplotypes of the SNP genotypes were constructed. There were a limited number of haplotypes within each casein locus; 6 for CSN1S1 and CSN2, 3 for CSN1S2, and 7 for CSN3. The limited number of haplotypes indicates strong linkage disequilibrium between SNPs within each locus. Future work will determine if the haplotypes have significant effects on health and production traits, and their potential for use in marker assisted selection.