Genetic variation of goat Y chromosome in the Sardinian population

Sardinian goat population is commonly considered a crossbred of autochthonous animals with improved Mediterranean breeds, mainly the Maltese. It has been demonstrated by using autosomal microsatellites that the Sardinian goats can be divided into three subpopulations: Sardinian, crossbred with Maltese, and Maltese. The aim of this study was to evaluate sequence variation at Y chromosome in Sardinian bucks and to integrate autosomal microsatellites data. Blood from 190 bucks from 68 farms spread in the main Sardinian goat farming areas was sampled. Three ECONOGENE project primer pairs plus an additional one corresponding to a total of 7 SNPs were used. For all common SNPs, the most frequent allele corresponded to the ECONOGENE one. The additional analysed SNP showed allelic frequencies similar to the other markers. The comparison with haplotypes based on the 6 common SNPs showed that the Sardinian most frequent haplotype corresponded to the predominant one in Central Europe. Results of this study showed that the Sardinian goat population has 8 haplotypes resulting in a large diversity of paternal lineages. The next step will be linking autosomal information to Y chromosome data. In fact, up to date, it seems unfeasible to detect recent upgrading breeds by using Y chromosome variation only.