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.