Characterization of biodiversity in six goat breeds reared in Southern Italy by means of microsatellite and SNP markers

An integrated analysis, using 20 microsatellite markers and 32 SNP markers belonging to the casein cluster has been carried out on 174 goats from 6 local goat breeds and populations from Southern Italy. Microsatellite markers provided 216 alleles (10.8 per locus; from 6.6 to 8.2 per breed). The average expected heterozygosity (He) was 0.732. Fis value (0.148) indicated a general heterozygosity deficiency. A high number of intragenic haplotypes (56) have been detected at casein loci, 25 at aS1 casein (CSN1S1), 12 at b casein (CSN2), 8 at aS2 casein (CSN1S2), 11 at k casein (CSN3), when 1% frequency was required for each breed. The breeds with higher production and management level, fixed the lowest number of combinations at casein loci (28). Molecular data have been used to calculate genetic distances and in clustering analysis.