Italian Goat Consortium : 50K BeadChip analyses in autochthonous goat breeds

An Italian Goat Consortium has been established to analyse the genomic diversity of Italian goat breeds reared in different conditions from the Alps to the main islands. To date, blood samples have been collected from 12 breeds and a total of 288 unrelated animals. Genomic DNA has been extracted using commercial kits and genotyped with the 53.347 SNPs Illumina Infinium iSelectHD Custom Bead Chip. Here we show preliminary results on Orobica, Bionda dell'Adamello and Valpassiria breeds, reared in Central and Eastern Alps, in Northern Italy, and on Grigia Ciociara, reared in Central Italy (n = 90). SNP call rate was on average 0.99 ± 0.016 (average ± SD). A total of 98.25% SNPs were polymorphic, 1.1% monomorphic and 0.5% gave no results. Observed average heterozygosity across breeds was 0.38 ± 0.11, while average expected heterozigosity 0.41± 0.11. The four breeds analysed had average MAF of 0.32 ± 0.12. Only 0.9% of SNPs were rare, and 97.6% had a MAF > 1%. Moreover 12.5% of SNPs were out of HW equilibrium. The analysis of other 8 local breeds from the Alps, and from Sicily and Sardinian islands is in progress. Large scale genomic information produced by new technologies has potential application in the genetic improvement of economic traits, in the traceability of typical goat products linked to local breeds and permits to select SNP subsets informative for parentage analysis. In addition, a detailed assessment of within and between and breed goat diversity is useful to reconstruct goat population history and demograpy and in the management and conservation of genetic resources. Genetic and genomic innovation, coupled to research, can enhance the sustainable productivity and the competitiveness of goat farms that play a strategic role in the economy of marginal rural areas. The research was also supported by the project "INNOVAGEN" (Italian MIPAAF Ministery).