The genome-wide structure of two economically important indigenous Sicilian cattle breeds

Genomic technologies, such as high-throughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to investigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (Ne), and the patterns of linkage disequilibrium (LD) in two economically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. In order to understand the genetic relationship and to place both Sicilian breeds in a global context, genotypes from others 134 domesticated bovid breeds were used. Principal component analysis showed that the Sicilian cattle breeds were closer to individuals of B. t. taurus from Eurasia and formed non-overlapping clusters with other breeds. Between the Sicilian cattle breeds, MOD was the most differentiated, whereas the animals belonging to CIN breed showed a lower value of assignment, the presence of substructure and genetic links with MOD breed. The average molecular inbreeding and coancestry coefficients were moderately high, and the current estimates of Ne were low in both breeds. These values indicated a low genetic variability. Considering levels of LD between adjacent markers, the average r2 in MOD breed was comparable to those reported for others cattle breeds, whereas CIN showed a lower value. Therefore, these results support the need of more dense SNP arrays for a high power association mapping and genomic selection efficiency in particular for CIN cattle breed. Controlling molecular inbreeding and coancestry would restrict inbreeding depression, the probability of losing beneficial rare alleles, and therefore, the risk of extinction. The results generated from this study have important implications for the development of conservation and/or selection breeding programs in these two local cattle breeds.