The Sicilian cattle breeds in a global context: genome-wide relationship with other worldwide cattle

Abstract

Genomic technologies, such as high-throughput genotyping based on Single Nucleotide Polymorphism (SNP) arrays, provide background information concerning genome structure in domestic animals. The aims of this study were to cluster animals, to explore the relationships among and within breeds, and to place the Sicilian breeds, Cinisara and Modicana, in a global context. The Illumina Bovine SNP50K v2 BeadChip genotyping data from 144 animals of Sicilian breeds and from other 1,543 animals belonging to 134 domesticated bovid breeds (DRYAD) were used. These breeds arose from 3 domesticated (sub)species: Bos javanicus, B. taurus indicus, and B. t. taurus. Principal Component Analysis (PCA) generated using PLINK and model-based clustering algorithm implemented in Admixture were performed. SNPs that did not satisfy the following quality criteria were discarded: SNP located on autosomes and common to all breeds; MAF ≥ 0.0005; SNP with genotyping rate ≥ 0.90. A total of 40,958 SNPs shared among all 136 breeds were analyzed. The Sicilian breeds showed outlier behavior for the values of PC2, with all individuals spread over the entire range of variability pertaining to the second component, therefore results of PCA were plotted using PC1 and PC3. The results showed the separation between B. t. taurus and B. t. indicus breeds and the divergences between African and Eurasian taurines. PC1 separated the individuals into several non overlapping clusters that corresponded with (sub)species and the geographical origin of each breeds. Using PC3, the Sicilian cattle breeds were closer to individuals of B. t. taurus from Europe that included some Italian cattle breeds, according to their geographic distribution, and to individuals of B. t. taurus from Asia. In fact, European cattle breeds were exported to Asia and admixed with Asian taurines. Ancestry models with 4 ancestral populations showed the 3 major groups of Asian indicine, Eurasian taurine, and African taurine; Sicilian cattle breeds formed a separate cluster, according to the findings based on the PCA using the first 2 components. These results reflected the differences between breeds resulting from separate domestic events, geographic dispersal and isolation, and breed formation.