6533b835fe1ef96bd129fd55

RESEARCH PRODUCT

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

subject

description

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 inves- tigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (N e ), and the patterns of linkage disequilibrium (LD) in 2 eco- nomically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. To understand the genetic rela- tionship and to place both Sicilian breeds in a global context, genotypes from 134 other domesticated bovid breeds were used. Principal component analysis showed that the Sicilian cattle breeds were closer to individuals of Bos taurus 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 the CIN breed showed a lower value of assignment, the presence of substruc- ture, and genetic links with the MOD breed. The average molecular inbreeding and coancestry coefficients were moderately high, and the current estimates of N e were low in both breeds. These values indicated a low genetic variability. Considering levels of LD between adjacent markers, the average r 2 in the MOD breed was compa- rable to those reported for others cattle breeds, whereas CIN showed a lower value. Therefore, these results sup- port the need of more dense SNP arrays for a high-power association mapping and genomic selection efficiency, particularly for the CIN cattle breed. Controlling molec- ular 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 2 local cattle breeds.