Estimation of linkage disequilibrium in the Nero Siciliano italian autochthonous breed using the Illumina 60K SNP array

Local breeds represent an important component of the overall farm animal diversity to be maintained and exploited. The new high-throughput molecular technologies allow a wide range of massive, simultaneous genomic analysis. Commercial SNP genotyping platforms, are a suitable tool for the genetic characterization and the study of inter-breeds diversity. Linkage disequilibrium, the nonrandom association of alleles at different loci, has received increasing attention in recent years as a result of the availability of genome sequences and large numbers of identified SNP. This study aims to assess the genomic structure of the Nero Siciliano pig, an Italian population reared in eastern Sicily, through the analysis of the extent and range of linkage disequilibrium using the SNP analyzed through the PorcineSNP60 Genotyping BeadChip. Moreover molecular data from other four Italian breeds/populations were also included in the linkage analysis. Linkage disequilibrium may reveal much about breed history, genetic relationships and represent an extremely valuable tool in planning the marker density required to be efficient in marker assisted selection. The Nero Siciliano breed showed the lowest value of average LD probably due to the lack of systematic selection strategies and variable LD rates were found in different genomic regions among the analyzed populations.