High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the whole-genome sequencing

Crossbreeding has been an effective method to improve crossbred performance in pig industry. To have a global view of a classic three-way crossbreeding system of Duroc x (Landrace x Yorkshire) (DLY), we identified SNPs for each pig breed and crossbred individual originated from a DLY pig family to estimate the influence of purebreds on crossbred offspring using whole-genome sequencing. To confirm the accuracy of the SNPs identified by whole-genome sequencing, therefore, we performed the porcine 60K BeadChip genotyping array (Illumina) for each sequenced pig individual. To confirm the accuracy of SNPs identified by whole-genome sequencing, we performed the porcine 60K BeadChip genotyping array (Illumina) for ten pig individuals of a DLY pig family.