Genomic analyses provide insights into genetic architecture of three-way crossbred pigs

Background Crossbreeding is effective for improving performance in poultry and livestock, which is mainly attributed to heterosis. For pork production, a classic three-way crossbreeding system of Duroc × (Landrace × Yorkshire) (DLY) is widely used to produce terminal crossbred pigs with stable and prominent performance. Nonetheless, studies on the transmission of genetic information and gene expression pattern of DLY have been limited. Findings We analyzed population-scale SNPs based on 30 individuals from these three purebreds and identified 529.93 K SNPs of breed-of-origin of alleles. We also applied whole-genome sequencing of ten individuals from a DLY pig family as well as transcriptome of four representative tissues (adipose, skeletal muscle, heart, and liver) for six DLY individuals. Based on above, we identified a large number of high-confidence ASE genes, among which four ASE genes ( KMO , PLIN4 , POPDC3 and UGT1A6 ) were found to be shared over all DLY individuals. Conclusion We suggest DLY is a more effective strategy of three-way crossbreeding among these three purebreds from genetic aspect. We suppose the numerous breed-of-origin of alleles have close association with improved performance of crossbred individuals. ASE may also play important roles on DLY three-way crossbreeding system. Our findings are valuable for understanding the transmission of genetic information and the gene expression in DLY three-way crossbreeding and may be used to guide breeding and production of pigs in the future.