The impact of haplotypes derived from Chinese pigs on genetic variation and economic traits in the Duroc breed

Abstract Background The historical importation of Chinese pigs into Western countries has facilitated the introduction of Chinese haplotypes into European pig breeds, thereby shaping their genetic diversity and phenotypic traits. However, the genetic and biological implications of this introgression remain poorly understood. Results Based on SNP chip and resequencing data, we confirmed significant genetic introgression from Chinese pigs into commercial European lines. The genetic origins of the introgressed segments predominantly derive from Southern Chinese domestic pigs (CSDP), with additional contributions from other populations, such as Eastern Chinese domestic pigs (CEDP). Our study demonstrates that the selection pressure for Chinese pig introgression was stronger in Duroc pigs compared to the Large White and Landrace breeds. Based on ancestral haplotypes from CEDP and CSDP, we conducted a genome-wide association study (GWAS) and identified 10 quantitative trait loci (QTLs), five of which were not identified in previous studies or using SNPs. Expression genome-wide association studies (eGWAS) based on these introgressed haplotypes, using gene expression profiles from the duodenum, liver, and muscle tissues in the Duroc population, revealed eGWAS signals that were enriched near transcript start sites. By integrating GWAS signals for loin muscle depth with eGWAS signals in muscle tissue, we confirmed that a region 300 Kb from TAF11 , which is enriched with open chromatin regions and encompasses a super-enhancer located within the same topologically associating domain as TAF11 , was associated with both TAF11 expression and loin muscle depth, highlighting the profound influence of Chinese introgression. Conclusions These findings offer valuable insights into the genetic influences of Chinese pig introgression on the Duroc breed, as well as the molecular basis for its effects on economically important traits in Duroc pigs.