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2025 ; 57
(1
): 58
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The impact of haplotypes derived from Chinese pigs on genetic variation and
economic traits in the Duroc breed
#MMPMID41131451
Fang S
; Guo C
; Liu H
; Wang Y
; Tan C
; Wu Z
; Zhao Y
; Hu X
; Yang R
Genet Sel Evol
2025[Oct]; 57
(1
): 58
PMID41131451
show ga
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.