Genome-Wide Analysis Reveals Copy Number Variant Gene TGFBR3 Regulates Pig Back Fat Deposition

Simple Summary: In this study, we conducted genome-wide copy number variation (CNV) analysis using next-generation sequencing data from Large White (LW) and Minzhu (MZ) pigs and integrated transcriptomic data from dorsal adipose tissues of 180-day-old LW and MZ pigs for expression quantitative trait loci (eQTL) analysis. Among the identified CNVs, the transforming growth factor beta receptor 3 (TGFBR3) gene was found to be associated with back fat thickness (BFT), with a dose effect observed between the TGFBR3 gene at the genomic and transcriptomic levels. In vitro experiments further demonstrated that TGFBR3 expression is involved in the proliferation and differentiation of porcine preadipocytes. BFT is closely related to meat quality and lean meat percentage in pigs. The BFT traits of European LW pigs significantly differ from those of Chinese indigenous fatty MZ pigs. CNV is a prevalent genetic variation that plays an important role in economically important traits in pigs. However, the potential contribution of CNV to BFT in LW and MZ pigs remains unclear. In this study, whole-genome CNV detection was performed using next-generation sequencing data from LW and MZ pigs, and transcriptome data from back fat tissue of 180-day-old LW and MZ pigs were integrated for expression quantitative trait loci (eQTL) analysis. We identified a copy number variation in the TGFBR3 gene associated with BFT, showing a dose effect between the genome and transcriptome levels of the TGFBR3 gene. In porcine preadipocytes, TGFBR3 expression continuously increased during differentiation. Knockdown of TGFBR3 using specific siRNA inhibited preadipocyte differentiation and proliferation. Our study provides insights into the genetic regulation of pork quality and offers a theoretical basis for improving carcass quality by modulating BFT in pigs.