| Summary: | Backfat thickness (BFT) is an important carcass composition trait and regarded as a breeding focus. Our initial transcriptome analysis of pig BFT identified GLI pathogenesis-related 1 (<i>GLIPR1</i>) as one of the promising candidate genes. This study was conducted to identify the expression profiles, polymorphisms, and genetic effects of the <i>GLIPR1</i> gene on BFT in pigs. The expression of the <i>GLIPR1</i> gene existed in every detected tissue, and there was a significantly higher expression in spleen and adipose tissue than others (<i>p</i> < 0.05). At the different ages of pig, the expression of the <i>GLIPR1</i> gene was low at an early age, increased with growth, and reached the highest level at 180 days. Genetic polymorphism analysis was detected in 553 individuals of the Large White × Minzhu F2 population. Four SNPs in the promoter significantly associated with 6–7 rib BFT (<i>p</i> < 0.05) were predicted to alter the transcription factor binding sites (TFBS), and the mutations of g.38758089 T>G and g.38758114 G>C were predicted to change the TFs associated with the regulation of adipogenesis. Haplotypes were formed by the detected SNPs, and one block showed a strong association with BFT (<i>p</i> < 0.05). In summary, our results indicate that the expression profiles and genetic variants of <i>GLIPR1</i> affected the BFT of pigs. To our knowledge, this study is the first to demonstrate the biological function and genetic effects of the <i>GLIPR1</i> gene on the BFT of pig and provide genetic markers to optimize breeding for BFT in pigs.
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