The effect of variants in the promoter of BMPER on the intramuscular fat deposition in longissimus dorsi muscle of pigs

•Two SNPs were found in the promoter of BMPER gene and interlock completely.•BMPER gene has an association with intramuscular fat content.•A–A haplotype could be used as a genetic marker for intramuscular fat deposition.

The aim of the study was to evaluate the contribution of BMPER promoter SNPs to the gene expression and intramuscular fat content in longissimus dorsi muscle. Firstly the promoter region of BMPER was comparatively scanned by direct sequencing with pool DNA of two groups (n = 15 for each group) with high (H) or low (L) IMF content. Two SNPs, c.− 1423A > G and c.− 1344A > C, were found to have reverse allele distribution in the two groups. Genotyping by PCR-SSCP in a larger population revealed that the two SNPs interlock completely to form only A–A or G–C haplotype. The IMF content and BMPER expression level of A–A/A–A genotype were higher than G–C/G–C genotype, and luciferase assay revealed that A–A haplotype promoter activity was also higher than G–C haplotype. Putative transcription factor prediction suggested that c.− 1344 A > C mutation might shift the promoter binding affinity with GATAs. We concluded that BMPER promoter polymorphisms have an effect on IMF content, and A–A haplotype could be used as a candidate genetic marker for preferable IMF deposition.