The Effect of BSCL2 Gene on Fat Deposition Traits in Pigs

SIMPLE SUMMARY: The study evaluated the mutation effects of BSCL2 variants on slaughter and fattening characteristics and meat quality traits. These mutations were selected based on variant calling analysis and χ test results within subcutaneous fat RNA-seq data. Potential genetic markers revealed significant genotype/allele distribution variations between high- and low-fat pigs. We suggested that the proposed variant calling derived from RNA-seq data might help develop genetic markers for complex pig traits. The results pinpoint that the selection of the BSCL2 G allele (rs341493267) could increase backfat thickness in pigs. In addition, observed polymorphisms also affected meat percentage, loin mass, and eye area. ABSTRACT: BSCL2 encodes seipin, a transmembrane endoplasmic reticulum protein associated with lipodystrophy and severe metabolic complications, including diabetes and hepatic steatosis. In pigs, BSCL2 expression increases during adipocyte differentiation. In the present study, we identified significant gene variants associated with fat deposition (FD)-related processes based on subcutaneous fat tissue RNA-seq data. In the association study, to prove our hypothesis, three Polish pig breeds were included: Złotnicka White (ZW, n = 72), Polish Landrace (PL, n = 201), and Polish Large White (PLW, n = 169). Based on variant calling analysis and χ(2) tests, BSCL2 mutations showing significantly different genotype/allele distribution between high- and low-fat pigs were selected for a comprehensive association study. Four interesting BSCL2 variants (rs346079334, rs341493267, rs330154033, and rs81333153) belonging to downstream and missense mutations were investigated. Our study showed a significant decrease in minor allele frequency for two BSCL2 variants (rs346079334 and rs341493267) in PL pigs in 2020–2021. In ZW, BSCL2 mutations significantly affected loin and ham fats, meat redness, and growth performance traits, such as feed conversion and daily feed intake. Similar observations were noted for PLW and PL, where BSCL2 mutations influenced fat depositions and meat traits, such as loin eye area, loin mass and fat, carcass yield, and growth performance traits. Based on the observation in pigs, our study supports the theory that BSCL2 expressed in subcutaneous fat is involved in the FD process.