Bivariate GWAS performed on rabbits divergently selected for intramuscular fat content reveals pleiotropic genomic regions and genes related to meat and carcass quality traits

Meat quality plays an important economic role in the meat industry and livestock breeding programmes. Intramuscular fat content (IMF) is one of the main meat quality parameters and its genetic improvement has led breeders to investigate its genomic architecture and correlation with other relevant traits. Genetic markers associated with causal variants for these traits can be identified by bivariate analyses. In this study, we used two rabbit lines divergently selected for IMF to perform bivariate GWAS with the aim of detecting pleiotropic genomic regions between IMF and several weight, fat, and meat quality traits. Additionally, whole-genome sequencing data from these lines were used to identify potential causal variants associated with the genetic markers. The main pleiotropic region was found on Oryctolagus cuniculus chromosome (OCC) 1 between 35.4 Mb and 38.2 Mb, explaining up to 2.66% of the IMF genetic variance and being associated with all traits analysed, except muscle lightness. In this region, the potentially causal variants found pointed to PLIN2, SH3GL2, CNTLN, and BNC2 as the main candidate genes affecting the different weight, fat depots and meat quality traits. Other relevant pleiotropic regions found were those on OCC3 (148.94–150.89 Mb) and on OCC7 (27.07–28.44 Mb). The first was associated with all fat depot traits and explained the highest percentage of genetic variance, up to 10.90% for scapular fat. Several allelic variants were found in this region, all located in the novel gene ENSOCUG00000000157 (orthologous to ST3GAL1 in other species), involved in lipid metabolism, suggesting it as the main candidate affecting fat deposition. The region on OCC7 was associated with most meat quality traits and explained 8.48% of the genetic variance for pH. No allele variants were found to segregate differently between the lines in this region; however, it remains a promising region for future functional studies. Our results showed that bivariate models assuming pleiotropic effects are valuable tools to identify genomic regions simultaneously associated with IMF and several weight, fat and meat quality traits. Overall, our results provided relevant insights into the correlations and relationships between traits at the genomic level, together with potential functional mutations, which would be relevant for exploration in rabbit and other livestock breeding programmes.