Author(s): GARCIA, I. S.; VIGNATO, B. S.; CESAR, A. S. M.; PETRINI, J.; SILVA, V. H. DA; MOROSINI, N. S.; GOES, C. P.; AFONSO, J.; SILVA, T. R. DA; LIMA, B. D.; CLEMENTE, L. G.; REGITANO, L. C. de A.; MOURÃO, G. B.; COUTINHO, L. L.

Summary: Intramuscular fat (IMF) and backfat thickness (BFT) are critical economic traits impacting meat quality. However, the genetic variants controlling these traits need to be better understood. To advance knowledge in this area, we integrated RNA-seq and single nucleotide polymorphisms (SNPs) identified in genomic and transcriptomic data to generate a linkage disequilibrium filtered panel of 553,581 variants. Expression quantitative trait loci (eQTL) analysis revealed 36,916 cis-eQTLs and 14,408 trans-eQTLs. We next used ATAC-Seq assay to identify and overlap eQTL and open chromatin regions. Six eQTLs were in regulatory regions, four in predicted insulators and possible CCCTC-binding factor DNA binding sites, one in an active enhancer region, and the last in a low signal region. Our results provided novel insights into the transcriptional regulation of IMF and BFT, unraveling putative regulatory variants.

Publication year: 2024

Types of publication: Journal article

Unit: Embrapa Southeastern Livestock

Keywords: Backfat thickness, Cytoskeleton remodeling, Expression quantitative trait loci, Immune response, Intramuscular fat, Iron transport, Phospholipid metabolism, Regulatory variants