Title:	Novel putative causal mutations associated with fat traits in Nellore cattle uncovered by eQTLs located in open chromatin regions.
Authors:	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.
Affiliation:	INGRID SOARES GARCIA, UNIVERSIDADE DE SÃO PAULO; BÁRBARA SILVA-VIGNATO, UNIVERSIDADE DE SÃO PAULO; ALINE SILVA MELLO CESAR, UNIVERSIDADE DE SÃO PAULO; JULIANA PETRINI, UNIVERSIDADE DE SÃO PAULO; VINICIUS HENRIQUE DA SILVA, UNIVERSIDADE DE SÃO PAULO; NATÁLIA SILVA MOROSINI, UNIVERSIDADE DE SÃO PAULO; CAROLINA PURCELL GOES, UNIVERSIDADE DE SÃO PAULO; JULIANA AFONSO; THAÍS RIBEIRO DA SILVA, UNIVERSIDADE DE SÃO PAULO; BEATRIZ DELCARME LIMA, UNIVERSIDADE DE SÃO PAULO; LUAN GASPAR CLEMENTE, UNIVERSIDADE DE SÃO PAULO; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; GERSON BARRETO MOURÃO, UNIVERSIDADE DE SÃO PAULO; LUIZ LEHMANN COUTINHO, UNIVERSIDADE DE SÃO PAULO.
Date Issued:	2024
Citation:	Scientific Reports, v. 14, 10094, 2024.
Description:	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.
NAL Thesaurus:	Intramuscular fat Immune response
Keywords:	Backfat thickness Expression quantitative trait loci Regulatory variants Cytoskeleton remodeling Iron transport Phospholipid metabolism
DOI:	https://doi.org/10.1038/s41598-024-60703-5
Type of Material:	Artigo de periódico
Access:	openAccess
Appears in Collections:	Artigo em periódico indexado (CPPSE)