Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus

Author(s)

Bruscadin, Jennifer Jessica ^[1] ; de Souza, Marcela Maria ^[2] ; de Oliveira, Karina Santos ^[1] ; Pereira Rocha, Marina Ibelli ^[1] ; Afonso, Juliana ^[3] ; Cardoso, Taina Figueiredo ^[4] ; Zerlotini, Adhemar ^[5] ; Coutinho, Luiz Lehmann ^[3] ; Meo Niciura, Simone Cristina ^[4] ; de Almeida Regitano, Luciana Correia ^[4]

Affiliation

^[1] Univ Fed Sao Carlos, Ctr Biol Sci & Hlth, Postgrad Program Evolutionary Genet & Mol Biol, Sao Carlos, SP - Brazil

^[2] Iowa State Univ, Dept Anim Sci, Ames, IA - USA

^[3] Univ Sao Paulo, Dept Anim Sci, ESALQ, Piracicaba, SP - Brazil

^[4] Embrapa Pecuaria Sudeste, POB 339, BR-13564230 Sao Carlos, SP - Brazil

^[5] Embrapa Informat Agr, Campinas, SP - Brazil

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 11, n. 1 APR 1 2021.
• Web of Science Citations: 0

Abstract

Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes. (AU)

• FAPESP's process: 12/23638-8 - Molecular basis of meat quality in Nelore beef cattle
• Grantee: Luciana Correia de Almeida Regitano
• Support Opportunities: Research Projects - Thematic Grants