Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes

Author(s):Show less -

de Souza, Marcela Maria ^{[1, 2]} ; Zerlotini, Adhemar ^[3] ; Pereira Rocha, Marina Ibelli ^{[1, 2]} ; Bruscadin, Jennifer Jessica ^{[1, 2]} ; da Silva Diniz, Wellison Jarles ^{[1, 2]} ; Cardoso, Taina Figueiredo ^[1] ; Mello Cesar, Aline Silva ^[4] ; Afonso, Juliana ^{[1, 2]} ; Nascimento Andrade, Bruno Gabriel ^[1] ; Mudadu, Mauricio de Alvarenga ^[3] ; Mokry, Fabiana Barichello ^{[1, 2]} ; Tizioto, Polyana Cristine ^[5] ; Neubern de Oliveira, Priscila Silva ^[1] ; Meo Niciura, Simone Cristina ^[1] ; Coutinho, Luiz Lehmann ^[4] ; de Almeida Regitano, Luciana Correia ^[1]

Affiliation

^[1] Embrapa Pecuaria Sudeste, Anim Biotechnol, Sao Carlos, SP - Brazil

^[2] Univ Fed Sao Carlos, Postgrad Program Evolutionary Genet & Mol Biol, Sao Carlos, SP - Brazil

^[3] Embrapa Informat Agr, Bioinformat Multiuser Lab, Campinas, SP - Brazil

^[4] Univ Sao Paulo, Dept Anim Sci, Piracicaba, SP - Brazil

^[5] NGS Solucoes Genom, Piracicaba, SP - Brazil

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 10, n. 1 JUN 23 2020.
• Web of Science Citations: 0

Abstract

Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770Kbp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3 ` UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits. (AU)

• FAPESP's process: 12/20328-8 - Allelic expression in genes associated with meat tenderness in Nellore by transcriptomic analysis
• Grantee: Marcela Maria de Souza
• Support Opportunities: Scholarships in Brazil - Doctorate
• 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