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

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 (770 K bp). 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.

Bibliographic Details

Main Authors:	SOUZA, M. M. de, ZERLOTINI NETO, A., ROCHA, M. I. P., BRUSCADIN, J. J., DINIZ, W. J. da S., CARDOSO, T. F., CESAR, A. S. M., AFONSO, J., ANDRADE, B. G. N., MUDADU, M. de A., MOKRY, F. B., TIZIOTO, P. C., OLIVEIRA, P. S. N. de, NICIURA, S. C. M., COUTINHO, L. L., REGITANO, L. C. de A.
Other Authors:	MARCELA MARIA DE SOUZA, UFSCar; ADHEMAR ZERLOTINI NETO, CNPTIA; MARINA IBELLI PEREIRA ROCHA, UFSCar; JENNIFER JESSICA BRUSCADIN, UFSCar; WELLISON JARLES DA SILVA DINIZ, UFSCar; TAINÃ FIGUEIREDO CARDOSO; ALINE SILVA MELLO CESAR, ESALQ/USP; JULIANA AFONSO, UFSCar; BRUNO GABRIEL NASCIMENTO ANDRADE, UFSCar; MAURICIO DE ALVARENGA MUDADU, CNPTIA; FABIANA BARICHELLO MOKRY, UFSCar; POLYANA CRISTINE TIZIOTO, NGS Soluções Genômicas, Piracicaba; PRISCILA SILVA NEUBERN DE OLIVEIRA; SIMONE CRISTINA MEO NICIURA, CPPSE; LUIZ LEHMANN COUTINHO, ESALQ/USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE.
Format:	Artigo de periódico biblioteca
Language:	Ingles English
Published:	2020-10-09
Subjects:	Expressão gênica, Regulação da expressão gênica, Allelic expression, Allele-specific expression, Bos Indicus, Gene expression regulation,
Online Access:	http://www.alice.cnptia.embrapa.br/alice/handle/doc/1125395 https://doi.org/10.1038/S41598-020-67089-0
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