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. 2020 Jun 23;10(1):10204.
doi: 10.1038/s41598-020-67089-0.

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

Marcela Maria de Souza  1   2 , Adhemar Zerlotini  3 , Marina Ibelli Pereira Rocha  1   2 , Jennifer Jessica Bruscadin  1   2 , Wellison Jarles da Silva Diniz  1   2 , Tainã Figueiredo Cardoso  1 , Aline Silva Mello Cesar  4 , Juliana Afonso  1   2 , Bruno Gabriel Nascimento Andrade  1 , Mauricio de Alvarenga Mudadu  3 , Fabiana Barichello Mokry  1   2 , Polyana Cristine Tizioto  5 , Priscila Silva Neubern de Oliveira  1 , Simone Cristina Méo Niciura  1 , Luiz Lehmann Coutinho  4 , Luciana Correia de Almeida Regitano  6
Affiliations

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

Marcela Maria de Souza et al. Sci Rep. .

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 (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.

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Conflict of interest statement

Author Polyana C. Tizioto was employed by company NGS Genomic Solutions. All the other authors declare no competing interests.

Figures

Figure 1
Figure 1
Allele-specific expression (ASE) profile in Nelore. (A) The number of ASE SNPs in function of tested SNPs per individual (R2 = 0.95, p = 0.006). Each blue dot represents a individual. (B) Number of ASE individuals in function of individuals tested per SNP (R2 = 0.74, p = 0.008). Each blue dot represents an SNP. (C) Percentage of individuals showing ASE for a given SNP as a proportion of the total individuals tested for the same SNP. (D) Distribution of occurrence of ASE through the individuals for each SNP.
Figure 2
Figure 2
Proportion of monoallelic expression. (A) Percentage of ASE individuals showing monoallelic expression for a given SNP as a proportion of the total of individuals with ASE for the same SNP. (B) Distribution of the number of monoallelic individuals for SNPs with 100% of monoallelic expression.
Figure 3
Figure 3
Genomic distribution of ASE SNPs. (A) Distribution of all allelic expression through the chromosomes. (B) Number of tested SNPs showing or not ASE in two scenarios (less than five samples and five or more samples) for each chromosome. Blue bars represent the SNPs showing biallelic expression in all tested individuals, dark red bars represent SNPs showing ASE in five or more samples (ASE SNPs > = 5 samples), and light red bars represent SNPs showing ASE in less than five individuals (ASE SNPs <5 samples).
Figure 4
Figure 4
Distribution of ASE variants according to their annotation.
See this image and copyright information in PMC

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