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

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.

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

“…Two ASE SNPs described by Guillocheau et al (2019) were identified here as aseQTLs: rs109170993, associated with the rs110850310 ASE SNP, and rs109842586, associated with the rs109372848 ASE SNP. The rs109842586 was also identified marking ASE in our population as well 5 .…”

“…Additionally, CMYA5 had 245 overlaps between aseQTLs and QTLs for b*FAT, CL, L*FAT, REA, WBSF0, WBSF7, and WHC traits. In addition, ASE genes in the bovine muscle functionally enriched for meat quality traits were previously identified in our population 5 and elsewhere 8 . Although these overlaps with QTLs might be useful for prioritizing SNPs for validation, a word of caution is necessary, as the confidence intervals for the QTLs might be considerable and could not be taken into account in our analyzes.…”

“…In this study, we identified 1134 aseQTLs associated with the ASE pattern of 126 SNPs in the Longissimus thoracis muscle of Nelore steers. Due to the sample requirement to associate each SNP marking ASE and aseQTL SNP, we tested 23% (192 out of 820) SNPs with significant ASE previously detected in the same population 5 and identified aseQTLs for 126 (66%) of them. Thirty-seven ASE SNPs associated with aseQTLs were also described in a previous ASE study developed with bovine muscle samples 8 .…”

“…The knowledge about regions with ASE and their regulatory mechanisms is relevant to improve animal breeding programs by increasing the accuracy of predictive models 4 . De Souza et al 5 identified SNPs in transcribed regions showing allele-specific expression patterns (ASE SNPs) in the muscle of Nelore ( Bos indicus ) related to meat tenderness, an important trait for meat consumer’s approval 6 , 7 . Many of these SNPs were located within genes responsible for essential biological functions for muscle development and meat tenderness 5 .…”

“…Herein, we investigated aseQTLs associated with allelic expression imbalance, evidenced by the number of reads corresponding to different SNP alleles in transcripts, previously described in a Nelore experimental population 5 . We then analyzed its involvement with predicted regulatory mechanisms, such as DNA methylation, whether they contained TFBS or miRNA binding sites.…”