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. 2022 Dec 11;13(12):2336.
doi: 10.3390/genes13122336.

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Jennifer Jessica Bruscadin  1   2 , Tainã Figueiredo Cardoso  2 , Wellison Jarles da Silva Diniz  3 , Marcela Maria de Souza  4 , Juliana Afonso  2 , Dielson Vieira  2   5 , Jessica Malheiros  6 , Bruno Gabriel Nascimento Andrade  7 , Juliana Petrini  8 , José Bento Sterman Ferraz  9 , Adhemar Zerlotini  10 , Gerson Barreto Mourão  8 , Luiz Lehmann Coutinho  8 , Luciana Correia de Almeida Regitano  2
Affiliations

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Jennifer Jessica Bruscadin et al. Genes (Basel). .

Abstract

Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation.

Keywords: ASE; beef; cis-regulation; phenotype.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Correlogram of mineral and fatty acid content phenotypes, carcass and meat quality traits. Red squares represent negative correlations, blue squares represent positive correlations and the white squares represent phenotypes without correlation in this population.
Figure 2
Figure 2
Differential allele-specific expression analysis results. (A) Manhattan Plot with all DASE analysis results. The points above the red line were the significant DASE SNPs (FDR ≤ 0.05). (B) Number of DASE SNPs per trait. The colors correspond to the sample group that presented more allelic imbalance: Orange color represent the number of DASE SNPs with more ASE in the high group (positive Log2FoldChange values), and the blue color represents the ones with more ASE in the low group (negative Log2FoldChange values).
Figure 3
Figure 3
KEGG metabolic pathways enriched in the DASE genes. (A) Enrichment of KEGG biological pathways showing the number and proportion of DASE genes in the given pathways. (B) Interaction network of the enriched KEGG pathways.
Figure 4
Figure 4
Gene set enrichment analysis of co-expression modules involving DASE genes for WBSF0 phenotype.
See this image and copyright information in PMC

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