Dataset Information

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

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.

SUBMITTER: Bruscadin JJ

PROVIDER: S-EPMC9777870 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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

Bruscadin Jennifer Jessica JJ Cardoso Tainã Figueiredo TF da Silva Diniz Wellison Jarles WJ de Souza Marcela Maria MM Afonso Juliana J Vieira Dielson D Malheiros Jessica J Andrade Bruno Gabriel Nascimento BGN Petrini Juliana J Ferraz José Bento Sterman JBS Zerlotini Adhemar A Mourão Gerson Barreto GB Coutinho Luiz Lehmann LL de Almeida Regitano Luciana Correia LC

Genes 20221211 12

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 <i>cis</i>-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 ...[more]

PMID: 36553605

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Dataset Information

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

Publications

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

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