Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality...

Area of Science:

• Genomics
• Livestock Genetics
• Molecular Biology

Background:

• Traditional transcriptomics identifies candidate genes but undercovers regulatory variants.
• Allele-specific expression (ASE) regions highlight cis-regulatory variants, crucial for enhancing genomic selection accuracy.

Purpose of the Study:

• To investigate single nucleotide polymorphisms (SNPs) in differential ASE (DASE) regions for beef quality traits in Nelore cattle.
• To identify regulatory variants impacting economically important livestock traits.

Main Methods:

• Utilized RNA sequencing data, imputed genotypes, and genomic estimated breeding values from 190 Nelore steers.
• Applied a beta-binomial model to identify DASE SNPs in 40 contrasting samples (20 per group).

Main Results:

• Identified 1479 DASE SNPs (False Discovery Rate ≤ 0.05) associated with 55 beef quality traits.
• Found that most DASE genes are involved in muscle homeostasis and tenderness, with a co-expression module enriched for protein ubiquitination.
• Observed overlap with epigenetics and phenotype data, suggesting DASE SNPs link to cis-regulatory variants modulating transcription and phenotype via chromatin state.

Conclusions:

• DASE SNPs are valuable for understanding genetic regulation of beef quality traits.
• Findings suggest a mechanism where cis-regulatory variants influence transcription and phenotype through chromatin modulation.
• This approach can improve genomic selection models for livestock breeding.