Abstract
Allele-specific expression (ASE) analysis improves the understanding of transcription’s cis-regulation. Herein, we used imputed SNPs along with RNA-Seq data from the Longissiumus thoracis muscle of 190 Nelore steers to identify functional cis-regulatory variants from ASE analysis. Using a Binomial Test, we identified 38,177 SNPs in ASE regions (ASE SNPs; FDR ≤0.05). We then searched for aseQTLs (SNPs potentially regulating the ASE) by comparing their heterozygosity to the measured allelic ratio under a Wilcoxon Rank Sum test. We identified 21,543 aseQTLs potentially regulating a total of 430 ASE SNPs (FDR ≤0.05). Based on a linear model, ASE SNPs and aseQTLs were associated with transcript abundance. We identified 3,333 SNPs acting as cis-eQTLs (FDR≤0.05). Results were integrated with previous ASE, functional regions, and meat quality-related differentially expressed genes data. This study described novel SNPs potentially regulating the transcription of genes that may affect beef traits.
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