Identification of eQTL and sQTL associated with meat quality in beef

Abstract

Background: Transcription has a substantial genetic control and genetic dissection of gene expression could help us understand the genetic architecture of complex phenotypes such as meat quality in cattle.Results: A total of 80 steers were selected for phenotyping, genotyping and RNA-seq evaluation. A panel of traits related to meat quality were recorded. Information on 112,042 SNPs and expression data on 8,588 autosomal genes and 87,770 exons from 8,467 genes were included in an expression and splicing quantitative trait loci (QTL) mapping (eQTL and sQTL, respectively). Expression of 1,352 genes was previously identified as associated with meat quality traits using a gene, exon and isoform differential expression (DE) analysis. The R package Matrix eQTL was used to perform the QTL mapping using linear regression. The identified QTLs were classified as cis or trans using 1 Mb as maximum distance between the associated SNP and the gene. Polymorphisms associated with expression of at least 20 genes, and splicing of at least 20 exons were considered QTL hot spots. A total of 8,377 eQTLs were identified, including 75.6% trans, 10.4% cis, 12.5% DE trans and 1.5% DE cis; 11,929 sQTLs were uncovered: 66.1% trans, 16.9% DE trans, 14% cis and 3% DE cis. Twenty seven expression master regulators and 13 splicing master regulators were identified and were classified as membrane associated or cytoskeletal proteins, transcription factors or DNA methylases These genes could control expression of other genes through cell signaling or by a direct transcriptional activation/repression mechanism. The ZNF804A, ALAD, OR13F1 and ENSBTAG00000000336 genes were identified as both expression and splicing master regulators.Conclusion: In the present analysis, we show that eQTL and sQTL mapping makes possible positional identification of gene and isoform expression regulators. Additionally, this mapping provides new insight into the regulatory network architecture in longissimus dorsi muscle in an Angus-Brahman multibreed population.