Abstract
Determining mechanisms regulating complex traits in pigs is essential to improve the production efficiency of this globally important protein source. MicroRNAs (miRNAs) are a class of non-coding RNAs known to post-transcriptionally regulate gene expression affecting numerous phenotypes, including those important to the pig industry. To facilitate a more comprehensive understanding of the regulatory mechanisms controlling growth, carcass composition, and meat quality phenotypes in pigs, we integrated miRNA and gene expression data from longissimus dorsi muscle samples with genotypic and phenotypic data from the same animals. We identified 23 miRNA expression Quantitative Trait Loci (miR-eQTL) at the genome-wide level and examined their potential effects on these important production phenotypes through miRNA target prediction, correlation, and colocalization analyses. One miR-eQTL miRNA, miR-874, has target genes that colocalize with phenotypic QTL for 12 production traits across the genome including backfat thickness, dressing percentage, muscle pH at 24 h post-mortem, and cook yield. The results of our study reveal genomic regions underlying variation in miRNA expression and identify miRNAs and genes for future validation of their regulatory effects on traits of economic importance to the global pig industry.
Highlights
Pork is the meat of choice worldwide, and global meat consumption is projected to continue to increase over the decade
295 miRNA expression profiles were included as response variables in the genomic best linear unbiased prediction (GBLUP)-based genome-wide association (GWA) analysis, and results for associating these miRNAs with 36,292 SNPs identified 315 significant miRNA-SNP associations (FDR < 0.05), comprising 23 significant miR-eQTL peaks
In addition to studying the genomic region surrounding the miR-eQTL peaks, we identified the miRNA whose expression was being affected by genomic variants and considered what the functional effects would be on their target gene(s)’ expression and related phenotypes
Summary
Pork is the meat of choice worldwide, and global meat consumption is projected to continue to increase over the decade. Pork producers will need to continue to improve the quality and consistency of pork products in order to enhance the prosperity of this global industry (USDA, 2020). Industry focus on increasing carcass leanness has historically neglected meat quality characteristics, increasing the incidence of inferior eating-quality pork and decreasing consumer satisfaction (Barbut et al, 2008; Schwab and Baas, 2008; Ciobanu et al, 2011). Many economically relevant production traits are controlled by complex interactions of gene and protein expression and regulation. While genomic selection has facilitated increased progress on those traits, a better understanding of the genetic architecture controlling phenotypic expression cannot only improve
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