Genetic control of longissimus dorsi muscle gene expression variation and joint analysis with phenotypic quantitative trait loci in pigs

Abstract

Background: Economically important growth and meat quality traits in pigs are controlled by cascading molecular events occurring during development and continuing throughout the conversion of muscle to meat. However, little is known about the genes and molecular mechanisms involved in this process. Evaluating transcriptomic profiles of skeletal muscle during the initial steps leading to the conversion of muscle to meat can identify key regulators of polygenic phenotypes. In addition, mapping transcript abundance through genome-wide association analysis using high-density marker genotypes allows identification of genomic regions that control gene expression, referred to as expression quantitative trait loci (eQTL). In this study, we perform eQTL analyses to identify potential candidate genes and molecular markers regulating growth and meat quality traits in pigs.

Results: Messenger RNA transcripts obtained with RNA-seq of longissimus dorsi muscle from 168 F2 animals from a Duroc x Pietrain pig resource population were used to estimate gene expression variation subject to genetic control by mapping eQTL. A total of 339 eQTL were mapped (FDR ≤ 0.01) with 191 exhibiting local-acting regulation. Joint analysis of eQTL with phenotypic QTL (pQTL) segregating in our population revealed 16 genes significantly associated with 21 pQTL for meat quality, carcass composition and growth traits. Ten of these pQTL were for meat quality phenotypes that co-localized with one eQTL on SSC2 (8.8-Mb region) and 11 eQTL on SSC15 (121-Mb region). Biological processes identified for co-localized eQTL genes include calcium signaling (FERM, MRLN, PKP2 and CHRNA9), energy metabolism (SUCLG2 and PFKFB3) and redox hemostasis (NQO1 and CEP128), and results support an important role for activation of the PI3K-Akt-mTOR signaling pathway during the initial conversion of muscle to meat.

Conclusion: Co-localization of eQTL with pQTL identified molecular markers significantly associated with both economically important phenotypes and gene transcript abundance. This study reveals candidate genes contributing to variation in pig production traits, and provides new knowledge regarding the genetic architecture of meat quality phenotypes.

Keywords: Pig; RNA-Seq; Skeletal muscle; Transcriptome; eQTL.

Fig. 1

eQTL map. The y-axis represents the absolute genomic position of the gene and the x-axis represents the genomic location of its associated SNP marker. Associations aligning on the diagonal are eQTL found on the same chromosome as the gene. A plausible position range was identified for each eQTL interval based on the peak’s flanking markers, and local regulation was determined when the gene position overlapped this range, shown in black. Plausible local regulators of gene expression (described in Figure S1 in Additional file 2) are shown in yellow. The eQTL intervals shown in green are distant regulators that map to the same chromosome as their associated gene. Distant regulators mapping to a different chromosome than the associated gene are shown in blue. The eQTL shown in red are plausible putative hotspots on SSC9 and SSC15

Fig. 2

Manhattan plots of meat quality and carcass composition pQTL co-localized with eQTL. The x-axis is the absolute genome position in mega-bases. The y-axis is the negative base 10 logarithm of q-values, with the red line representing the significance threshold. Manhattan plots in shades of blue are for the pQTL (FDR ≤ 0.05), and those in shades of orange are for the eQTL (FDR ≤ 0.01). SNPs associated with an eQTL co-localizing with a pQTL, and whose association is no longer significant after performing the conditional analysis are shown in black

Fig. 3

Manhattan plots of growth pQTL co-localized with eQTL. The x-axis is the absolute genome position in mega-bases. The y-axis is the negative base 10 logarithm of q-values, with the red line representing the significance threshold. Manhattan plots in shades of blue are for the pQTL (FDR ≤ 0.05), and those in shades of orange are for the eQTL (FDR ≤ 0.01). SNPs associated with an eQTL co-localizing with a pQTL, and whose association is no longer significant after performing the conditional analysis are shown in black

Fig. 4

Proportion of variance explained by peak pQTL SNP for phenotypes (blue) and gene transcript abundance (green). Traits are shown on the x-axis, and the proportion of phenotypic variance explained by the SNP marker is shown on the y-axis. Directionality of bar plots indicates SNP effect on phenotype or gene expression (i.e., increase or decrease)