Abstract
BackgroundEconomically 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.ResultsMessenger 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.ConclusionCo-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.
Highlights
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
The number of single nucleotide polymorphisms (SNP) associated with an expression quantitative trait loci (eQTL) was on average 9.09 ± 15.07, and the size of each eQTL interval was on average 11.59 ± 22.30-Mb (Table 1)
A total of five eQTL intervals contained an additional peak determined through conditional analysis by fixing the peak eQTL SNP
Summary
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. Genomic regions harboring single nucleotide polymorphisms (SNP) accounting for a significant portion of phenotypic variation for economically important traits have been identified and implemented in marker assisted selection [1,2,3] In pigs, these efforts have identified candidate genes affecting meat quality (e.g., CRC1, PRKAG3, CAST), weight gain (e.g., MC4R) and litter size (e.g., ESR) [4]. Expression quantitative trait loci (eQTL) maps provide a foundation to study divergent molecular processes in livestock species [2, 14] This approach has been successful in identifying candidate genes, causative variants and molecular networks regulating phenotypic traits in swine, including back fat [15], drip loss [16], glycolytic potential [13], plasma cortisol levels [10] and lipid metabolism [17]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
