Identification of eQTL in swine muscle and liver based on RNAm sequencing

Abstract

This project aims to identify single nucleotide polymorphisms (SNP) located in coding regions of the DNA, identified from the complete mRNA sequencing, and associate them with the level of gene expression in pig muscle and liver fed with different sources of fatty acids. A total of 72 genetically lean immunocastrated male pigs were used in a 98-day study to evaluate the effects of including 3% soybean oil (SO), canola oil (CO), or fish oil (FO) in the diets vs. feeding a standard commercial diet with 1.5% SO (control) on growth performance, carcass and meat quality traits of the longissimus lumborum (LL) muscle. Pigs were grouped by initial body weight (BW; 28.44 ± 2.95 kg) and assigned to one of four treatments, with six replicate pens per treatment and three pigs per pen. The animals were slaughtered with an average live weight of 132.7±10.9 kg. Subsequently, muscle and liver tissue samples were collected for extraction and sequencing of mRNA. Subsequently, an association analyses of the eQTLs with performance traits (e.g., live weight, carcass yield, intramuscular fat, ribeye area, and fat thickness) will be conducted based on different statistical methods. A quantitative genomics approach for summarizing the findings of this study and integrating the results in genomic prediction methods will be proposed. In summary, this project will contribute for advancing the knowledge and developing practical tools in the area of functional genomics of pork quality and nutrient utilization in pigs. (AU)