Identifying candidate functional SNPs associated with the fatty acid profile of pork loin intramuscular fat

Abstract

Pork meat is one of the most consumed animal proteins around the world. Due to its economic and nutritional importance, pigs (Sus scrofa) are also used as an animal model in human research. Pork has a high nutritional value and is an important source of unsaturated fatty foods for human consumption. In this context, the main objectives of this project are to identify candidate functional single nucleotide polymorphism (SNP) and expression quantitative trait loci (eQTL) associated with traits related to the profile of monounsaturated, polyunsaturated, and omega-3 fatty acids, based on large-scale genotyping data and muscle transcriptome of immunocastrated male Large White pigs fed a diet with different fatty acid profiles. For this, genotyping information (SNP chip - Porcine GGP 50k) and mRNA sequencing (RNA sequencing; RNA-Seq) of 72 males of the Large White breed, immunocastrated and homozygous-negative halothane (NN), were slaughtered with a weight average of 130 kg. The animals were fed four diets: basal with 1.5% degummed soybean oil; basal with 3% soybean oil; basal with 3% canola oil; and basal with 3% of fish oil (mouth mangrove sardines; Cetengraulis edentulus). Liver and loin (Longissimus lumborum, LL) samples of the animals were collected at the time of slaughter for later genotyping and gene expression analyses. It is expected that this study will allow the identification of potentially functional polymorphisms associated with phenotypes of economic and consumer health interest. From the RNA-Seq data, a SNP call analysis was performed and the information obtained was combined with the genotyping data. The genomic datasets will be used for performing association analyses with the total gene expression data and eQTL will be identified using the Matrix eQTL package of the R program. Subsequently, the fatty acid profile data will be associated with eQTL and then the co-expression network analysis. In addition, while at Purdue University, the student will participate in graduate courses, journal clubs, lab meetings, and will attend the International Plant and Animal Genome (PAG) conference to be held in San Diego, California (USA) in January/2024. (AU)