Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs.

BACKGROUND: Mapping expression quantitative trait loci (eQTLs) in skeletal muscle tissue in pigs is crucial for understanding the relationship between genetic variation and phenotypic expression of carcass traits in meat animals. Therefore, the primary objective of this study was to evaluate the impact of different sets of single nucleotide polymorphisms (SNP), including scenarios removing SNPs pruned for linkage disequilibrium (LD) and SNPs derived from SNP chip arrays and RNA-seq data from liver, brain, and skeletal muscle tissues, on the identification of eQTLs in the Longissimus lumborum tissue, associated with carcass and body composition traits in Large White pigs. The SNPs identified from muscle mRNA were combined with SNPs identified in the brain and liver tissue transcriptomes, as well as SNPs from the GGP Porcine 50 K SNP chip array. Cis- and trans-eQTLs were identified based on the skeletal muscle gene expression level, followed by functional genomic analyses and statistical associations with carcass and body composition traits in Large White pigs. RESULTS: The number of cis- and trans-eQTLs identified across different sets of SNPs (scenarios) ranged from 261 to 2,539 and from 29 to 13,721, respectively. Furthermore, 6,180 genes were modulated by eQTLs in at least one of the scenarios evaluated. The eQTLs identified were not significantly associated with carcass and body composition traits but were significantly enriched for many traits in the "Meat and Carcass" type QTL. The scenarios with the highest number of cis- (n = 304) and trans- (n = 5,993) modulated genes were the unpruned and LD-pruned SNP set scenarios identified from the muscle transcriptome. These genes include 84 transcription factor coding genes. CONCLUSIONS: After LD pruning, the set of SNPs identified based on the transcriptome of the skeletal muscle tissue of pigs resulted in the highest number of genes modulated by eQTLs. Most eQTLs are of the trans type and are associated with genes influencing complex traits in pigs, such as transcription factors and enhancers. Furthermore, the incorporation of SNPs from other genomic regions to the set of SNPs identified in the porcine skeletal muscle transcriptome contributed to the identification of eQTLs that had not been identified based on the porcine skeletal muscle transcriptome alone.

Effect of dietary soybean oil inclusion on liver-related transcription factors in a pig model for metabolic diseases.

Dietary fatty acids (FA) are components of the lipids, which contribute to membrane structure, energy input, and biological functions related to cellular signaling and transcriptome regulation. However, the consumers still associate dietary FA with fat deposition and increased occurrence of metabolic diseases such as obesity and atherosclerosis. Previous studies already demonstrated that some fatty acids are linked with inflammatory response, preventing metabolic diseases. To better understand the role of dietary FA on metabolic diseases, for the first time, a study to identify key transcription factors (TF) involved in lipid metabolism and inflammatory response by transcriptome analysis from liver samples of animal models was performed. The key TF were identified by functional enrichment analysis from the list of differentially expressed genes identified in liver samples between 35 pigs fed with 1.5% or 3.0% soybean oil. The functional enrichment analysis detected TF linked to lipid homeostasis and inflammatory response, such as RXRA, EGFR, and SREBP2 precursor. These findings demonstrated that key TF related to lipid metabolism could be modulated by dietary inclusion of soybean oil. It could contribute to nutrigenomics research field that aims to elucidate dietary interventions in animal and human health, as well as to drive food technology and science.

A comparative review of serological assays for the detection of rabies virus-specific antibodies.

Rabies is a major public health problem with a fatality rate close to 100%, caused by a virus of the Lyssavirus genus, of which rabies virus (RABV) is the prototype. Nonetheless, the complete prevention can be achieved by the induction of neutralizing antibodies by pre- or post-exposure prophylaxis. According to the world health organization (WHO) and World Organization for animal health (OIE), serum titers of rabies virus neutralizing antibodies (RVNA) that are higher or equal to 0.5 international units (IU)/ml indicate adequate immune response after vaccination against rabies. Currently, RFFIT and FAVN are the gold standard tests recommended by both WHO and OIE for detecting and quantitating RVNA in biological samples from individuals or animals previously vaccinated and/or subjects suspected of having been infected by RABV. Although the tests RFFIT and FAVN are efficient, they are time-consuming, labor-intensive manual tests and not cost-effective for routine use. Following the previously mentioned, approaches with alternative methods have been developed to detect RVNA or rabies-specific antibodies in human or animal serum, but with variable success. This work summarizes the advances in the serological assays for the detection of neutralizing antibodies or rabies antibodies and assesses the individual immune status after vaccination against rabies, as well as the mechanisms of RABV neutralization mediated by antibodies. Therefore, the main alternative methods for the determination of RABV or rabies-specific antibodies are exposed, with promising results, besides being easy to execute, of low cost, and representing a possibility of being applied, according to the proposal of each test to the network of Rabies Surveillance Laboratories.