Abstract We have used a RNA-seq approach to investigate differential expression in the skeletal muscle of swine (N = 52) with divergent lipid profiles i.e. HIGH (increased intramuscular fat and saturated monounsaturated fatty acid contents, higher serum concentrations fatness) LOW pigs (leaner an increased polyunsaturated content). The number mRNAs non-coding RNAs (ncRNAs) expressed porcine gluteus medius were 18,104 1,558, respectively. At nominal level significance ( P -value ≤ 0.05), we...

Abstract Background Genetic pressure in animal breeding is sparking the interest of breeders for selecting elite boars with higher sperm quality to optimize ejaculate doses and fertility rates. However, molecular basis not yet fully understood. Our aim was identify candidate genes, pathways DNA variants associated swine by analysing 25 sperm-related phenotypes integrating genome-wide association studies (GWAS) RNA-seq under a systems biology framework. Results By GWAS, we identified 12...

The identification of genes differentially expressed in the skeletal muscle pigs displaying distinct growth and fatness profiles might contribute to identify genetic factors that influence phenotypic variation such traits. So far, majority porcine transcriptomic studies have investigated differences gene expression at a global scale rather than mRNA isoform level. In current work, we differential isoforms gluteus medius (GM) 52 Duroc HIGH (increased backfat thickness, intramuscular fat...

Feed efficiency (FE) has a major impact on the economic sustainability of pig production. We used systems-based approach that integrates single nucleotide polymorphism (SNP) co-association and gene-expression data to identify candidate genes, biological pathways, potential predictors FE in Duroc population. applied an association weight matrix (AWM) analyse results from genome-wide studies (GWAS) for nine associated production traits using 31K SNPs by defining residual feed intake (RFI) as...

Abstract Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we combined phenotypic and microarray expression data to map loci with potential effects five meat recorded longissimus dorsi (LD) gluteus medius (GM) muscles 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH ), electric conductivity (CE) muscle redness (a*), lightness (L*) yellowness (b*). We found significant genome-wide associations for CE LD...

Intramuscular fat (IMF) content and composition have a strong impact on the nutritional organoleptic properties of porcine meat. The goal current work was to compare patterns gene expression genetic determinism IMF traits in gluteus medius (GM) longissimus dorsi (LD) muscles.

The genetic determinism of blood lipid concentrations, the main risk factor for atherosclerosis, is practically unknown in species other than human and mouse. Even model organisms, little known about how determinants traits are modulated by age-specific factors. To gain new insights into this issue, we have carried out a genome-wide association study (GWAS) cholesterol (CHOL), triglyceride (TRIG) low (LDL) high (HDL) density lipoprotein concentrations measured Duroc pigs at two time points...

The genetic basis of muscle fat deposition in pigs is not well known. So far, we have only identified a limited number genes involved the absorption, transport, storage and catabolism lipids. Such information crucial to interpret, from biological perspective, results genome-wide association analyses for intramuscular content composition traits. Herewith, investigated how ingestion food changes gene expression gluteus medius Duroc pigs.By comparing mRNA fasted (T0) with that sampled 5 h (T1)...

In this study we investigated the impact of dietary protein and carotene levels on microbial functions composition during last month purebred fattening Duroc pigs. Fecal microbiota was characterized using 16S ribosomal RNA sequencing at two points live, 165 (T1) 195 (T2) days. From 70 to days age, 32 pigs were divided into groups fed either a standard-protein (SP) or low-protein (LP) diet. (165-195 days), all received LP diet, carotene-enriched (CE) not (NC). Significant differences observed...

We performed a genome-wide association study to map the genetic determinants of carcass traits in 350 Duroc pigs typed with Porcine SNP60 BeadChip. Association analyses were carried out using gemma software. The proportion phenotypic variance explained by SNPs ranged between negligible moderate (hSNP2= 0.01-0.30) depending on trait under consideration. At level, we detected one significant backfat thickness 3rd and 4th ribs six mapping SSC12 (37-40 Mb). also identified several...

Intramuscular fat (IMF) content is a relevant trait for high-quality meat products such as dry-cured ham, but increasing IMF has the undesirable correlated effect of decreasing lean growth. Thus, there need to find selection criteria independent from In pigs, proportion linoleic (C18:2) and arachidonic (C20:4) acids decline with deposition therefore they can be considered indicators fatness. The aim this research was estimate genetic variation C18:2 C20:4 in their correlations growth traits,...

Integration of high throughput DNA genotyping and RNA-sequencing data enables the discovery genomic regions that regulate gene expression, known as expression quantitative trait loci (eQTL). In pigs, efforts to date have been mainly focused on purebred lines for traits with commercial relevance such growth meat quality. However, little is genetic variants mechanisms associated robustness an animal, thus its overall health status. Here, liver, lung, spleen, muscle transcriptomes 100 three-way...

The role of non-coding RNAs in the porcine muscle metabolism is poorly understood, with few studies investigating their expression patterns response to nutrient supply. Therefore, we aimed investigate changes microRNAs (miRNAs), long intergenic (lincRNAs) and mRNAs before after food intake.We measured miRNA, lincRNA mRNA levels gluteus medius 12 gilts a fasting condition (AL-T0) 24 fed ad libitum during either 5 h. (AL-T1, N = 12) or 7 (AL-T2, prior slaughter. small RNA fraction was...

This is the first study to explore genetic diversity and population structure of domestic water buffalo ( Bubalus bubalis ) in Germany their potential relations herds other parts Europe or worldwide. To this end, animals from different Germany, Bulgaria, Romania, Hungary were genotyped compared genotypes populations with worldwide distribution open public. The pilot analyzed structure, phylogenetic tree, inbreeding events our samples. In buffalos a mixed make-up contributions Bulgaria...

The molecular basis of compensatory growth in monogastric animals has not yet been fully explored. Herewith, this study we aim to determine changes the pig skeletal muscle transcriptome profile during following a feed restriction period. A RNA-Seq experiment was performed with total 24 females belonging Duroc commercial line. Half received either restricted (RE) or ad libitum (AL) diet first fattening period (60–125 d age). After that, all gilts were fed for further ~30 until age ~155 d,...

The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene genetically regulated a context-dependent manner. In the current work, we have compared transcriptomic and eQTL profiles two porcine (skeletal muscle liver) which typically show highly divergent profiles, 103 Duroc pigs genotyped with Porcine SNP60 BeadChip (Illumina) available microarray-based measurements hepatic mRNA levels. Since structural variation could effects on...

<title>Abstract</title> Background: Integration of high throughput DNA genotyping and RNA-sequencing data enables the discovery genomic regions that regulate gene expression, known as expression quantitative trait loci (eQTL). In pigs, efforts to date have been mainly focussing on purebred lines for traits with commercial relevance growth meat quality. However, little is genetic variants mechanisms associated robustness an animal, thus its overall health status. Here, liver, lung, spleen,...

The animal gastrointestinal tract contains a complex microbiome whose composition ultimately reflects the co-evolution of microorganisms with their host and host’s environment. This study aimed to gain insights into adaptation microbiota local Egyptian cattle three different ecosystems (Upper Egypt, Middle Lower Egypt) distributed across 11 governorates (with an average 12 animals per governorate) using amplicon sequencing. We analyzed from 136 fecal samples through 16S rRNA gene sequencing...

Abstract The red-legged partridge ( Alectoris rufa ) is a popular game bird species that in decline several regions of southwestern Europe. introduction farm-reared individuals distinct genetic make-up hunting reserves can result swamping wild populations. Here we present de novo genome assembly for the based on long-read sequencing technology. assembled size 1.14 Gb, with scaffold N50 37.6 Mb and contig 29.5 Mb. Our highly contiguous contains 97.06% complete avian core genes. Overall,...

A comprehensive and systematic view of the genetic regulation lipid metabolism genes is still lacking in pigs. Herewith, we have investigated 63 porcine with crucial roles uptake, transport, synthesis catabolism lipids. With this aim, performed an expression QTL (eQTL) scan 104 pigs available genotypes for Illumina Porcine SNP60 chip microarray measurements gene gluteus medius muscle. Analysis data gemma software revealed 13 cis- 18 trans-eQTL modulating 19 loci. Genes regulated by eQTL...

Abstract Background The composition of intramuscular fat depends on genetic and environmental factors, including the diet. In pigs, we identified a haplotype three SNP mutations in stearoyl-coA desaturase ( SCD ) gene promoter associated with higher content monounsaturated fatty acids fat. second these SNPs (rs80912566, C &gt; T) affected putative retinol response element promoter. effect dietary vitamin A restriction over is controversial as it pig line duration restriction. This study aims...

Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed other cattle, in particular candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used evaluate the genetic structure GWH relation cattle by carrying out principal components model-based clustering analyses. Secondly, identified integrating findings from: a) a genome-wide association...

In general, the relationship between predicted functional consequences of missense mutations mapping to genes known be involved in human diseases and severity disease manifestations is weak. this study, we tested pigs whether single nucleotide polymorphisms (SNPs), have on function related lipid metabolism are associated with phenotypes. Association analysis demonstrated that nine out 72 nominally SNPs were classified as "highly" or "very highly consistent" silico-predicted did not show...

The red-legged partridge (Alectoris rufa) is a popular game bird species that in decline several regions of southwestern Europe. introduction farm-reared individuals distinct genetic make-up hunting reserves can result swamping wild populations. Here we present de novo genome assembly for the based on long-read sequencing technology. assembled size 1.14 Gb, with scaffold N50 37.6 Mb and contig 29.5 Mb. Our highly contiguous contains 97.06% complete avian core genes. Overall, quality this...