A5034605866- Genetic and phenotypic traits in livestock
- Animal Nutrition and Physiology
- Genetic Mapping and Diversity in Plants and Animals
- Livestock and Poultry Management
- Adipose Tissue and Metabolism
- Animal Genetics and Reproduction
- Cancer-related molecular mechanisms research
- Fatty Acid Research and Health
- Meat and Animal Product Quality
- Animal Virus Infections Studies
- Chromosomal and Genetic Variations
- Cardiovascular Disease and Adiposity
- Circular RNAs in diseases
- Nutritional Studies and Diet
- MicroRNA in disease regulation
- Genomics and Phylogenetic Studies
- Peroxisome Proliferator-Activated Receptors
- Diet and metabolism studies
- Genomic variations and chromosomal abnormalities
- Muscle Physiology and Disorders
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Molecular Biology Techniques and Applications
- Nutrition, Genetics, and Disease
- Identification and Quantification in Food
University of Liège
2018-2024
Universidade Federal de Ouro Preto
2024
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2024
Biologie de la Reproduction, Environnement, Epigénétique et Développement
2024
Université de Versailles Saint-Quentin-en-Yvelines
2024
Université Paris-Saclay
2024
Universidade Federal do Espírito Santo
2023
Purdue University West Lafayette
2023
Genomics (United Kingdom)
2020-2022
Universidade de São Paulo
2014-2021
Abstract Standardised analysis pipelines are an important part of FAIR bioinformatics research. Over the last decade, there has been a notable shift from point-and-click pipeline solutions such as Galaxy towards command-line Nextflow and Snakemake. We report on recent developments in nf-core frameworks that have led to widespread adoption across many scientific communities. describe how adopting standards enables faster development, improved interoperability, collaboration with >8,000...
Clinical mastitis (CM) is an inflammatory disease occurring in the mammary glands of lactating cows. CM under genetic control, and a prominent resistance QTL located on chromosome 6 was reported various dairy cattle breeds. Nevertheless, biological mechanism underpinning this has been lacking. Herein, we mapped, fine-mapped, discovered putative causal variant underlying Dutch population. We identified ~12 kb multi-allelic copy number (CNV), that perfect linkage disequilibrium with lead SNP,...
Abstract Five to ten percent of mammalian genomes is occupied by multiple clades endogenous retroviruses (ERVs), that may count thousands members. New ERV arise retroviral infection the germline followed expansion reinfection and/or retrotransposition. mobilization a source deleterious variation, driving emergence silencing mechanisms, leaving “DNA fossils”. Here we show ERVK[2-1-LTR] clade still active in bovine and disease-causing alleles. We develop method measure rate mobilization,...
Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a whole genome scale. Intramuscular fat (IMF) content carcass composition play important roles in metabolic physiological processes mammals because they influence insulin sensitivity consequently prevalence diseases such obesity type 2 diabetes. However, limited information is available genetic...
Natural and artificial selection leads to changes in certain regions of the genome resulting signatures that can reveal genes associated with selected traits. Selection may be identified using different methodologies, which some are based on detecting contiguous sequences homozygous identical-by-descent haplotypes, called runs homozygosity (ROH), or estimating fixation index (FST) genomic windows indicates genetic differentiation. This study aimed identify a paternal broiler TT line at...
Abstract Background Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation complex traits, not only in humans, but also livestock animals. We identified CNVs along the chicken genome analyzed their association with performance traits. Genome-wide were inferred from Affymetrix® high density SNP-chip data for broiler population. concatenated into segments analyses performed linear mixed models considering...
Chicken feed efficiency (FE) traits are the most important economic in broiler production. Several studies evaluating genetic factors affecting food consumption chickens available. However, of these identified genomic regions containing putative quantitative trait loci for each separately. It is still a challenge to find common gene networks related traits. Therefore, here, genome-wide association study (GWAS) was conducted explore candidate responsible Feed Intake (FI), Body Weight Gain...
Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying adaptation to environment imposed challenges. In broiler chickens, conventional production systems in tropical environments lead animals with favorable genotypes be naturally selected, increasing frequency these alleles next generations. this study, ~1400 chickens from a paternal line were genotyped 600 K Affymetrix® Axiom®...
Meat and egg-type chickens have been selected for several generations different traits. Artificial natural selection phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, aims this study were to sequence 28 from two Brazilian lines (meat white egg-type) use information characterize genome-wide variations, identify putative regions under using Fst method, find pathways selection. A total 13.93 million SNPs 1.36 INDELs...
Abstract Excessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat and health concern consumers. We genotyped 497 birds from Brazilian F 2 Chicken Resource Population, using high-density SNP array (600 K), to estimate genomic heritability related traits identify regions positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks data previous whole genome sequencing...
Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer's palatability. In this study, RNA-Seq was used in network analysis better understand the biological processes that lead differences tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed 22 differentially expressed transcripts identified. Among...
Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with deposition the carcass allows identification positional candidate genes (PCGs) that might regulate and be useful for selection against excess chicken's carcass. This study aimed to estimate genomic heritability coefficients identify QTLs PCGs abdominal (ABF) skin (SKIN) traits broiler chicken population, originated from White Plymouth Rock Cornish breeds. ABF SKIN are moderately...
Performance traits are economically important and targets for selection in breeding programs, especially the poultry industry. To identify regions on chicken genome associated with performance traits, different genomic approaches have been applied last years. The aim of this study was application CornellGBS approach (134,528 SNPs generated from a PstI restriction enzyme) Genome-Wide Association Studies (GWAS) an outbred F2 population. We validated 91.7% these 134,528 after imputation missed...
Understanding the architecture of gene expression is fundamental to unravel molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These are economically important for beef industry since they affect carcass meat quality. Our main goal was identify regulatory polymorphisms within genomic regions (QTL) associated with IMF BFT Nellore cattle. For that, we used RNA-Seq data from 193 steers perform SNP calling analysis....
Structural variants (SVs) are chromosomal segments that differ between genomes, such as deletions, duplications, insertions, inversions and translocations. The genomics revolution enabled the discovery of sub-microscopic SVs via array whole-genome sequencing (WGS) data, paving way to unravel functional impact SVs. Recent human expression QTL mapping studies demonstrated play a disproportionally large role in altering gene expression, underlining importance including genetic analyses....
Abstract Dietary fatty acids (FA) are components of the lipids, which contribute to membrane structure, energy input, and biological functions related cellular signaling transcriptome regulation. However, consumers still associate dietary FA with fat deposition increased occurrence metabolic diseases such as obesity atherosclerosis. Previous studies already demonstrated that some linked inflammatory response, preventing diseases. To better understand role on diseases, for first time, a study...
Abdominal fat content is an economically important trait in commercially bred chickens. Although many quantitative loci (QTL) related to deposition have been detected, the resolution for these regions low and functional variants are still unknown. The current study was conducted aiming at increasing a region previously shown QTL associated with deposition, detect novel from this annotate those delineate potentially ones as candidates future studies. To achieve this, 18 chickens parental...
Poultry breeding programs have been focused on improvement of growth and carcass traits, however, this has resulted in correlated changes internal organ weights increased incidence metabolic disorders. These disorders can affect feed efficiency or even cause death. We used a high density SNP array (600 K, Affymetrix) to estimate genomic heritability, perform genome-wide association analysis, identify regions positional candidate genes (PCGs) associated with traits an F2 chicken population....
Pigs (Sus scrofa) are an animal model for metabolic diseases in humans. Pork is important source of fatty acids (FAs) the human diet, as it one most consumed meats worldwide. The effects dietary inclusion oils such canola, fish, and soybean on pig gene expression mostly unknown. Our objective was to evaluate FA composition, identify changes liver male pigs fed diets enriched with different profiles, impacted pathways networks enlighten biological mechanisms' variation. Large White were...
We report the generation of an organism-wide catalog 976,813 cis -acting regulatory elements for bovine detected by assay transposase accessible chromatin using sequencing (ATAC-seq). regroup these in 16 components nonnegative matrix factorization. Correlation between genome-wide density peaks and transcription start sites, correlation peak accessibility expression neighboring genes, enrichment factor binding motifs support their potential. Using a previously established 12,736,643 variants,...
Cohorts of individuals that have been genotyped and phenotyped for genomic selection programs offer the opportunity to better understand genetic variation associated with complex traits. Here, we performed an association study traits related body size muscular development in intensively selected beef cattle. We leveraged multiple trait information refine interpret significant associations.After a multiple-step genotype imputation sequence-level 14,762 Belgian Blue (BBB) cows, genome-wide...
Diagnosing canine visceral leishmaniasis (CVL) in Brazil faces challenges due to the limitations regarding sensitivity and specificity of current diagnostic protocol. Therefore, it is urgent map new antigens or enhance existing ones for future techniques. Immunoinformatic tools are promising identification potential epitopes antigen candidates. In this study, we evaluated peptides selected by epitope prediction CVL serodiagnosis ELISA assays. Ten B-cell were immunogenic silico, but two...