Frederique Pitel

Frederique Pitel
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Génétique, Physiologie et Systèmes d'Elevage (GenPhySE)

About

244
Publications
29,098
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
4,107
Citations
Additional affiliations
October 1995 - present

Publications

Publications (244)
Article
Early experiences, including prenatal environment, are known to influence a wide variety of mechanisms involved in the phenotype elaboration. We investigated the effect of the addition of endocrine disruptors or of a methyltransferase inhibitor during the embryonic development of quails from different genetic backgrounds (four different quail lines...
Article
Full-text available
Early development is a critical period during which environmental influences can have a significant impact on the health, welfare, robustness and performance of livestock. In oviparous vertebrates, such as birds, embryonic development takes place entirely in the egg. This allows the effects of environmental cues to be studied directly on the develo...
Article
Full-text available
Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the fraction usually studied is harbored in protein-coding regions because potential impacts on proteins are relatively easy to predict by popular tools such as the Variant Effect Predictor. These tools annotate variants independently without considering the potentia...
Article
Full-text available
In addition to their common usages to study gene expression, RNA-seq data accumulated over the last 10 years are a yet-unexploited resource of SNPs in numerous individuals from different populations. SNP detection by RNA-seq is particularly interesting for livestock species since whole genome sequencing is expensive and exome sequencing tools are u...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
Long non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken genes enriched in LNC (http://www.fragencode.org/), built from the Ensembl reference extended using novel LNC modelled here from 364 RNA-seq and...
Chapter
In poultry breeding, epigenetics is not a common used element in the selection of parents to breed the next generations. That is surprising as epigenetics can influence gene function, is inherited via mitosis and / or meiosis and can occur both from the female and male lines. Epigenetics have been shown to affect gene-expression and can thereby pla...
Article
Full-text available
Background: The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. Results: We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics,...
Article
Full-text available
Background: Production conditions of layer chicken can vary in terms of temperature or diet energy content compared to the controlled environment where pure-bred selection is undertaken. The aim of this study was to better understand the long-term effects of a 15%-energy depleted diet on egg-production, energy homeostasis and metabolism via a mult...
Article
Full-text available
Background: In quail, two feather colour phenotypes i.e. fawn-2/beige and yellow are associated with the ASIP locus. The aim of our study was to characterize the structural modifications within this locus that explain the yellow mutation (large deletion) and the fawn-2/beige mutation (assumed to be caused by a different structural modification). Re...
Article
Full-text available
In mammals, leptin and tumor-necrosis factor (TNF) are prominent interacting adipokines mediating appetite control and insulin sensitivity. While TNF pleiotropically functions in immune defense and cell survival, leptin is largely confined to signaling energy stores in adipocytes. Knowledge about the function of avian leptin and TNF is limited and...
Article
Full-text available
In mammals, leptin and tumor-necrosis factor (TNF) are prominent interacting adipokines mediating appetite control and insulin sensitivity. While TNF pleiotropically functions in immune defense and cell survival, leptin is largely confined to signaling energy stores in adipocytes. Knowledge about the function of avian leptin and TNF is limited and...
Article
Full-text available
The effects of maternal nutrition on offspring phenotypes have been mainly documented over the past years in mammals, and are now studied in poultry as well. In the present study, we investigated the effects of a reduced level of dietary Methionine (Met) on laying performances of common laying ducks and their impacts on the phenotype of their mule...
Article
Full-text available
Les animaux d'élevage sont confrontés à de multiples contraintes environnementales auxquelles ils doivent s'adapter. De plus en plus d'études s'intéressent à l'impact de l'environnement précoce sur les phénotypes des animaux et leurs capacités à s'adapter aux différents challenges rencontrés ultérieurement. Dans cette revue, nous nous intéresserons...
Preprint
Full-text available
The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromos...
Book
Full-text available
Poultry meat and eggs are major sources of nutrients in the human diet. The long production career of laying hens expose them to biotic or abiotic stressors, lowering their production. Understanding the mechanisms of adaptation to stress is crucial for selecting robust animals and meeting the needs of a growing human population. In this study, fina...
Article
Full-text available
While it has been shown that epigenetics accounts for a portion of the variability of complex traits linked to interactions with the environment, the real contribution of epigenetics to phenotypic variation remains to be assessed. In recent years, a growing number of studies have revealed that epigenetic modifications can be transmitted across gene...
Article
Full-text available
Over the years, farmed birds have been genetically selected to improve performance traits. However, many studies have shown that phenotype not only depends on genetics: gene expression is also influenced by the environment, through epigenetic changes that may alter the phenotypes of the animals. Since high-throughput sequencing techniques are extre...
Article
Full-text available
Background Misidentification of the chicken leptin gene has hampered research of leptin signaling in this species for almost two decades. Recently, the genuine leptin gene with a GC-rich (~70%) repetitive-sequence content was identified in the chicken genome but without indicating its genomic position. This suggests that such GC-rich sequences are...
Article
Full-text available
Correction: After the publication of this work [1] an error was noticed in one of the author surnames. The author name Leif Anderson should be spelt as Leif Andersson.
Article
Full-text available
Over the years, farmed birds have been selected on various performance traits mainly through genetic selection. However, many studies have shown that genetics may not be the sole contributor to phenotypic plasticity. Gene expression programs can be influenced by environmentally induced epigenetic changes that may alter the phenotypes of the develop...
Article
Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans increases detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to acco...
Conference Paper
Full-text available
La récente mise à disposition du génome de référence de la caille japonaise (mars 2016) a rendu possible la caractérisation moléculaire par séquençage haut débit de mutations causales de phénotypes dont le locus impliqué est connu, comme le phénotype Beige (Fawn) impliquant le gène ASIP. Les lectures appairées obtenues par séquençage de deux caille...
Chapter
Phenotype variability depends on genetics and environmental factors. Improving farm animal performances relies on genetic variability, but the possible improvement of selection schemes taking into account nongenetic transgenerational inheritance has become a topic of choice. Indeed, the parental diet may influence the adult phenotype of the offspri...
Book
Phenotype variability depends on genetics and environmental factors. Improvingfarm animal performances relies on genetic variability, but the possible improvementof selection schemes taking into account nongenetic transgenerationalinheritance has become a topic of choice. Indeed, the parental diet may influencethe adult phenotype of the offspring,...
Article
Full-text available
Background Environmental exposures, for instance to chemicals, are known to impact plant and animal phenotypes on the long term, sometimes across several generations. Such transgenerational phenotypes were shown to be promoted by epigenetic alterations such as DNA methylation, an epigenetic mark involved in the regulation of gene expression. Howeve...
Article
Full-text available
Japanese quail (Coturnix japonica) is an important model animal in poultry studies. In the present study a large F2-cross design to map QTL for PU and other correlated traits on 14 chromosomes was used. Next to PU, the traits calcium utilization, body weight gain, and feed per gain ratio were investigated. Because the marker density was only sparse...
Article
Full-text available
RNA editing is a post-transcriptional process leading to differences between genomic DNA and transcript sequences, potentially enhancing transcriptome diversity. With recent advances in high-throughput sequencing, many efforts have been made to describe mRNA editing at the transcriptome scale, especially in mammals, raising contradictory conclusion...
Article
Full-text available
In mammals, multigenerational environmental effects have been documented by either epidemiological studies in human or animal experiments in rodents. Whether such phenomena also occur in birds for more than one generation is still an open question. The objective of this study was to investigate if a methionine deficiency experienced by a mother (G0...
Article
Full-text available
Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans allows increasing the detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score appr...
Article
Full-text available
Contents 79 The Chicken Leads the Way in Avian Genomics. Prepared by J. Smith. 80 The Chicken Genome: Current Status of Genome Assembly and Annotations. Prepared by D.W. Burt, L. Eöry, A.L. Archibald, B.L. Aken, P. Flicek, K. Howe, W. Chow, M. Dunn, J.M.D. Wood, R. Nag, and W.C. Warren. 83 The Avian RNAseq Consortium: A Community Effort to Annot...
Article
Il existe chez les animaux et l'Homme une mémoire de l'environnement embryonnaire (nutrition, stress, polluants...) qui peut influencer le métabolisme des individus à l'âge adulte. Cette mémoire de l’environnement précoce est expliquée en partie par des variations de l’état épigénétique des gènes, transmises au cours des divisions cellulaires au co...
Article
Full-text available
RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I)...
Article
Full-text available
Free fatty acid receptors (FFAR) belong to a family of five G-Protein Coupled Receptors that are involved in the regulation of lipid metabolism, so that their loss of function increases the risk of obesity. The aim of this study was to determine the expansion of genes encoding paralogs of FFAR2 in the chicken, considered as a model organism for dev...
Conference Paper
Very few causal genes have been identified by quantitative trait loci (QTLs) mapping because of the large size ofQTLs, and most of them were identified thanks to functional links already known with the targeted phenotype.Here we propose to combine selection signature detection, SNP annotation, and expression analyses to identifycausal genes underly...
Article
More and more studies show that epigenetic information affects the phenotypes of individuals. Little is knownabout the epigenetic mechanisms in birds, although, as in many animal and plant species, these mechanisms maybe involved in trait variability. Little is known about epigenetic mechanisms in birds with the exception of thephenomenon of dosage...
Article
The epigenetic phenomena, such as the DNA methylation, which participate to the regulation of gene expression,can influence the phenotypes and recent studies show that the epigenetic information can be transmitted acrossgenerations. In the context of the ANR research program EpiBird, we conducted a pilot study to estimate thephenotypic differences...
Article
Full-text available
Very few causal genes have been identified by quantitative trait loci (QTLs) mapping because of the large size of QTLs, and most of them were identified thanks to functional links already known with the targeted phenotype. Here we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify po...
Article
Full-text available
Background Behavioral traits such as sociability, emotional reactivity and aggressiveness are major factors in animal adaptation to breeding conditions. In order to investigate the genetic control of these traits as well as their relationships with production traits, a study was undertaken on a large second generation cross (F2) between two lines o...
Article
Full-text available
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific...
Preprint
Full-text available
RNA editing corresponds to a post-transcriptional nucleotide change in the RNA sequence, creating an alternative nucleotide, not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-...
Conference Paper
Full-text available
Little is known about epigenetic mechanisms in birds, except the phenomenon of dosage compensation of sex chromosomes, although such mechanisms could be involved in the phenotypic variability of birds, as in several livestock species. This paper reviews the literature on epigenetic mechanisms that could contribute significantly to trait variability...
Conference Paper
Full-text available
Abstract Text: Little is known about epigenetic mechanisms in birds, except the phenomenon of dosage compensation of sex chromosomes, although such mechanisms could be involved in the phenotypic variability of birds, as in several livestock species. This paper reviews the literature on epigenetic mechanisms that could contribute significantly to...
Conference Paper
Abstract Text: The social behavior of animals, which is partly controlled by genetics, is involved in their adaptation to large breeding groups. Genetic relationships between different social behaviors, fear behaviors and production traits were estimated in a second generation cross of two lines of Quail divergently selected for their social reinst...
Conference Paper
Abstract Text: Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for haplotype information in genome scans for selection allows increasing the detection power, but haplotype-based methods require individual genotypes and are not applicable when only allele frequencies are available. We pr...
Conference Paper
Full-text available
P4079 Simultaneous characterization of ge-nomic regions associated with two feather traits and two eggshell colors in domestic Japanese Quail (Coturnix japonica). Bertrand Bed'Hom (INRA, AgroParisTech), Fré dé rique Pitel, Patrice Dehais and Sophie Leroux (INRA, ENVT, ENSAT), David Gourichon and Sandrine Riviè re (INRA), Nicolas Bruneau (INRA, Ag-r...
Article
Full-text available
Gene loss is one of the main drivers in the evolution of genomes and species. The demonstration that a gene has been lost by pseudogenization is truly complete when one finds the pseudogene in the orthologous genomic region with respect to active genes in other species. In some cases, the identification of such orthologous loci is not possible beca...