Pour ameliorer la resistance et le bien-etre des poulets en croissance a la chaleur sans affecter leurs performances, il est possible de les acclimater au chaud pendant l’incubation des oeufs. Ce traitement d’acclimatation (A) correspond a une incubation des oeufs a 39,5°C pendant 12 heures par jour (E7 a E16), la temperature d’incubation des oeufs temoins (T) etant de 38,7°C. Le traitement thermique embryonnaire induit des changements d’expression d’un certain nombre de genes cibles identifies par une approche transcriptomique dans le cadre du projet ANR Thermochick. L’objectif du CI EpiTherm est d’identifier des variations de methylation de l’ADN associees ou non avec les variations du transcriptome afin de mieux comprendre les mecanismes moleculaires regulant la production de chaleur dans ce modele.
Molecular genetic analyses in quail will benefi t greatly from a higher density of
genetic markers. We chose therefore to obtain high numbers of SNP (Single Nucleotide
Polymorphism) by high-throughput sequencing (Titanium 454 GS-FLX, Roche) of two
main types of reduced representations of the genome: restriction digested fractions
of genomic DNA and EST (Expressed Sequence Tag), representing the expressed
genes. The genomic fractions were generated as AFLP (Amplifi ed Fragment Length
Polymorphism) fragments and the expressed ones by preparing cDNA libraries from
two tissues: embryo and brain. To optimize the information content of the SNP
detected for subsequent analyses, libraries were prepared from individuals selected
in the two lines involved in a QTL cross and each individual in the AFLP library
was tagged. Sequencing runs produced 399,189 sequence reads from cDNA, and
1,107,451 from genomic fragments, covering over 433 Mb of sequence in total
and allowing the detection of 17,400 putative SNP. Further analyses using the tags
information will allow the estimation of heterozygozity in the F1 males.
Besides the interest of the production of a large number of new SNP, this
technology should allow to sequence GC rich regions corresponding to the smallest
microchromosomes for which there is no or few sequence in chicken. The comparison
of the quail sequences with the chicken genome assembly will allow a virtual
mapping of the SNP obtained, based on the high synteny conservation between
these two avian species.
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) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation sequencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome.
Summary A quantitative trait loci (QTL) study was undertaken to identify genome regions involved in the control of fearfulness in Japanese quail ( Coturnix japonica ). An F2 cross was made between two quail lines divergently selected over 29 generations on duration of tonic immobility (DTI), a catatonic‐like state of reduced responsiveness to a stressful stimulation. A total of 1065 animals were measured for the logarithm of DTI (LOGTI), the number of inductions (NI) necessary to induce the immobility reaction, open‐field behaviour including locomotor activity (MOVE), latency before first movement (LAT), number of jumps (JUMP), dejections (DEJ) and shouts (SHOUT), corticosterone level after a contention stress (LOGCORT) and body weight at 2 weeks of age (BW2). A total of 310 animals were included in a genome scan using selective genotyping with 248 AFLP markers. A total of 21 suggestive or genome‐wide significant QTL were observed. Two highly significant QTL were identified on linkage group 1 (GL1), one for LOGTI and one for NI. In the vicinity of the QTL for LOGTI, a nearly significant QTL for SHOUT and a suggestive QTL for LAT were also identified. On GL3, genome‐wide significant QTL were observed for JUMP and DEJ as well as suggestive QTL for LOGTI, MOVE, SHOUT and LAT. A significant QTL for BW2 was observed on GL2 and a nearly significant one on GL1. These results may be useful in the understanding of fearfulness in quail and related species provided that fearfulness has the same genetic basis.
Avian coccidiosis is a major parasitic disease of poultry, causing severe economical loss to poultry production by affecting growth and feed efficiency of infected birds. Current control strategies using mainly drugs and more recently vaccination are showing drawbacks and alternative strategies are needed. Using genetic resistance that would limit the negative and very costly effects of the disease would be highly relevant. The purpose of this work was to detect for the first time QTL for disease resistance traits to Eimeria tenella in chicken by performing a genome scan in an F2 cross issued from a resistant Fayoumi line and a susceptible Leghorn line. The QTL analysis detected 21 chromosome-wide significant QTL for the different traits related to disease resistance (body weight growth, plasma coloration, hematocrit, rectal temperature and lesion) on 6 chromosomes. Out of these, a genome-wide very significant QTL for body weight growth was found on GGA1, five genome-wide significant QTL for body weight growth, plasma coloration and hematocrit and one for plasma coloration were found on GGA1 and GGA6, respectively. Two genome-wide suggestive QTL for plasma coloration and rectal temperature were found on GGA1 and GGA2, respectively. Other chromosme-wide significant QTL were identified on GGA2, GGA3, GGA6, GGA15 and GGA23. Parent-of-origin effects were found for QTL for body weight growth and plasma coloration on GGA1 and GGA3. Several QTL for different resistance phenotypes were identified as co-localized on the same location. Using an F2 cross from resistant and susceptible chicken lines proved to be a successful strategy to identify QTL for different resistance traits to Eimeria tenella, opening the way for further gene identification and underlying mechanisms and hopefully possibilities for new breeding strategies for resistance to coccidiosis in the chicken. From the QTL regions identified, several candidate genes and relevant pathways linked to innate immune and inflammatory responses were suggested. These results will be combined with functional genomics approaches on the same lines to provide positional candidate genes for resistance loci for coccidiosis. Results suggested also for further analysis, models tackling the complexity of the genetic architecture of these correlated disease resistance traits including potential epistatic effects.
Dans le cadre d'une étude mixte pré-expérimentale sur le projet d'accompagnement-citoyen PRO-COM auprès d'enfants et d'adolescents avec une lésion neurotraumatique, cette analyse qualitative vise à approfondir notre compréhension de la perspective des familles et des accompagnateurs sur l'acceptabilité et la faisabilité de ce type d'intervention dans la communauté. Sur les six familles recrutées au départ, trois d'entre elles ainsi que les accompagnateurs des jeunes âgés entre 8 et 18 ans ont complété une première entrevue semi-dirigée; alors qu'une seule famille et l'accompagnateur du jeune ont participé à la deuxième entrevue prévue. Une analyse thématique des journaux de bord des accompagnateurs et des verbatim d'entrevues contribue à identifier les caractéristiques facilitantes pour les accompagnements, ainsi que les éléments liés à l'acceptabilité et à la faisabilité du projet. Malgré ses limites, cette étude laisse entrevoir une intervention suffisamment prometteuse pour être explorée davantage dans des études ultérieures.
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