[Avian cytogenetics goes functional] Third report on chicken genes and chromosomes 2015

High-density gridded libraries of large-insert clones using bacterial artificial chromosome (BAC) and other vectors are essential tools for genetic and genomic research in chicken and other avian species... Taken together, these studies demonstrate that applications of large-insert clones and BAC libraries derived from birds are, and will continue to be, effective tools to aid high-throughput and state-of-the-art genomic efforts and the important biological insight that arises from them

Epigénétique et variabilitlé des caractères : quelle importance en aviculture ?

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 compensation of sex chromosomes, although such mechanisms could be involved in thephenotypic variability of birds, as in several livestock species. This paper reviews the literature on epigeneticmechanisms that could contribute significantly to trait variability in birds, and compares the results to theexisting knowledge of epigenetic mechanisms in mammals. The main issues addressed in this paper are: (1)Does genomic imprinting exist in birds? (2) How does the embryonic environment influence the adult phenotypein avian species? (3) Does the embryonic environment have an impact on phenotypic variability across severalsuccessive generations? The potential for epigenetic studies to improve the performance of individual animalsthrough the implementation of limited changes in breeding conditions or the addition of new parameters inselection models is still an open question.De plus en plus d'études révèlent que l'information épigénétique a une influence sur les phénotypes desindividus. On sait peu de choses sur les mécanismes épigénétiques chez les oiseaux, bien que, comme dansplusieurs espèces animales et végétales, ces mécanismes pourraient être impliqués dans la variabilité desperformances. Cet article passe en revue la littérature sur les mécanismes épigénétiques qui pourraient contribuerde manière significative à la variabilité des caractères chez les oiseaux, et compare les résultats à la connaissanceactuelle des mécanismes épigénétiques chez les mammifères. Les principales questions abordées sont lessuivantes: (1) L'empreinte génomique parentale existe-t-elle chez les oiseaux? (2) En quoi l'environnementembryonnaire influence le phénotype adulte chez les espèces aviaires? (3) Dans quelle mesure l'environnementembryonnaire a-t-il un impact sur la variabilité phénotypique sur plusieurs générations successives ? Le rôlepotentiel des études épigénétiques dans l’amélioration des performances individuelles des animaux à travers lamise en oeuvre de changements, même restreints, dans les conditions d'élevage, ou par l'ajout de nouveauxparamètres dans les modèles de sélection, est encore une question ouverte

Epigenetics and long-term effects if embryonic environment in avian species

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Epigenetics and phenotypic variability:interesting insights from birds and long-term effects of embryonic environment in avian species

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Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events

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-I) and from cytidine to uridine (C-to-U). This phenomenon is more and more described in mammals, notably since the availability of next generation sequencing technologies allowing a whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken are still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, to understand to what extent this phenomenon is conserved in vertebrates. We performed RNA and DNA sequencing from 8 embryos. Being aware of common pitfalls inherent to sequence analyses leading to false positive discovery, we stringently filtered our datasets and found less 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 editing level increase with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, and provide support of an absence of non A-to-I events from the chicken transcriptome

Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates

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

Transcriptome-wide investigation of genomic imprinting in chicken

Session : Genetic diversity and polymorphismsThe question of evolution of imprinting in vertebrates and its existence in birds is evoked in the literature, but not yet definitely answered. Genomic imprinting is an epigenetic modification leading to parent-oforigin- specific expression of certain genes. It has been observed in eutherian mammals and marsupials, but not in birds. So far, the allelic expression of imprinted gene orthologs has been analyzed in the chicken, without any reliable evidence of imprinting. Several imprinted QTL have been found in poultry; as some of them may finally be considered as not relevant to genomic imprinting, others appeared to be consistent, when using appropriate animal design and methodology. Our main objectives are to detect genes for which variation in expression is observed according to the allele, either because of an allele-specific expression or a parent-of-origin dependent expression. We screened the entire genome for allele-specific differential expression on whole embryonic transcriptomes by using high-throughput sequencing. Two chicken lines were used, as inbred and as genetically distant as possible, to unquestionably identify the parental origin of each observed haplotype. Two families from 2 reciprocal crosses were produced and transcripts from 20 embryos (4.5 d) have been tagged and sequenced through 6 HiSeq2000 lanes. About 200 Gb have been generated and are under analysis

Y a-t-il de l'empreinte chez la poule ?

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Transcriptome-wide investigation of genomic imprinting in chicken

Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken

Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail

Chantier qualité GABackground: As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of a QTL for a fear-related behaviour, namely tonic immobility, previously localized on Coturnix japonica chromosome 1. To this aim, two reduced representations of the genome were analysed through high-throughput 454 sequencing: AFLP (Amplified Fragment Length Polymorphism) fragments as representatives of genomic DNA, and EST (Expressed Sequence Tag) as representatives of the transcriptome. Results: The sequencing runs produced 399,189 and 1,106,762 sequence reads from cDNA and genomic fragments, respectively. They covered over 434 Mb of sequence in total and allowed us to detect 17,433 putative SNP. Among them, 384 were used to genotype two Advanced Intercross Lines (AIL) obtained from three quail lines differing for duration of tonic immobility. Despite the absence of genotyping for founder individuals in the analysis, the previously identified candidate region on chromosome 1 was refined and led to the identification of a candidate gene. Conclusions: These data confirm the efficiency of transcript and AFLP-sequencing for SNP discovery in a non-model species, and its application to the fine mapping of a complex trait. Our results reveal a significant association of duration of tonic immobility with a genomic region comprising the DMD (dystrophin) gene. Further characterization of this candidate gene is needed to decipher its putative role in tonic immobility in Coturnix