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International audience; Duck species are known to have different ability to fatty liver production in response to overfeeding and gene expression analyses can help to characterize mechanisms involved in these differences. This data article reports the sequencing of RNAs extracted from the liver of Pekin and Muscovy duck species and of their reciprocal hybrids, Mule and Hinny ducks fed ad libitum or overfed. Libraries were prepared by selecting polyadenylated mRNAs and RNA Sequencing (RNASeq) was performed using Illumina HiSeq2000 platform. RNASeq data presented in this article were deposited in the NCBI sequence read archive (SRA) under the accession number SRP144764 and links to these data were also indicated in the Data INRAE repository (https://doi.org/10.15454/JJZ3QQ). Transcriptome analyses of these data were published in Hérault et al. (2019) and Liu et al. (2020)

Additional file 3. Numbers of enriched GO terms as a function of DEG numbers found with reference based and/or DRAP methods.

Additional file 1. Examples of interactions between feeding and genetic type effect.

National audience; Avian breeders are currently putting in place genomic selection in their selection schemes. One key parameter to optimize selection schemes, and so genetic gain of selected populations, is to correctly predict the accuracy of genomic evaluation. In a previous study, it has been shown that genomic selection at birth was a very promising strategy for breeders selection in purebred. As crossbred between pure lines is commonly used in avian selection schemes, raises the question about the use of crossbred offspring in breeders evaluation, and their impact on evaluation accuracy. In this study, we had 2 goals. First, estimation of genetic correlation, for the same egg quality trait, between performance from pure line, and cross line layers. Then, estimation of the differences in evaluation accuracy, by adding crossbred information to pure line evaluation. Results shown that genetic correlation between purebred and crossbred trait is strong, but did not allow to consider that it is the same trait. Adding crossbred performances into evaluations allowed to obtain better results, globally, than in separated evaluations.; Depuis quelques années, la sélection génomique commence à se mettre en place dans la filière avicole. Dans le but d’optimiser les schémas de sélection, et donc le progrès génétique des populations sélectionnées, il est important de connaître la précision de l’évaluation génomique, comparativement à l’évaluation génétique. Dans une étude précédente, il avait été observé que l’usage de la sélection génomique à la naissance était une stratégie très prometteuse pour la sélection des reproducteurs en race pure. Le croisement entre lignées pures étant utilisé à large échelle par les schémas de sélection avicoles, il s’est posé la question de l’utilisation des données des descendantes croisées sur l’évaluation des reproducteurs, et de leur influence sur la précision de l’évaluation. Dans le cadre de cette étude, 2 objectifs ont été poursuivis. Tout d’abord, estimer la corrélation génétique, pour un même caractère de qualité d’œuf, entre la performance exprimée par des poules de lignée pure, et celle des poules croisées. Ensuite, estimer les différences de précision apportées par l’intégration des données des croisées à l’évaluation en lignée pure. Les résultats ont montré que la corrélation génétique entre caractère pur et croisé est forte, mais ne permet pas de considérer qu’il s’agit du même caractère. L’ajout des performances de croisées aux évaluations a permis d’obtenir des résultats globalement meilleurs qu’en évaluations séparées.

La structure du déséquilibre de liaison (DL) au sein des populations en sélection impacte fortement la précision obtenue lors des études de cartographie de QTL ou lors de l’évaluation génomique des reproducteurs. Chez les oiseaux, la structure hétérogène du génome nécessite de décrire précisément le DL pour optimiser la sélection. L’utilisation des puces SNP haute densité pour le génotypage des populations de volailles est une opportunité pour approfondir notre connaissance de la structure du DL de ces populations. L’objectif de cette étude est d’acquérir une connaissance haute résolution de la structure du DL au sein de populations de poules de types ponte et chair. Nous avons analysé les génotypes (puce 600 K Affymetrix® Axiom® HD SNP) de 1541 animaux issus de 3 populations. L’étendue et le niveau du DL ont été estimés par le r2 moyen à distance physique donnée entre SNP. Cette étude met en évidence des différences importantes de structure du DL entre lignées et entre chromosomes. L’étendue et le niveau du DL sont plus importants dans les lignées de type ponte ou pour les macro-chromosomes et le chromosome Z. Ce niveau important de DL peut faciliter la détection de QTL sur ces chromosomes, mais peut également compliquer la localisation fine de polymorphismes causaux. A l’inverse, le faible niveau de DL observé sur les micro-chromosomes nécessite l’utilisation d’une forte densité de SNP pour détecter une association avec un phénotype, mais devrait permettre la cartographie fine d’un polymorphisme causal. Ces différences sont à prendre en considération pour définir une stratégie de génotypage économique et efficace pour la cartographie fine de QTL ou l’évaluation génomique., Knowledge of the linkage disequilibrium (LD) pattern is useful in animal genetic studies as it underlies mapping studies and genomic selection. This is all the more important in birds given the heterogeneous structure of the avian karyotype. Recently, the availability of the high density 600 K Affymetrix® Axiom® HD SNP genotyping array allowed to assess an in-depth knowledge of the LD pattern in chicken genome. The aim of the present study was to assess a higher resolution of the LD pattern in chicken genome in layer and broiler lines. In this study, we analyzed genotypes of 1541 animals from layers and broiler commercial populations to characterize their LD pattern. LD was measured by the average r2 value at a given physical distance between SNP. LD extended over a larger region for layer lines than for broiler line. Most differences between lines appeared at small interval distances (< 0.5Mb). LD extent and decay differed considerably between chromosomes categories. Average r2 values were higher for Z chromosome than for macro, intermediates and microchromosomes. The extent of useful LD observed for autosomal chromosomes was at least ten-fold longer for layer lines than for broiler. Finally, this study shed light on high LD for Z chromosome. The differences in LD pattern observed between chromosomes and chicken lines should be taken into account to define an economically efficient genotyping strategy.

Liver weights. Ap: Common Pekin duck; Cm: Muscovy duck; mu: Mule duck; hi: Hinny duck. (DOCX 24 kb)

Clusters of enriched GO terms associated to differentially expressed genes defined by semantic similarity. (PDF 2017 kb)

Gene expression analysis of duck liver steatosis from hybrid and parental species. Journées Ouvertes Biologie, Informatique et Mathématiques (Jobim)

The main goal of selection is to choose breeders of the next generation among a set of selection candidates. In genomic selection, the choice of breeders is based on the use of information on DNA polymorphisms, in particular SNP, in addition of performance measures. Since 2013, a commercial high density genotyping chip (600,000 markers) for chicken allowed the implementation of genomic selection in layer and broiler breeding. However, genotyping costs with this chip still remain high for a routine use on a large number of selection candidates. Consequently, it is interesting to develop, at a lower cost, low density genotyping chips. To do so, a set of SNP markers has to be selected to enable an imputation (prediction) of missing genotypes with high accuracy on a high density chip (HD chip). In this perspective, we conducted various simulation studies to choose the optimal strategy for low density genotyping of two different lines of laying hen. Different low density genotyping chips were designed according to two methodologies: a choice of SNP depending on a clustering of SNP based on linkage disequilibrium threshold or a choice of SNP at regular intervals (kb) along each chromosome. Imputation accuracy was assessed as the mean correlation between true and imputed genotypes. Results showed that correlations were more sensitive to false imputation of SNPs with low Minor Allele Frequency (MAF) with the equidistant methodology. Imputation accuracy improved with SNP density and when a higher LD threshold is used for SNP selection. Given the particular structure of the avian genome with chromosomes of very heterogeneous sizes and extents of LD, imputation accuracy differed according to the type of chromosome. All the simulation studies showed that linkage disequilibrium methodology enabled to get better results of imputation than with equidistant methodology.

The main goal of selection is to choose breeders of the next generation among a set of selection candidates. In genomic selection, the choice of breeders rests on the use of information on DNA polymorphisms, in particular SNP, in addition of performance measures. Since 2013, a commercial high density genotyping chip (600,000 markers) for chicken allowed the implementation of genomic selection in layer and broiler breeding. However, genotyping costs with this chip still remain high for a routine use on a large number of selection candidates. Consequently, it is interesting to develop, at a lower cost, low density genotyping chips. To do so, a set of SNP markers has to be selected to enable an imputation (prediction) of missing genotypes on a high density chip (HD chip). This imputation enables to predict missing genotypes of all selection candidates from high density genotyping of a reference population with phenotypes. In this perspective, according to the reference population, various simulation studies were conducted to choose the best strategy for low density genotyping of laying hen lines. Two different low density genotyping chips of 10K SNP were designed according to two methodologies: a choice of SNP depending on a clustering based on linkage disequilibrium threshold or a choice of SNP at regular intervals (kb) along each chromosome. Imputation accuracy was assessed as the mean correlation between true and imputed genotypes. Focusing on populationnal factors that can influence imputation accuracy, it is shown that imputation accuracy improves with an increase in the size of the reference population. By decreasing the kinship degree between reference and candidate population, it is seen that imputation accuracy decreases. Most importantly, results show that a key point in getting good imputations is to have the direct parents in the reference population. Finally, all different genotyping strategies focused on population factors show that linkage disequilibrium methodology enables to get better results of imputation than with equidistant methodology.

Knowledge of the linkage disequilibrium (LD) pattern is useful in animal genetic studies as it underlies mapping studies and genomic selection. Recently, the availability of the high density 600K Affymetrix® Axiom® HD SNP genotyping array allows to asses a higher resolution of the LD structure in chicken genome. In this study, we analysed genotypes of 1541 animals from layers and broiler commercial populations to characterize their LD pattern. LD was measured by the average r2 value at a given physical distance between SNP. LD extends over a larger region for layers line than for broiler line. Most differences between lines appeared at small interval distance (< 0.5Mb). LD extent and decay differed considerably between chromosome categories. Average r2 values were higher for Z chromosome than for macro, intermediates and microchromosomes. The extent of useful LD observed for autosomal chromosomes is at least tenfold longer for layers line than for broiler. Finally, this study shed light on high LD for the Z chromosome. The differences in LD pattern observed between chromosomes and chicken lines should be taken into account to define an economically efficient genotyping strategy.

Background Coccidiosis is the most common and costly disease in the poultry industry and which caused by protozoans from the genus of Eimeria. The current control of coccidiosis, based on the use of anticoccidial drugs and vaccination, faces serious obstacles such as drug resistance and the high costs for development of efficient vaccines, respectively. Therefore, the present control programs must be expanded with complementary approaches such as the use of genetics for improvement of the host’s response to Eimeria infections. Recently, we have performed a large-scale challenge study on Cobb500 broilers using E. maxima where we investigated variability among animals in response to the challenge. Taking advantage of size and structure of the large-scale challenge study, we performed a genome-wide association study (GWAS) with the aim to identify genomic regions underlying variability of the measured traits in the response to Eimeria maxima in broilers. Furthermore, we conducted a post-GWAS functional analysis with the aim of gaining a better biological understanding of the underlying response to Eimeria maxima challenge in broilers. Results In total, we identified 22 single nucleotide polymorphisms (SNP) with q-value

Additional file 11: Figure S4. Title: Distribution of the most frequent significant biological pathways. Description: Distribution of the most frequent biological pathways being significantly enriched with genes in genomic regions associated with measured traits during the large-scale challenge study. The distribution is considerably different when all measured traits are considered together and when PC measurements are excluded.

Use of genetic tools for improvement of host’s response is considered as a promising complementary approach for coccidiosis control. Therefore, we performed genome wide association study (GWAS) for response to Eimeria maxima challenge in broilers. The challenge was done on 2024 Cobb500 broilers. We phenotyped animals on two levels: global phenotyping performed on all animals and deep phenotyping on a subset of 184 extreme animals. The global phenotyping included: body weight gain, hematocrit, plasma coloration and rectal temperature and the deep phenotyping included: blood cell count, plasma proteins profiles, oocyst count and lesion score. GWAS was conducted on 1975 animals which were genotyped using 580K Affymetrix® Axiom® HD genotyping array. Quality control procedures involved the following criteria: SNP call rate (1%). GWAS was carried out in GEMMA software using standard univariate linear mixed model. The false-discovery rates (FDR) were calculated using the R package q-value and the cut-off of the significant association was set at q-value ≤ 0.05. We identified several genomic regions associated with measured parameters. Among the most promising results, robust associations have been identified between albumin levels and one region on GGA2, alpha 1 globulin and one region on GGA1, alpha 2 globulin and two regions on GGA1 and GGA6 and plasma coloration and one region on GGA6. To our knowledge this is the largest association study that has been conducted in a commercial broiler product to ascertain the genetic components driving the response of chickens to coccidiosis.

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International audience; Afin de mieux comprendre les réseaux de régulation des gènes impliqués dans le métabolisme des lipides chez le poulet, nous avons entrepris la réalisation d'une puce dédiée. Le foie étant le lieu principal de la lipogénèse chez les oiseaux, 220 gènes à expression hépatique, intervenant dans ce métabolisme, et ce toutes espèces confondues, ont été répertoriés d'après les données bibliographiques. Afin d’isoler ces gènes chez le poulet, deux stratégies ont été mises en place, utilisant d’une part des séquences homologues (dont des EST) et des séquences hétérologues d’autre part. Au total, 124 gènes aviaires ont été amplifiés par PCR et clonés sous forme de fragments de 300 bases localisés dans les régions codantes. Les produits PCR et des ADNc contrôles (spikes), permettant de normaliser les hybridations, ont ensuite été déposés sur membranes pour être hybridés. Les premiers résultats obtenus montrent des problèmes de sensibilité nous conduisant encore à quelques mises au point. Une fois ces dernières achevées, cet outil pourra être utilisé dans différents dispositifs d’animaux (caractérisés par des génotypes, des états nutritionnels ou des états physiologiques différents) afin de mieux étudier la régulation de ce métabolisme chez les espèces aviaires et de mieux appréhender son implication dans les variations phénotypiques observées.

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Cytotoxic necrotizing factor types 1 and 2 (CNF1 and -2) produced by pathogenic Escherichia coli strains have 90% conserved residues over 1,014-amino-acid sequences. Both CNFs are able to provoke a remarkable increase in F-actin structures in cultured cells and covalently modify the RhoA small GTPases. In this study, we demonstrated that CNF2 reduced RhoA GTPase activity in the presence and absence of P122 RhoGAP . Subsequently, peptide mapping and amino acid sequencing of CNF2-modified FLAG-RhoA produced in E. coli revealed that CNF2 deamidates Q63 of RhoA-like CNF1. In vitro incubation of the C-terminal domain of CNF2 with FLAG-RhoA resulted also in deamidation of the FLAG-RhoA, suggesting that this region contains the enzymatic domain of CNF2. An oligopeptide antibody (anti-E63) which specifically recognized the altered G-3 domain of the Rho family reacted with glutathione S -transferase (GST)-RhoA and GST-Rac1 but not with GST-Cdc42 when coexpressed with CNF2. In addition, CNF2 selectively induced accumulation of GTP form of FLAG-RhoA and FLAG-Rac1 but not of FLAG-Cdc42 in Cos-7 cells. Taken together, these results indicate that CNF2 preferentially deamidates RhoA Q63 and Rac1 Q61 and constitutively activates these small GTPases in cultured cells. In contrast, anti-E63 reacted with GST-RhoA and GST-Cdc42 but not with GST-Rac1 when coexpressed with CNF1. These results indicate that CNF2 and CNF1 share the same catalytic activity but have distinct substrate specificities, which may reflect their differences in toxic activity in vivo.

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The cytopathic effect (CPE) of Escherichia coli producing cytotoxic necrotizing factor type 1 (CNF1) was investigated by using a human epithelial cell (HeLa) model of infection with CNF1-producing E. coli BM2-1. This strain was shown to bind loosely, but massively, to HeLa cells. A 4-h interaction between bacteria and eukaryotic cells triggered the delayed appearance of a progressive dose-dependent CPE characterized by (i) intense swelling of cells accompanied by the formation of a dense network of actin stress fibers, (ii) inhibition of cell division due to a complete block in the G 2 phase of the cell cycle, and (iii) nucleus swelling and chromatin fragmentation. These alterations resulted in cell death starting about 5 days after interaction. The absence of multinucleation clearly distinguished the CPE from the effect produced by free CNF1, which was shown to result in a true endomitosis. Moreover, the CPE was neither produced by cell-free culture supernatants of infected cells nor prevented by a CNF1-neutralizing antiserum. Pathogenicity was completely abolished after Tn5::phoA insertion mutagenesis in the cnf-1 structural gene but not restored by trans complementation with a recombinant plasmid containing intact cnf-1 and its promoter. These results suggest that a gene downstream of cnf-1, essential to the induction of the CPE, was affected by the mutation. On the other hand, transformation of the wild-type strain BM2-1 with the same recombinant plasmid leads to a significant increase in both CNF1 activity and CPE, demonstrating the direct contribution of CNF1 to the CPE. In conclusion, the pathogenicity of E. coli BM2-1 for HeLa cells results from a complex interaction involving cnf-1 and associated genes and possibly requiring a preliminary step of binding of bacterial organisms to target cells.

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