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International audience; Feed efficiency is a complex trait of interest in animal breeding to reduce environmental impact of livestock herding and the cost of animal feed. A divergent selection on feed efficiency was carried out in pigs for more than 10 generations at an INRAE experimental unit, establishing lines of relative high- and low-feed efficiency in large white pigs. The objective of this study was to identify the molecular mechanisms underlying the divergence in feed efficiency between the two pig lines in the duodenum. We focused on the duodenum because of its sensory role in the hunger satiety pathways.Duodenum mucosal samples were collected in post-weaning pigs from the two divergent lines either after a 12 h period of feed restriction, or with a 10 h period of feed restriction followed by a 2 h period of ad libitum feed access (n = 6 per group and per line). Transcritomes and methylomes were analysed by poly-A RNA sequencing (RNA-seq) and by methylated DNA precipitation followed by sequencing (MeDP-seq), respectively. Transcriptomic reads were analysed with nf-core/rnaseq and limma-voom. MeDP-seq reads were analysed with nf-core/chipseq and the BayMeth method.A total of 962 genes were differentially expressed in the duodenum mucosa between the conditions (fasted vs fed), in contrast with 318 differentially expressed genes when comparing the divergent lines. The DNA methylome of the duodenum mucosa was unaffected by short term feed intake, but was distinct between the lines. More transcripts were affected by short term feed intake in the feed-efficient line than in the other line, including genes of the incretine secretion pathways involved in the production of GIP and GLP-1.Thus the duodenum transcriptomic response to short term feed intake was distinct in feed efficient and less efficient pig lines. These differences might in part be due to differences in DNA methylation profiles.

International audience; Identifying causal mutations responsible of phenotypes in a time and cost-effective manner remains a challenge still for all species. Although the portfolio of next-generation sequencing methodologies offers a broad range of opportunities nowadays, having the right and suitable molecular genetic tools in non-model organisms is often an issue. For the European rabbit (Oryctolagus cuniculus), considered as an animal model for experimental research, the OryCun2.0 reference genome was released in 2009 and the Affymetrix AxiomOrcun SNP Array was made available in 2016. This novel beadchip gives the possibility to develop conveniently genome-wide association studies (GWAS) in rabbits without however freeing itself from the subsequent steps of causal mutation characterization. Whole exome sequencing (WES) appears as a direct and suitable strategy to target and sequence variants all at once. Unfortunately, no exome enrichment tool exist for rabbits. Here, we proposed to capture the rabbit exome using the marketed human panel since human and rabbit genomes are closely related on the phylogenetic tree of species. We performed heterologous hybridization for 48 rabbits from 7 different populations and generated 2 billion sequencing reads for the whole dataset. The quality of the heterologous hybridization allowed the capture of the rabbit exome and enabled a dataset of 40,000 confident variants that specifically target both protein-coding and extended exons. This method also presents a unique opportunity to investigate both (i) the genetic diversity of different rabbits’ breeds and (ii) the mendelian determinism of specific phenotypes in rabbits without resorting to costly customized tools.

Additional file 9: Figure S5. Sex assignment for the 1159 goats sampled in VarGoats. Representation of the ratio of read number between the autosomes and the X chromosome and the read number on the Y chromosome for each animal to determine its sex. The horizontal bar corresponds to the threshold of 25 reads from the Y scaffold allowing to differentiate males from females.

Additional file 6: Figure S4. Tranche plot produced by VariantRecalibrator for SNPs. Description: Partition of the call sets into quality tranches. The tranches correspond to certain levels of sensitivity relative to the truth sets (the highest tranche corresponds to a high accuracy call set but with the lowest value of sensitivity).

Additional file 3: Figure S1. Distribution of the concordance rates. Concordance rates (CR) between sequence variants and 50 k genotypes for 457 individuals. The figure shows a clear disruption in the distribution of CR, thus we found it easy and relevant to discard the samples below a concordance rate of 70% between sequence and chip SNP data.

Additional file 5: Figure S3. Pairwise comparisons of the annotations chosen in VQSR for InDels. Description: Modeling report generated by GATK VariantRecalibrator for every pairwise combination of annotations used (QD, DP, FS, MQRankSum, ReadPosRankSum and SOR), with a 2D projection of the Gaussian mixture model.

International audience; Junctional Epidermolysis Bullosa (EB) is a severe congenital disease affecting the skin at the extremities of the limbs and the mucous membranes. In sheep, this recessive disease causes perinatal death of affected lambs. Multiple observations of EB cases were recently reported in the French Mouton Vendéen meat sheep breed. Skin biopsies of 6 affected lambs and when available, blood samples from the parents (n= 7) and unaffected full-sib lambs (n = 4) were collected for genomic DNA extraction. From a bibliography study and analysis of the OMIM database (Online Mendelian of Human Genes and Genetic Disorders), we have focused on 12 candidate genes mainly belonging to the collagen, laminin, integrin and keratin families. Based on the hypothesis of a recessive transmission of a deleterious variant, we have performed whole-genome sequencing of 2 unrelated EB-affected lambs (supposed homozygous carriers) and 1 unaffected full-sib (supposed heterozygous or non-carrier). Using the GATK workflow on a Galaxy platform, we have identified a novel SNP in the exon 23 of the ITGB4 gene of the integrin family (OAR11_v4.0, g. 54799925 G > A (p.885 R > *)) whose variant allele causes a premature stop codon. By a specific RFLP assay, we have determined that all EB-affected lambs were homozygous for this variant allele, their parents were heterozygous and the full-sibs were either heterozygous or non-carrier, fitting well with the working hypothesis. Following this primary discovery, a larger set of Mouton Vendéen animals was genotyped. We estimated the population allele frequency at 6.8% by genotyping a cohort of renewal ewe lambs (n = 1227). We also found a 5.7% allele frequency among the breeding rams present in 2018 (n = 1007) in artificial insemination center, progeny-testing station, and for natural mating in farms. Moreover, the specific genotyping of producing ewes in the most EB-affected flocks revealed a variant allele frequency up to 13.3%, due to overuse of inbreeding strategy. In conclusion, the discovery of a new mutation in ITGB4 causing EB in sheep will improve the selection scheme management of the Mouton Vendéen breed to limit the dissemination of this disease.

International audience; The segregation of the L prolific mutation in the FecL major gene was described in the meat strain of Lacaune sheep. The L mutation was shown to not only affect the prolificacy, but also the fertility after insemination and the growth and mortality of lambs born from L carrier ewes. In order to increase our knowledge about the potential pleiotropic effect of the L prolific mutation, we have observed 20 ++ and 23 L+ Lacaune ewe lambs from birth to adulthood. We have recorded their growth, average daily gain (ADG), endocrine hormone profiles, onset of puberty and fertility after first natural mating. The L mutation did not affect the birth weight or the ADG among the analyzed period. In contrast, these two traits were significantly decreased by the twin or triplet mode of birth compared to single. Interestingly, by checking circulating progesterone level (>0.5ng/ml), L+ ewe lambs have shown precocious ovulation events one month earlier on average than ++ (5 vs. 6, P

Gastrointestinal nematodes (GIN) are a major constraint for small ruminant production. Due to the rise of anthelmintic resistance throughout the world, alternative control strategies are needed. The development of GIN resistance breeding programs is a promising strategy. However, a better understanding of the mechanisms underlying genetic resistance might lead to more effective breeding programmes. In this study, we compare transcriptome profiling of abomasal mucosa and lymph node tissues from non-infected, resistant and susceptible infected Creole goats using RNA-sequencing. A total of 24 kids, 12 susceptible and 12 GIN resistant based on the estimated breeding value, were infected twice with 10,000 L3 Haemonchus contortus. Physiological and parasitological parameters were monitored during infection. Seven weeks after the second infection, extreme kids (n = 6 resistant and 6 susceptible), chosen on the basis of the fecal egg counts (FEC), and 3 uninfected control animals were slaughtered. Susceptible kids had significantly higher FEC compared with resistant kids during the second infection with no differences in worm burden, male and female worm count or establishment rate. A higher number of differentially expressed genes (DEG) were identified in infected compared with non-infected animals in both abomasal mucosa (792 DEG) and lymph nodes (1726 DEG). There were fewer DEG in resistant versus susceptible groups (342 and 450 DEG, in abomasal mucosa and lymph nodes respectively). 'Cell cycle' and 'cell death and survival' were the main identified networks in mucosal tissue when comparing infected versus non-infected kids. Antigen processing and presentation of peptide antigen via major histocompatibility complex class I were in the top biological functions for the DEG identified in lymph nodes. The TGF beta 1 gene was one of the top 5 upstream DEG in mucosal tissue. Our results are one of the fist investigating differences in the expression profile induced by GIN infection in goats.

National audience

Notice à Reprendre après le Congres; Insights on the genetic determinism and evolution of recombination rates by combining multiple genome-wide datasets in the Sheep. 68. Annual Meeting of the European Associationfor Animal Production (EAAP)

International audience; The Flemish sheep breed is of the dairy type and currently considered as a rare breed in Flanders (Belgium). The original breeding objective of the Flemish sheep was wool production (18th century) but it was also known for its high litter size and good maternal capacity. In order to support conservation efforts, pedigree data (n=5,095) and litter size information (2,385 litters on 1,224 ewes) were analysed. In the period 2010-2015, there were on average 38 sires and 238 ewes used for breeding annually. The average inbreeding coefficient was estimated at 0.055 and the effective population size was 124 (based on increase of coancestry) and 55 (based on increase of inbreeding). Average prolificacy (2002-2015) attained 2.02±0.87 (mean ±stand. deviation) with up to five lambs born. Using a linear animal model and a Gibbs sampling algorithm, a relatively high heritability coefficient of 0.25 was obtained for prolificacy This result warranted a screening of the breed for major fecundity (Fec) genes known to affect litter size. Fifty-eight individuals of the breed (20 rams and 38 ewes) were screened at the 4 Fec gene loci for all known mutations in ovine BMP15, GDF9, BMPR1B and B4GALNT2. Four individuals (3 ewes and 1 ram) were identified as carriers of the FecXGr mutation in the BMP15 gene originally evidenced in the French Grivette breed and no other mutations were detected. This finding warrants: (1) a population wide screening of the breed for this mutation; and (2) an investigation into the effects of the mutation on prolificacy in this breed. This discovery also underlines the importance of conservation and investigation of endangered breeds because they may harbour valuable alleles for future use.

Identification of two major genes affecting prolificacy in the French Noire du Velay sheep. 36. Conference of the International Society for Animal Genetics (ISAG)

National audience; Mastitis is an infectious disease mainly caused by bacteria invading the mammary gland. Genetic control of susceptibility to mastitis has been widely evidenced in dairy ruminants, but the genetic basis and underlying mechanisms are still largely unknown. We describe here the discovery, fine mapping and functional characterization of a genetic variant associated with mastitis in dairy sheep. After implementing genome-wide association studies, we identified a major QTL associated with an elevated milk leukocyte count on ovine chromosome OAR3. Fine mapping of the region, using full sequencing of the genomes of three animals with a 12X coverage, provided one strong SNP candidate that mapped to the coding sequence of a highly conserved gene, suppressor of cytokine signaling 2 (Socs2). The frequency of the allele associated with increased susceptibility to mastitis was 21.7% and the Socs2 genotype explained 12% of the variance of the trait. The point mutation induces the R96C substitution in the SH2 functional domain of SOCS2, i.e. the binding site of the protein to various ligands, as well-established for the growth hormone receptor GHR. Using surface plasmon resonance we show that the R96C point mutation completely abrogated SOCS2 binding affinity for the phosphopeptide of GHR. Additionally, the body size, body weight and milk production in R96C homozygote sheep, were significantly increased by 24%, 18%, and 4.4%, respectively, when compared to wild type sheep, supporting the view that the point mutation causes a loss of SOCS-2 functional activity. Altogether these results provide strong evidence for a causal mutation controlling mastitis in sheep and highlight the major role of SOCS-2 as a tradeoff between the host’s inflammatory response to mammary infections, and body growth and milk production, which are all mediated by the JAK/STAT signaling pathway.; Les mammites sont principalement liées à des infections de la glande mammaire par diverses bactéries. L’existence d’une variabilité génétique naturelle de la résistance des ruminants laitiers aux mammites a été largement établie, mais les gènes sous-jacents restent majoritairement inconnus. Dans cet article, nous rapportons les résultats de détection, de cartographie fine et de caractérisation fonctionnelle d’un variant génétique associé à la prédisposition aux mammites chez les ovins laitiers. En premier lieu, une analyse d’association basée sur le génotypage de 1009 béliers avec la puce Illumina 50K OvineSNP50Beadchip a permis d’identifier une région QTL, associée à des concentrations de cellules somatiques (CCS) élevées, sur le chromosome ovin OAR3. La cartographie fine de la région basée sur le séquençage complet de 3 animaux chez qui les allèles ségrégeaient a permis d’identifier un SNP candidat localisé dans la séquence codante d‘un gène hautement conservé dans le règne animal, Suppressor Of Cytokine Signaling 2 (Socs2). La fréquence de l’allèle associé à des CCS élevés est de 21,7% et le « génotype Socs2» explique 12% de la variance du caractère dans la population où il a été identifié. La mutation induit une substitution R96C dans le domaine fonctionnel SH2 de SOCS-2, le site de fixation de la protéine à de nombreux ligands tels que le récepteur à l’hormone de croissance (GHR). A l’aide d’un test fonctionnel basé sur la résonance des plasmons de surface, nous avons montré que la mutation R96C abroge l’affinité de SOCS-2 pour la tyrosine phosphorylée du domaine intracellulaire de GHR. Par ailleurs, nous avons montré que la croissance et la taille à l’âge adulte des brebis portant l’allèle muté étaient supérieures à celles des brebis de génotype sauvage, en adéquation avec l’hypothèse d’une invalidation de la fonction de SOCS-2. De plus, la mutation est également associée à une production laitière supérieure. L’ensemble de ces résultats conforte le fait que la mutation identifiée est probablement responsable du QTL pour les CCS sur OAR3. Ces résultats suggèrent un rôle de SOCS-2 dans le contrôle de l’inflammation médié par la voie de signalisation JAK/STAT et suggèrent un potentiel effet pléiotropique de cette mutation sur la croissance et les caractères de production.

Les mammites sont principalement liées à des infections de la glande mammaire par diverses bactéries. L’existence d’une variabilité génétique naturelle de la résistance des ruminants laitiers aux mammites a été largement établie, mais les gènes sous-jacents restent majoritairement inconnus. Dans cet article, nous rapportons les résultats de détection, de cartographie fine et de caractérisation fonctionnelle d’un variant génétique associé à la prédisposition aux mammites chez les ovins laitiers. En premier lieu, une analyse d’association basée sur le génotypage de 1009 béliers avec la puce Illumina 50K OvineSNP50Beadchip a permis d’identifier une région QTL, associée à des concentrations de cellules somatiques (CCS) élevées, sur le chromosome ovin OAR3. La cartographie fine de la région basée sur le séquençage complet de 3 animaux chez qui les allèles ségrégeaient a permis d’identifier un SNP candidat localisé dans la séquence codante d‘un gène hautement conservé dans le règne animal, Suppressor Of Cytokine Signaling 2 (Socs2). La fréquence de l’allèle associé à des CCS élevés est de 21,7% et le « génotype Socs2» explique 12% de la variance du caractère dans la population où il a été identifié. La mutation induit une substitution R96C dans le domaine fonctionnel SH2 de SOCS-2, le site de fixation de la protéine à de nombreux ligands tels que le récepteur à l’hormone de croissance (GHR). A l’aide d’un test fonctionnel basé sur la résonance des plasmons de surface, nous avons montré que la mutation R96C abroge l’affinité de SOCS-2 pour la tyrosine phosphorylée du domaine intracellulaire de GHR. Par ailleurs, nous avons montré que la croissance et la taille à l’âge adulte des brebis portant l’allèle muté étaient supérieures à celles des brebis de génotype sauvage, en adéquation avec l’hypothèse d’une invalidation de la fonction de SOCS-2. De plus, la mutation est également associée à une production laitière supérieure. L’ensemble de ces résultats conforte le fait que la mutation identifiée est probablement responsable du QTL pour les CCS sur OAR3. Ces résultats suggèrent un rôle de SOCS-2 dans le contrôle de l’inflammation médié par la voie de signalisation JAK/STAT et suggèrent un potentiel effet pléiotropique de cette mutation sur la croissance et les caractères de production., Mastitis is an infectious disease mainly caused by bacteria invading the mammary gland. Genetic control of susceptibility to mastitis has been widely evidenced in dairy ruminants, but the genetic basis and underlying mechanisms are still largely unknown. We describe here the discovery, fine mapping and functional characterization of a genetic variant associated with mastitis in dairy sheep. After implementing genome-wide association studies, we identified a major QTL associated with an elevated milk leukocyte count on ovine chromosome OAR3. Fine mapping of the region, using full sequencing of the genomes of three animals with a 12X coverage, provided one strong SNP candidate that mapped to the coding sequence of a highly conserved gene, suppressor of cytokine signaling 2 (Socs2). The frequency of the allele associated with increased susceptibility to mastitis was 21.7% and the Socs2 genotype explained 12% of the variance of the trait. The point mutation induces the R96C substitution in the SH2 functional domain of SOCS2, i.e. the binding site of the protein to various ligands, as well-established for the growth hormone receptor GHR. Using surface plasmon resonance we show that the R96C point mutation completely abrogated SOCS2 binding affinity for the phosphopeptide of GHR. Additionally, the body size, body weight and milk production in R96C homozygote sheep, were significantly increased by 24%, 18%, and 4.4%, respectively, when compared to wild type sheep, supporting the view that the point mutation causes a loss of SOCS-2 functional activity. Altogether these results provide strong evidence for a causal mutation controlling mastitis in sheep and highlight the major role of SOCS-2 as a tradeoff between the host’s inflammatory response to mammary infections, and body growth and milk production, which are all mediated by the JAK/STAT signaling pathway.

National audience

International audience; Gastro-intestinal nematodes are of major concern to sheep health worldwide. Identifying the causative genes responsible for resistance would augment the efficiency of selection. Previously, back-cross (BC) sheep (Black Belly * Romane breeds) were genotyped with a 50K SNP chip and were measured for faecal egg count after two successive experimental challenges by H. contortus. The most significant QTL were identified on chromosomes 5, 12, 13, 21. A customized assay including 1000 SNP was created to increase the density ofmarker coverage in these regions and others major QTL regions affecting parasitism resistance in natural infection conditions. In the present study, 277 Romane lambs were experimentally challenged with H contortusand genotyped with the dedicated 1000 SNP. Six out of the eight tested QTL regions have an effect in the Romane pure Breed population.

National audience

National audience

International audience

Goat breeds, including dairy, meat and fiber breeds, are adapted to a wide range of breeding conditions, and have a large economic impact. Currently, however, they benefit from fewer genomic research tools compared to cattle or sheep. At present, the International Goat Genome Consortium (www.goat.genome.org) federates 3 projects, aiming at the improvement of knowledge of goat genome: - de novo goat genome sequence - RH panel and whole genome high density RH maps - 50K SNP chip. An update will be made on these three topics. Details will be given on the international goat SNP chip, developed using whole genome de novo sequencing and reduced representation libraries of the genome of Alpine, Saanen, Creole, Boer, Kacang and Savanna breeds. More than 500,000 SNP were chosen by filtering on flanking sequence data, minimum allele frequency, technological qualities and categorized depending on the number of breeds in which the 2 alleles were observed. 60,000 high quality SNPs were finally spaced on the goat genome, using goat contigs. 59,000 out of the 60,000 SNPs were aligned on the bovine genome. 100 % of the SNPs were observed as heterozygous in milk breeds, 97% in meat breeds. This chip, based on Illumina Infinium technology, has been used to generate cluster files on 288 animals, using both the breeds used for SNP discovery and Skopelos, Angora and Jinlan breeds.