From preimplantation diagnosis to herd monitoring: what does genomics bring to breeders?

Genomic selection is now fully implemented in breeding programs conducted by French breeding companies in Holstein, Normande and Montbeliard breeds. Initially, genotyping has been implemented by companies in selection schemes. This method enables to estimate the genetic potential of an animal at birth, thus shortening considerably the schedule of selection schemes and lowering its cost. In this context, optimizing reproductive biotechnologies has become a strategic priority. This may be achieved through different scenarii combining production of in vivo derived embryos and embryo transfer (ET) and the oocyte retrieval. Nowadays, one of the major challenges for reproductive biotechnologies is the realization of a pre-implantation diagnosis, from a small number of cells taken from the embryo, which opens new perspectives. In addition, since the opening of a genotyping service to French dairy farmers in 2011, genomic selection moved apace in farms from Montbeliard, Holstein, Red Pie and Normande breeds. In farms, genotyping of females is a new management tool enabling to sort heifers from birth, to refine the choice of bulls for an optimized breeding management, to control inbreeding together with genetic level and to anticipate breeding plans (choice of reproduction type and / or use of sexed semen). These tools may help to reach sustainable breeding practices, at collective and individual levels and are expected to evolve with the continuous optimization of genotyping toolsLa sélection génomique est aujourd’hui pleinement appliquée dans les programmes de sélection menés par les entreprises de sélection françaises Prim’Holstein, Normande et Montbéliarde. Dans un premier temps, le génotypage a été principalement valorisé par les entreprises dans la mise en oeuvre des schémas de sélection. Optimiser les techniques de reproduction est devenu un axe stratégique, en combinant la production d’embryons, l’utilisation de la superovulation et du transfert d’embryon (TE), ainsi que la ponction d’ovocytes. Aujourd’hui, un des défis majeurs des biotechnologies de la reproduction est la réalisation d’un diagnostic pré-implantatoire, à partir d’un petit nombre de cellules prélevées chez l’embryon, qui ouvre de nouvelles perspectives. En outre, depuis l’ouverture du service de génotypage aux éleveurs bovins laitiers français en 2011, la sélection génomique s’installe à grands pas au sein des élevages des races Montbéliarde, Prim’Holstein, Pie Rouge et Normande. En élevage, le génotypage des femelles est un nouvel outil de management, facilitant le tri des génisses de renouvellement, permettant d’affiner les accouplements par un choix des taureaux optimisé, de contrôler la consanguinité au niveau génétique et d’anticiper les plans d’accouplement (choix du mode de reproduction et/ou utilisation de semence sexée). Ces applications doivent permettre d’atteindre des pratiques de reproduction durables, au niveau collectif autant qu’individuel et devraient encore évoluer avec l’amélioration continue des outils de génotypag

Vers une amélioration de la détection des chaleurs dans les troupeaux bovins grâce à une nouvelle méthode de diagnostic et de conseil (DetŒstrus)

La détection des chaleurs est une étape clé de la mise à la reproduction dans les troupeaux pratiquant l'insémination animale (IA). La qualité de la détection est difficile à évaluer rendant délicat le conseil dans ce domaine. "DetŒstrus" est une nouvelle méthode de diagnostic et de conseil centrée sur la détection des chaleurs et utilisable par les conseillers dans les troupeaux bovins où l'IA est pratiquée. L'objectif de ce document est de présenter cette méthode et sa première évaluation sur le terrain. Cette méthode est innovante dans la mesure où elle permet de distinguer les problèmes liés à la vache (défaut de cyclicité post-partum, de niveau d'expression des chaleurs) de ceux liés aux pratiques de l'éleveur (défaut de sensibilité, de spécificité de la détection), et ainsi de proposer des solutions ciblées et adaptées aux contraintes et objectifs de l'éleveur. La méthode se présente sous la forme d'un document Excel® organisé en fiches qui servent de support lors de l'audit et se décline en deux versions (laitière et allaitante). La version laitière comprend une estimation de la sensibilité et de la spécificité de la détection grâce à des équations de prédiction utilisant des données facilement accessibles en exploitation et prenant en compte le niveau d'expression des chaleurs des vaches. La version allaitante comprend un simulateur permettant d'estimer la reprise de cyclicité post-partum dans le troupeau, et donc de planifier la surveillance des chaleurs pour une utilisation facilitée de l'IA. Un premier test en exploitation de la méthode montre que 89% des conseillers (40/45) et la totalité des éleveurs (24/24) ont jugé l'audit satisfaisant. 91% des éleveurs (21/23) se sentent "mieux armés" sur la détection des chaleurs après l'audit. La durée totale de l'audit (préparation et intervention) a été de 3h ± 1h en troupeaux laitiers et 2h10 ± 42min en troupeaux allaitants. Les retours de l'essai ont permis d'optimiser la méthode prochainement disponible en téléchargement gratuit sur le site de l'Institut de l'Elevage

Reproductive Technologies and Genomic Selection in Cattle

The recent development of genomic selection induces dramatic changes in the way genetic selection schemes are to be conducted. This review describes the new context and corresponding needs for genomic based selection schemes and how reproductive technologies can be used to meet those needs. Information brought by reproductive physiology will provide new markers and new improved phenotypes that will increase the efficiency of selection schemes for reproductive traits. In this context, the value of the reproductive techniques including assisted embryo based reproductive technologies (Multiple Ovaluation Embryo Transfer and Ovum pick up associated to in vitro Fertilization) is also revisited. The interest of embryo typing is discussed. The recent results obtained with this emerging technology which are compatible with the use of the last generation of chips for genotype analysis may lead to very promising applications for the breeding industry. The combined use of several embryo based reproductive technologies will probably be more important in the near future to satisfy the needs of genomic selection for increasing the number of candidates and to preserve at the same time genetic variability

Phylogeography and Genetic Diversity of Francisella tularensis subsp. holarctica in France (1947-2018)

In France, tularemia is caused by Francisella tularensis subsp. holarctica and is a sporadic disease affecting mainly wildlife animals and humans. F. tularensis species presents low genetic diversity that remains poorly described in France, as only a few genomes of isolates from the country are available so far. The objective of this study was to characterize the genetic diversity of F. tularensis in France and describe the phylogenetic distribution of isolates through whole-genome sequencing and molecular typing. Whole genomes of 350 strains of human or animal origin, collected from 1947 to 2018 in France and neighboring countries, were sequenced. A preliminary classification using the established canonical single nucleotide polymorphism (canSNP) nomenclature was performed. All isolates from France (except four) belonged to clade B.44, previously described in Western Europe. To increase the resolution power, a whole-genome SNP analysis was carried out. We were able to accurately reconstruct the population structure according to the global phylogenetic framework, and highlight numerous novel subclades. Whole-genome SNP analysis identified 87 new canSNPs specific to these subclades, among which 82 belonged to clade B.44. Identifying genomic features that are specific to sublineages is highly relevant in epidemiology and public health. We highlighted a large number of clusters among a single clade (B.44), which shows for the first time some genetic diversity among F. tularensis isolates from France, and the star phylogeny observed in clade B.44-subclades revealed that F. tularensis biodiversity in the country is relatively recent and resulted from clonal expansion of a single population. No association between clades and hosts or clinical forms of the disease was detected, but spatiotemporal clusters were identified for the first time in France. This is consistent with the hypothesis of persistence of F. tularensis strains found in Western Europe in the environment, associated with slow replication rates. Moreover, the presence of identical genotypes across long periods of time, and across long distances, supports this hypothesis but also suggests long-distance dispersal of the bacterium.This work was supported by the French National Research Agency (ANR) and the Direction Générale de l’Armement (DGA) (No. ANR-15-ASTR-0021-01). MK is a Ph.D. student co-supported by Université Paris-Est and DGA grants

Comparative Genomics and in vitro Infection of Field Clonal Isolates of Brucella melitensis Biovar 3 Did Not Identify Signature of Host Adaptation

Brucella spp. are responsible for brucellosis, a widespread zoonosis causing reproductive disorders in animals. Species-classification within this monophyletic genus is based on bacteriological and biochemical phenotyping. Traditionally, Brucella species are reported to have a preferential, but not exclusive mammalian host. However, this concept can be challenged since many Brucella species infect a wide range of animal species. Adaptation to a specific host can be a driver of pathogen variation. It is generally thought that Brucella species have highly stable and conserved genomes, however the degree of genomic variation during natural infection has not been documented. Here, we investigated potential genetic diversity and virulence of Brucella melitensis biovar 3 field isolates obtained from a single outbreak but from different host species (human, bovine, small ruminants). A unique MLVA-16 pattern suggested all isolates were clonal. Comparative genomic analyses showed an almost non-existent genetic diversity among isolates (only one SNP; no architectural rearrangements) and did not highlight any signature specific to host adaptation. Similarly, the strains showed identical capacities to enter and replicate in an in vitro model of macrophage infection. In our study, the absence of genomic variability and similar virulence underline that B. melitensis biovar 3 is a broad-host-range pathogen without the need to adapt to different hosts

Phenotypic and Molecular Characterization of Brucella microti-Like Bacteria From a Domestic Marsh Frog (Pelophylax ridibundus)

Several Brucella isolates have been described in wild-caught and “exotic” amphibians from various continents and identified as B. inopinata-like strains. On the basis of epidemiological investigations conducted in June 2017 in France in a farm producing domestic frogs (Pelophylax ridibundus) for human consumption of frog's legs, potentially pathogenic bacteria were isolated from adults showing lesions (joint and subcutaneous abscesses). The bacteria were initially misidentified as Ochrobactrum anthropi using a commercial identification system, prior to being identified as Brucella spp. by MALDI-TOF assay. Classical phenotypic identification confirmed the Brucella genus, but did not make it possible to conclude unequivocally on species determination. Conventional and innovative bacteriological and molecular methods concluded that the investigated strain was very close to B. microti species, and not B. inopinata-like strains, as expected. The methods included growth kinetic, antimicrobial susceptibility testing, RT-PCR, Bruce-Ladder, Suis-Ladder, RFLP-PCR, AMOS-ERY, MLVA-16, the ectoine system, 16S rRNA and recA sequence analyses, the LPS pattern, in silico MLST-21, comparative whole-genome analyses (including average nucleotide identity ANI and whole-genome SNP analysis) and HRM-PCR assays. Minor polyphasic discrepancies, especially phage lysis and A-dominant agglutination patterns, as well as, small molecular divergences suggest the investigated strain should be considered a B. microti-like strain, raising concerns about its environmental persistence and unknown animal pathogenic and zoonotic potential as for other B. microti strains described to date

Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae

Schmallenberg virus experimental infection of sheep

International audienceSince late 2011, a novel orthobunyavirus, named Schmallenberg virus (SBV), has been implicated in many cases of severely malformed bovine and ovine offspring in Europe. In adult cattle, SBV is known to cause a mild transient disease; clinical signs include short febrile episodes, decreased milk production and diarrhoea for a few days. However, the knowledge about clinical signs and pathogenesis in adult sheep is limited. In the present study, adult sheep of European domestic breeds were inoculated with SBV either as cell culture grown virus or as virus with no history of passage in cell cultures. Various experimental set-ups were used. Sampling included blood collection at different time points during the experimental period and selected organ material at autopsy. Data from this study showed, that the RNAemic period in sheep was as short as reported for cattle; viral genome was detectable for about 3-5 days by real-time RT-PCR. In total, 13 out of 30 inoculated sheep became RNAemic, with the highest viral load in animals inoculated with virus from low cell culture passaged or the animal passaged material. Contact animals remained negative throughout the study. One RNAemic sheep showed diarrhoea for several days, but fever was not recorded in any of the animals. Antibodies were first detectable 10-14 days post inoculation. Viral RNA was detectable in spleen and lymph nodes up to day 44 post inoculation. In conclusion, as described for cattle, SBV-infection in adult sheep predominantly results in subclinical infection, transient RNAemia and a specific antibody response. Maintenance of viral RNA in the lymphoreticular system is observed for an extended period

Modification chimique de polyesters aliphatiques biorésorbables par voie anionique (une nouvelle voie d'accès à des copolyesters fonctionnalisés)

MONTPELLIER-BU Pharmacie (341722105) / SudocPARIS-BIUP (751062107) / SudocSudocFranceF