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GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech
Research highlights for 2020: an illustration of our main research results
Accelerometers provide early genetic selection criteria for the jumping horse
Selection of jumping horses is based on two criteria: evaluation by experts during a breeding show at the age of 3 years or show performances from the age of 4 years until adult age. Our study identified an early selection criterion that is objective and efficient, and measurable during horse shows: take-off time during free jumping. This take-off time is measured using a miniaturized accelerometer (Equimetrix ®), has a reasonable heritability (0.16), and is highly genetically correlated with show performance (0.59). Thus, breeder’s associations now have a tool for selection that can be used during competitions and complements style scores without replacing them. The French Saddle Stub Book has already begun a partnership with a saddlery to put the tool into practice and integrate it in the selection schemes.
Contact: BIGE Team, Eric Barrey
Symposium: Non-coding RNA in mitochondrial and nuclear crosstalk
Today, non-coding RNAs (ncRNAs) that are either encoded by the mitochondrial genome or imported into mitochondria represent an emerging field because of their importance for human and animal health. The objective of this symposium was to share the latest advances on the diversity of ncRNAs, the underlying molecular mechanisms, and their impact on mitochondrial functions and nuclear-mitochondrial crosstalk. These findings open new horizons for developing diagnostic and therapeutic strategies for diseases such as cancers, cardiovascular, muscular and mitochondrial diseases.
Contact: BIGE Team, Eric Barrey
A new method for long-read sequencing of mitochondrial genomes
Mitochondria have many cell functions including the production of chemical energy as ATP by oxidative phosphorylation. The study of the genetic variability of the mitochondrial genome is interesting for the detection of mitochondrial diseases (mutations that impact their functions) but also for genetic selection of sports performances, notably in the horse.
The mitochondrial genome of mammals is small and encodes 37 genes without taking non-coding RNAs into account, which are now being more and more studied. We established a reliable method for sequencing the complete horse mitochondrial genome that can detect polymorphisms between individuals, and thus provides information on the genetic diversity of mitochondrial genomes, in addition to the nuclear genome data. The method was developed on the equine mitochondrial genome but can easily be adapted to other species. This new-generation sequencing method, which combines a low error rate and sequence length, opens the way to field analyses due to the miniaturization of the method
Contact: BIGE Team, Eric Barrey and Sophie Pollet
Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows
Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. Within the Microficient project, the rumen microbiome from Holstein cows was characterized by DNA sequencing. Methane production and dry matter intake (DMI) were individually measured over 4 to 6 weeks to estimate methane production per kg ingested. Three groups of microorganisms were identified, one of which was associated with higher methane production. The taxonomic composition presented a lower abundance of Succinivibrionaceae and Methanosphaera, and higher abundance of Ruminococcaceae, Christensenellaceae and Lachnospiraceae. Metagenomic analysis revealed that this group contained an overrepresentation of genes associated with methanogenesis, including the methyl‐coenzyme M reductase enzyme. A group of 86 discriminant bacterial OTU (operational taxonomic unit), which include bacteria families linked to methane emission such as Succinivibrionaceae, Ruminococcaceae, Christensenellaceae, Lachnospiraceae and Rikenellaceae, explains 24% of the phenotypic variance of methane emission, whereas the host genome’s contribution was ~14%. These microbial biomarkers are relevant criteria for targeted methane reduction selection programs in the dairy cattle industry.
Contact: G2B Team, Didier Boichard
Improved dairy cattle mating plans at the herd level using genomic information
IINRAE and MO³, which is a shared Research-Development structure for the Montbeliarde cattle breed, have investigated whether systematic genotyping of young females is interesting for breeding. Genomic information allows an improved early prediction of the genetic value of cows but it also provides a true measure of the kinship between bulls and cows and an appropriate management of genetic defects or major genes. Three different mating methods (random, sequential or linear optimization) based on genomic information on males and females were compared for 160 real herds of Montbeliarde cattle. Clearly, planning intra-farm matings using linear optimization improves the economic result while reducing inbreeding in offspring and the probability of conceiving an embryo with a genetic defect. This approach was implemented in the field for the Montbeliarde breed. This study was performed as part of the PhD work of Marie Bérodier, defended in 2020.
Contact: G2B Team, Vincent Ducrocq
Gene networks for three feed efficiency criteria reveal shared and specific biological processes
Feed efficiency is a major determinant for the competitiveness of a farm. However, it is a complex trait to analyze because measuring animal intake on a large scale is difficult. In addition, it is a trait that can be evaluated according to different non-equivalent criteria. By combining phenotypic and sequence data, this study aimed at identifying genes and metabolic pathways involved in feed efficiency. Towards this aim, we studied 789 Charolais bulls, which were phenotyped for intake quantity and for three efficiency criteria. These animals were genotyped using an SNP array and their complete genome sequence was imputed statistically. Data analysis included a genome-wide association study (GWAS) at the genome sequence level combined with an analysis of the gene networks identified. These networks included 426 to 626 genes. The most enriched biological processes included salivary, gastric and mucin secretions and metabolic and cardiovascular processes. Several hormones were also identified and are candidate biomarkers for feed efficiency.
Contact: G2B Team, Sébastien Taussat (Allice), Gilles Renand, Pauline Martin
Survey of mitochondrial sequences integrated into the bovine nuclear genome
Nuclear copies of the mitochondrial DNA (NUMTs) have already been described in several species. In this context, we identified and analysed 166 bovine NUMT regions with a total length of 430 kbp, representing about 0.02% of the cattle nuclear genome. Copies of all mitochondrial regions were detected in the nuclear genome, with distinct degrees of sequence similarity to the mitogenome. Some NUMT regions include large mitogenome segments and show high similarity to the organelle genome sequence. NUMT regions are frequently modified by insertion of repetitive sequences and by sequence rearrangements. We confirmed the existence of 29 NUMT regions by PCR amplification using DNA from the cow (Dominette) which was used to generate the bovine genome reference sequence, ruling out the possibility that these NUMT could be artifacts of the genome assembly. As there are NUMT regions with high similarity to the mitogenome, special care is needed when designing primers for mitochondrial DNA amplification. Our results can therefore be used to avoid co-amplification of bovine nuclear sequences similar to mitochondrial DNA.
Contact: G2B Team, Dominique Rocha
Identification of candidate genes for resistance to paratuberculosis from sequence-based GWAS in Holstein and Normande dairy cattle
Bovine paratuberculosis is a contagious and incurable disease caused by Mycobacterium avium paratuberculosis. Genetics can help control the disease. Within the PICSAR-PARADIGM multidisciplinary project financed by INRAE (GISA metaprogram), APIS-GENE and GDS-France, the healthy or diseased status (clinical or subclinical) of 2293 cows (1644 Holstein and 649 Normande) was characterized by at least four concordant diagnoses, using a case-control type method. After imputation of the whole genome sequence for each cow, an association analysis showed three QTL on chromosomes 12, 13 and 23 that target specifically three genes, i.e. ABCC4, CBFA2T2 and IER3, and are also good functional candidates.
Confirmed effects of candidate variants for milk production, udder health, and udder morphology in dairy cattle
Thanks to the data from the international consortium “1000 bovine genomes”, it is possible to impute, i.e. to statistically reconstitute, all bovine DNA polymorphisms for which genotyping data on SNP arrays are available. These data, combined with performance data recorded on farms, allow the identification of genome regions (QTL) and polymorphisms that are involved in the genetic determinism of traits via an association analysis. By applying this approach to the data from 11,039 bulls (via the mean of the corrected performances of their daughters) from the Holstein, Montbeliarde and Normande breeds for five milk production, two udder health and eight udder morphology traits, we identified 48, 24 and 12 QTL for the three breeds, respectively. In these QTL regions, “candidate” polymorphisms were selected, added to the genotyping chip used in routine genomic selection analyses, then tested on 85,303 cows from the three breeds to confirm their effects. We also confirmed 54 QTL regions, in which we identified genes that are functionally associated with the milk production traits studied. The polymorphisms with confirmed effects are available for routine genomic evaluation of dairy cattle in France and should allow more accurate prediction of milk production traits in young cattle that are breeding candidates.
Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities
Taking account of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, which are small molecules with regulatory properties present in large quantities in milk. Analysis of the variation in milk microRNA composition according to genetic background using high-throughput sequencing shows that milk from Holstein and Normande cattle are respectively composed of 2038 and 2030 microRNA, with 1771 shared microRNAs. Comparison of these two cattle breeds, with distinct dairy production characteristics, revealed 182 microRNA displaying significant differences in abundance. They are involved in the regulation of the lipid metabolism and in mammary morphogenesis and development, which can affect lactation. Our findings provide new insights into the regulation of molecular mechanisms involved in milk production
Contact: GaLac Team, Sandrine Le Guillou
Broilers divergently selected for digestibility differ in their digestive microbial ecosystems
Reducing the competition of animal nutrition on foods intended for human consumption involves using alternative foods that are, however, more difficult to digest. Thus, one of today’s challenges in animal nutrition is to improve the digestive efficiency of animals fed with this type of food. Two divergent broiler chicken lines, D+ and D- (high vs. low digestive efficiency), genetically divergently selected for their digestive efficiency is an interesting biological tool to study the biological mechanisms involved in digestive performance. Since previous studies showed that selection of these lines had an impact on the intestinal microbiota, we characterized the ileal, jejunal and caecal microbiota of animals with different digestibilities from the D+ and D- lines via sequencing of the rRNA 16S gene. Our objective was to compare the taxonomic composition of the microbiota of animals with contrasting digestibility levels as well as the associated functions from a prediction of their metagenome. Our results indicate that the original intestinal segment is the main structuring factor of the microbiota. The caecal microbiota is the most concerned by differences in digestive efficiency, with 41 bacterial species that have different abundances between highly and poorly efficient animals. In addition, we predicted that the caecal microbiota of efficient animals could be enriched in genes that contribute to degrading short chain fatty acids (SCFA) from non-starch polysaccharides. These results confirm the impact of genetic selection on digestibility of the caecal microbiota and open the way to the identification of host genes that control the taxonomic composition of the digestive microbiota in the chicken.
Contact: GeMS Team, Fanny Calenge and Marion Borey
“Livestock Metagenomics” Special Issue
Following an Editorial on the potential of metagenomics for animal genetics studies by Jordi Estellé in 2019 (Estellé, 2019), the Journal of Animal Breeding and Genetics invited him to act as Guest Editor together with Miguel Pérez-Enciso (CRAG, Spain) for a special issue dedicated to Livestock Metagenomics (Estellé & Pérez-Enciso, 2020). This special issue selected nine research papers on the topic, among which three included INRAE co-authors working on bovine, porcine and horse species. In bovine rumen, Ramayo-Caldas et al. (2020) used multivariate analysis to identify a series of taxons associated with methane emission, and suggested a partial genetic control by both the microbiome and the host of this phenotype. In pigs, Massacci et al. (2020) analysed the role of host genetics on diarrhoea in pigs naturally infected by E. coli. In horses, Massacci et al. (2020), performed a longitudinal study to uncover the differences in the microbiota among six horse breeds.
Contact: GeMS Team, Jordi Estellé
A relationship exists between the intestinal microbiota dn variability to vaccine response in pigs
Improving the efficiency of vaccines is a priority in farming, associated with a reduced use of antibiotics. An individual variability to vaccine response exists that may lead to a heterogeneity in the level of protection of vaccinated animals within a given population. Within this context, it is important on the one-hand to improve vaccines and knowledge of the mechanisms that regulate host-pathogen interactions, and on the other hand, to identify the determinants of individual variability observed. Our study showed that, in pigs, there is an association between the intestinal microbiota and immune response to a vaccine directed against Mycoplasma hyopneumoniae, a bacteria responsible for pulmonary pathogens. We show that the microbial profiles obtained from feces collected before vaccination at 28 days-of-age differ between high and low responders to vaccination, and contain predictive information at all levels of response. An overabundance of bacteria of the Prevotella, Anaerovibrio and Sutterella genera seem to favor a better immune response to vaccination. These results open the way to the use of the microbiota as a lever in the optimization of vaccination strategies in the pig.
Contact: GeMS Team, Claire Rogel-Gaillard
Sources of variation of DNA methylation in rainbow trout: combined effects of temperature and genetic background
In order for aquaculture to be economically sustainable but also respectful of the environment and societies’ constraints, improvement of the robustness of fish, i.e. their capacity to maintain a high level of production in varying environments, has become a major challenge. Epigenetic mechanisms are molecular mechanisms that can modulate gene activity without modifying the information contained within the genes themselves. It has been established that epigenetic markers, and notably DNA,methylation play a role in the modulation of responses to environmental changes, and therefore in the development of robustness. To improve our understanding of the underlying mechanisms of fish robustness, one of the challenges is now to understand how the different genotypes modify their epigenetic markers in response to an environmental change and therefore more or less adapt to this change. A study financed by the AQUAEXCEL2020 European project, shows that the temperature (11°C vs. 16°C) during the early phases of development modify epigenetic marks. Using original animal material composed of isogenic lines, we showed that an early temperature regime modifies DNA methylation patterns and that these changes seem to depend on the genotype. This study opens up perspectives for the study of the genetic determinism of epigenetic markers.
Contact: GenAqua Team, Delphine Lallias
Male or female? Genetic control is not that simple in the rainbow trout
In the rainbow trout (Oncorhynchus mykiss), sex is governed by a simple chromosome system (XX/XY) and the major sex determinant is the sdY gene. This characteristic is used to produce completely female populations (XX), which are more interesting than bisexual populations. However, male individuals are regularly observed in these XX populations. A team of scientists from INRAE studied the origin of such spontaneous masculinization, in partnership with colleagues from the trout sector. They showed that masculinization has a high heritability and is more frequent in the offspring of certain individuals. A genomic analysis revealed that several genes other than sdY, are involved in the development of the male sex in XX individuals, and genetic markers associated with masculinization were identified in the population studied. This study shows that several genetic factors that control sex coexist with the XX/XY system. These results are a first step towards the understanding of the mechanisms that control masculinization in XX individuals. They also pave the way to applications in fish farming, with the use of genetic markers to identify mutations that favor masculinization.
Contact: GenAqua Team, Florence Phocas
Publication of the book« Génétique des animaux d’élevage – Diversité et adaptation dans un monde changeant »
Whereas the world is currently undergoing global changes and a climate crisis, many questions have been raised on the role and position of breeding. This work provides an overview of the history and changes in methods and dynamics that have been ongoing in the last decade and which will shape the future of animal selection. Domestication of animals and their selection are founded on a long, shared history between man, animals and territories. This has been fed by a continuous flow of new knowledge and methodological approaches that permit the characterization of genetic diversity and progress in the choice of sires adapted to production systems that are more and more diversified in relation with the world's agroecological transition and food safety. Genetic improvement has contributed to shaping the living, raising ethics questions that are reinforced and renewed by the opportunities provided genomics tools and "big data".
Contact: GenPhySE and GABI, Etienne Verrier, Denis Milan, Claire Rogel-Gaillard
A new approach to calculate individualized pathway deviation scores using multi-omics integration
Comprehensive genetic and molecular profiles of living organisms can be obtained using omics data, and studies with matched multi-omic data collected from the same samples hold promise for providing holistic insight into complex biological processes. Advanced multivariate statistical techniques provide a useful integrative framework for multi-omic data to help unravel the associations among various multi-omic data. Using a multivariate, multi-table framework, we proposed a new approach called padma to quantify and characterize individualized pathway-specific multi-omic aberrations within a sampled population. Our tool padma is both a hypothesis generator and an exploratory data analysis approach, and we illustrated its biological relevance by using a large-scale public multi-omic dataset in oncology.
Contact: Equipe GiBBS, Andréa Rau, Florence Jaffrezic, Denis Laloë
INRAE Journal Genetics Selection Evolution
Created in 1969 as Annales de Génétique et de Sélection Animale, renamed Génétique Sélection Evolution in 1983 then Genetics Selection Evolution in 1989, this INRAE journal was the first to be published in open access in 2009 by BioMed Central. This change of model was accompanied by an unprecedented development with an internationalization of its reading committee, readership and submissions, an increase in the number of articles submitted and published, and an increase in the impact factor, which in 2020 (impact factor calculated over 2019) reached a record level of 3.94. As of 2012, it ranks among the top three journals in its category 'Agriculture, Dairy and Animal Science' and in the first quarter of the very broad category 'Genetics & Heredity' in the Journal of Citation Reports. Even if the impact factor is not an absolute criterion, Genetics Selection Evolution is today internationally recognized as the reference journal for the publication of research results in genetics and breeding of farm animal species and contributes to the scientific influence in these fields.
Although the Prion protein (PrP) has raised much attention via its implication in transmissible spongiform encephalopathies, the related Shadoo protein has for a long time remained in the shadow of its big sister. With colleagues from INSERM, CEA and SAPS, we developed knock-out mice at the locus that codes for Shadoo using genome editing and we analyzed their phenotypes. The absence of this protein, expressed from the very first stages of embryo development and present in many organs, does not prevent the mice from being viable and fertile. However, this invalidation results in a decreased size of litters associated with an early, post-implantation lethality of the embryo. It also causes intra-uterine growth problems and alters the development/differentiation of the mammary gland and the composition of milk, at least regarding the lipids, thus inducing a slower growth of the young pups. Thus, this study helps understand several poorly known roles of the Shadoo protein at different stages of development.
Contact: MoDiT Team, Bruno Passet
An improved LC–MS method to profile and quantify molecular diversity of the six main bovine milk proteins in their native state
This article describes a reference method based on liquid chromatography and mass spectrometry (LC-MS) which provides an accurate identification of the six main proteins of cow’s milk, including allelic and splicing variants along with isoforms resulting from post-translational modifications, with a level of resolution never seen before. Proteins are identified from their molecular masses observed compared to theoretical masses of intact proteins indexed in the “internal” database that includes nearly 3000 molecules. Quantification is done using UV (214 nm) spectra or a mass signal. Thus, up to one-hundred molecules, derived from the six main milk proteins, can be identified and quantified from a single individual sample of milk. The method is transferable to several other mammalian species including small ruminants, camelids, equines, rabbits, …. along with humans. It leads to new perspectives for the nutritional valorization of milk and the optimization of associated techniques.
Contact: @BRIDGe Team, Guy Miranda, Leonardo Bianchi, Agnès Delacroix-Buchet
Optimization of the animal cryobank operating costs
INRAE (UMR GABI) coordinated the European project IMAGE (imageh2020.eu) for an innovative management of gene banks. One of the innovations of this project was to bring together a team of economists from Edinburgh University with cryobank leaders, notably in France, Spain and the Netherlands. The optimization of the management of frozen semen collections for farm species was studied using a mathematical modeling method that maximizes the cost-efficiency ratio in terms of the number of preserved breeds. IDELE, another partner of the project, provided data on operating costs of the national cryobank, as well as 10 other gene banks in Europe, in order to establish a rationalization strategy on the European level. Then, the method was applied to the rationalization of collections in the country, by considering Spain, which has a large number of animal cryobanks. Thus, this method assesses the economic relevance of the organization of an infrastructure as long as the operating costs are well identified. It could be tested on the RARe infrastructure. In any case, application of this modeling tool will be useful at INRAE
Contact: Michèle Tixier-Boichard
A new reference work on poultry genetics and genomics
This book provides a state-of-the-art of today’s knowledge in four main fields: genetic diversity of poultry, determinism of major traits for poultry production, recent evolution in genomics and selection, and finally emerging concepts or technologies that are susceptible to transform selection such as nutrigenomics, epigenetics or genome editing. Two books summarizing knowledge in poultry genetics were published in 1990 and 2003. Thus, it was time to pool all the significant advancements from the use of genomics in a reference document for the poultry industry, amateur breeders, scientists and students in poultry sciences along with decision makers. The Animal Genetics Division of INRAE is particularly well represented in the editor-in-chief committee and in eight of the 21 chapters, with nine authors from four units of the division leading genetic research in poultry species, that are part of a genetic poultry network, RESAVI, which also associates scientists from the Animal Physiology & Breeding Division. The impact of genomics is particularly visible with the use of molecular markers for selection, analysis of genetic architecture of traits and the identification of causal mutations.