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We identified and analyzed &alpha, 2,8-sialyltransferases sequences among 71 ray-finned fish species to provide the first comprehensive view of the Teleost ST8Sia repertoire. This repertoire expanded over the course of Vertebrate evolution and was primarily shaped by the whole genome events R1 and R2, but not by the Teleost-specific R3. We showed that duplicated st8sia genes like st8sia7, st8sia8, and st8sia9 have disappeared from Tetrapods, whereas their orthologues were maintained in Teleosts. Furthermore, several fish species specific genome duplications account for the presence of multiple poly-&alpha, 2,8-sialyltransferases in the Salmonidae (ST8Sia II-r1 and ST8Sia II-r2) and in Cyprinus carpio (ST8Sia IV-r1 and ST8Sia IV-r2). Paralogy and synteny analyses provided more relevant and solid information that enabled us to reconstruct the evolutionary history of st8sia genes in fish genomes. Our data also indicated that, while the mammalian ST8Sia family is comprised of six subfamilies forming di-, oligo-, or polymers of &alpha, 2,8-linked sialic acids, the fish ST8Sia family, amounting to a total of 10 genes in fish, appears to be much more diverse and shows a patchy distribution among fish species. A focus on Salmonidae showed that (i) the two copies of st8sia2 genes have overall contrasted tissue-specific expressions, with noticeable changes when compared with human co-orthologue, and that (ii) st8sia4 is weakly expressed. Multiple sequence alignments enabled us to detect changes in the conserved polysialyltransferase domain (PSTD) of the fish sequences that could account for variable enzymatic activities. These data provide the bases for further functional studies using recombinant enzymes.

To investigate the dynamics of circRNA expression in pig testes, we designed specific strategies to individually study circRNA production from intron lariats and circRNAs originating from back-splicing of two exons. By applying these methods on seven Total-RNA-seq datasets sampled during the testicular puberty, we detected 126 introns in 114 genes able to produce circRNAs and 5,236 exonic circRNAs produced by 2,516 genes. Comparing our RNA-seq datasets to datasets from the literature (embryonic cortex and postnatal muscle stages) revealed highly abundant intronic and exonic circRNAs in one sample each in pubertal testis and embryonic cortex, respectively. This abundance was due to higher production of circRNA by the same genes in comparison to other testis samples, rather than to the recruitment of new genes. No global relationship between circRNA and mRNA production was found. We propose ExoCirc-9244 (SMARCA5) as a marker of a particular stage in testis, which is characterized by a very low plasma estradiol level and a high abundance of circRNA in testis. We hypothesize that the abundance of testicular circRNA is associated with an abrupt switch of the cellular process to overcome a particular challenge that may have arisen in the early stages of steroid production. We also hypothesize that, in certain circumstances, isoforms and circular transcripts from different genes share functions and that a global regulation of circRNA production is established. Our data indicate that this massive production of circRNAs is much more related to the structure of the genes generating circRNAs than to their function. Abbreviations: PE: Paired Ends; CR: chimeric Read; SR: Split Read; circRNA: circular RNA; NC: non conventional; ExoCirc-RNA: exonic circular RNA; IntroLCirc-: name of a porcine intronic lariat circRNA; ExoCirc-: name of a porcine exonic circRNA; IntronCircle-: name of a porcine intron circle; sisRNA: stable intronic sequence RNA; P: porcine breed Pietrain; LW: porcine breed Large White; RT: reverse transcription/reverse transcriptase; Total-RNA-seq: RNA-seq obtained from total RNA after ribosomal depletion; mRNA-seq: RNA-seq of poly(A) transcripts; TPM: transcripts per million; CR-PM: chimeric reads per million; RBP: RNA binding protein; miRNA: micro RNA; E2: estradiol; DHT: dihydrotestesterone

Emotions, unlike mood, are short-lived reactions associated with specific events. They can be characterized by two main dimensions, their arousal (bodily activation) and valence (negative versus positive). Knowledge of the valence of emotions experienced by domestic and captive animals is crucial for assessing and improving their welfare, as it enables us to minimize the negative emotions that they might experience and to promote positive ones. Emotions can affect vocalizations directly or indirectly through the brain, lungs, larynx or vocal tract. As a result, vocal expression of emotions has been observed across species, and could serve as a non-invasive and potentially very reliable tool to assess animal emotions. In pigs (Sus scrofa), vocal expression of emotions has been relatively well studied. However, it is not known if the vocal indicators revealed in previous studies are valid across call types and contexts. To find this out, we conducted a meta-analysis of the effects of emotional valence on pig vocalizations, including calls recorded in the most common emotional situations encountered by pigs throughout their lives, from birth to slaughter. Our analyses revealed that pigs produced calls characterized by a higher center of gravity, a shorter duration, less noise (lower Wiener entropy), lower formants (measured using the formant dispersion) and LPC coefficients in positive compared to negative contexts. Overall, these vocal parameters could be very useful for developing automated methods to monitor pig welfare on-farm.

International audience; Although the functions of most of circular RNAs (circRNAs) are not characterized, they likely impact many biological processes. Indeed, in addition to generating a linear transcript many protein-coding genes produce circRNAs that are tightly regulated.By analyzing Total-RNaseq from 7 pubertal testis samples we detected 126 introns in 114 genes able to produce intronic circRNAs and 5,236 exonic circRNAs produced by 2,516 genes. Comparison of Total-RNaseq data sets from porcine testis, embryonic cortex and postnatal muscle stages revealed a high abundance of intronic and exonic circRNAs for 2 samples from pubertal testis and embryonic cortex, respectively. In pubertal testis with circRNAs in abundance, 24% of protein-coding genes produced linear and circular transcripts. This abundance was due to higher production of circRNA by the same genes than in other testis samples rather than to the recruitment of new genes. No global relationship between exonic circRNA and mRNA productions was found in pubertal testis. We showed that exonic circRNAs are typically produced by large genes that are also able to produce mRNAs. We suggest ExoCirc-9244 (origin: SMARCA5) to be a marker of circRNA abundance in testis. Among 76 pubertal testes analyzed by RT-PCR, we identified 12 transcriptomes containing a large quantity of ExoCirc-9244 and which are therefore suspected to have an overall high circRNAs abundance. By qRT-PCR, we confirmed results concerning ExoCirc-9244 and showed that samples expressing ExoCirc-9244 had low steroid synthesis potential (confirmed by plasma estradiol level).Even though our data indicate that this massive production of circRNAs is much more related to the structure of genes generating circRNAs than to their function, we highlighted with ExoCirc-9244, a particular stage of pubertal testis development characterized by a low steroid production and an abundance of circRNA. We suggest that bursts of circRNAs might be linked to an abrupt switch of the cellular metabolism: a distinct stage in developmental processes of embryonic cortex or pubertal testis may require circRNAs. In these circumstances the number of circRNAs would be more important than their individual characteristics, which would be a unique feature in the transcripts world.

International audience; The future sustainability of cattle production will require improved resource use efficiency, reduced GHG emissions, and improved animal health and welfare. Facing this challenge needs far more complex animal traits than previously and they need to be assessed under a range of conditions. For example, the concepts of feed efficiency, robustness and sensitivity to health disorders are more difficult to include in selection indices than simple productivity traits. It is now time to look for means to investigate complex animal traits using smart technologies and rapid analytical methods in a standardised way applied in many contexts. At the same time, the European Strategy Forum on Research Infrastructures (ESFRI) roadmap clearly identified the need for improved coordination, harmonisation and access to European research infrastructures (RIs) on farm animals. The SmartCow project (www.smartcow.eu) answering the call H2020-INFRAIA2016-2017 was selected by the European Commission for 4 years funding starting from 1st February 2018. Three types of activities are developed to increase the phenotyping capabilities of the cattle European sector. Networking activities will create, thanks to an inventory and an interactive map, a unique portal to key European cattle RIs. The project will ensure that existing guidelines are adopted [e.g., the ICAR Guidelines for Bovine Functional Traits (section 7) are cited in distinct guidelines generated by the Networking activities]. When no international standard exists (e.g. feed efficiency, digestive, behavioural traits…), the project works towards the use of unified measurement methods through common standards and guidelines. The development of the cattle ontology of traits (ATOL and EOL; www.atol-ontology.com) through SmartCow will also be an important step to unify research methodologies and link definition of traits with standardized methods. A cloud-based database platform developed by Agrimetrics using web semantic will ensure integration, sharing and interoperability of data generated by the project leading to an open European database on cattle traits and phenotypes. Joint research activities will generate innovations for the research community on cattle towards the use of less-invasive methods and high-throughput phenotyping. Refining in vivo methods to evaluate feed efficiency and emissions will generate innovations in experimental design and planning for more accuracy. The development of new biomarkers (proxies) that can be easily measured in milk, faeces, urine, or blood through rapid analytical methods (NIRS) will bring new phenotyping capacities. The development of tools to generate new and improved information from animal sensors and other routinely collected data (e.g. prediction of individual cow status in terms of health and welfare) will also enable a more efficient phenotyping and genetic selection of cattle. Finally, the project organizes transnational access to major RIs: INRA in France, Scotland’s Rural College and University of Reading in the UK, Wageningen University and WUR/DLO in the Netherlands, FBN-Leibniz in Germany, Teagasc in Ireland, Aarhus University in Denmark and IRTA in Spain. It provides access to around 2500 dairy and 1000 beef cattle and facilitate up to 30 research projects to be financed by the SmartCow project after selection through specific calls. Eleven projects have already been selected after the first call.

Theatre 1; SmartCow is an H2020 Research Infrastructure European project which integrates key European cattle research infrastructures to promote their coordinated use and development, and thereby help the European cattle sector face the challenge of sustainable production. SmartCow has been launched on 1st February. This session shall just introduce the project (which has not achieved any results yet). Covering all the relevant scientific fields and the diversity of cattle types and production systems, SmartCow will provide the academic and private research communities with easy access to 11 major research infrastructures from 7 countries of high quality services and resources. These are needed to develop innovative and ethical solutions for efficient use of animal and feed resources that reduce greenhouse gas emissions and promote animal welfare and healthy livestock. SmartCow combines strong scientific and technical skills in animal nutrition (in vivo methods for nutrient utilization and emissions measurements), genetics (genotyped animals, phenotyping capabilities), health and welfare (sensors and automatic recordings of physiological and behavioral traits) and ethics in animal experimentation. A central promotion and management of transnational access to the research infrastructures will provide access to around 10,000 cow-weeks and facilitate up to 30 research projects. Networking activities will harmonize and standardize procedures in animal care and measurements, design of experiments, data recording and analysis thanks to a cloud-based data-platform. Joint research activities will produce refined methods and proxies to evaluate feed efficiency and emissions, develop new protocols to reduce the use of animals and produce new methods to exploit sensor data for cattle husbandry. Promotion of transnational access and dissemination of SmartCow outcomes will be supported by a Stakeholder Platform composed of pre- and post-farm gate industry, farmer organizations, NGOs, policy makers at national and EU levels.

Despite decades of intensive research on injurious behaviours like aggression and tail biting in pigs, these problems persist on many farms. In Europe, stricter enforcement of legislation against routine tail docking puts additional pressure on farmers, and researchers are asked to find solutions. However, remedial measures are dependent on early diagnosis of the problem. The European PigWatch Project (https://pigwatch.net, Anihwa ERA-Net) aims to sensitize stock persons to early signs which predict injurious behaviours and to develop automatic measurement techniques that could help farmers to manage their herd. We developed, testedand adapted an on-farm observation protocol in the five participating countries of the project (Netherlands, France, Switzerland, Germany and Denmark) to train stock persons to observe their animals in a different way. The use of the protocol by the farmers showed that the position of the tail (tucked, hanging or curled) seems to be a good indicator for underlying problems that might culminate in harmful behaviour. Some farmers state that using the protocol changed the way they look at their animals. Furthermore, as increased behavioural activity is a clear sign for ongoing aggressive acts, a sensor is being developed in France measuring animal activity and sending an alarm when detecting a sustained fighting. In a first test, the behaviour of 32 pigs (4 pens with 8 pigs each, 110-150 days of age) was observed for 30 h via video and annotated for episodes of fighting (head knock, biting). Three pigs per pen (n=12) were equipped with the activity sensor via an ear tag and alarms were compared with the video analyses. Results showed that the sensors detected 42% of the fighting, with 62% true positives. Its sensitivity and specificity will be improved through additional observations and recordings. Moreover, the sensor will be tested soon on-farm in Germany. In addition to the advantages on the farms, these technologies should enable standardised and efficient animal monitoring. The project will end in 2019, with tools to help farmers to identify early signs of aggression and tail biting in their pigs.

From many endangered or threatened species which are expected to profit from assisted reproduction techniques, mainly epididymal sperm of dead or freshly castrated males are available. These sperm had contact to epididymal secretion products but not to seminal fluid components. Notably, products of accessory sex glands have been shown in domestic animals to condition sperm for fertilization, in particular by mediating sperm-oviduct interaction. We report for the first time that motile epididymal sperm from domestic cats are able to bind to fresh oviduct epithelial cell explants from preovulatory females (median [min, max] of 10 [8, 16] and 10 [8, 17] sperm per 0.01 mm(2) explant surface from both isthmic and ampullar regions, respectively). More sperm attach to the explants when epididymal sperm were preincubated for 30 minutes with seminal fluid separated from electroejaculates of mature tomcats (median [min, max] of 17 [13, 25] and 16 [12, 21] sperm per 0.01 mm(2) explant surface from isthmus and ampulla, respectively). The proportion of bound sperm increased from a median of 54% to 62% by seminal fluid treatment. Sperm-oviduct binding could be facilitated by the decelerated sperm motion which was observed in seminal fluid-treated samples or supported by seminal fluid proteins newly attached to the sperm surface. Seminal fluid had no effect on the proportion of sperm with active mitochondria. Extent and pattern of sperm interaction in vitro were independent of explant origin from isthmus or ampulla. Sperm were attached to both cilia and microvilli of the main epithelial cell types present in all explants. In contrast to published sperm-binding studies with porcine and bovine oviduct explants where predominantly the anterior head region of sperm was attached to ciliated cells, the tails of some cat sperm were firmly stuck to the oviduct cell surfaces, whereas the heads were wobbling. Whether this response is a preliminary step toward phagocytosis or a precondition to capacitation and fertilization remains to be determined. In conclusion, treatment of epididymal sperm with seminal fluid or particular protein components should be considered in future investigations for its potential to improve the outcome of artificial insemination in felids.

We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance. © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)

Background Spermatozoa interact with oviduct secretions before fertilization in vivo but the molecular players of this dialog and underlying dynamics remain largely unknown. Our objectives were to identify an exhaustive list of sperm-interacting proteins (SIPs) in the bovine oviduct fluid and to evaluate the impact of the oviduct anatomical region (isthmus vs. ampulla) and time relative to ovulation (pre-ovulatory vs. post-ovulatory) on SIPs number and abundance. Methods Pools of oviduct fluid (OF) from the pre-ovulatory ampulla, pre-ovulatory isthmus, post-ovulatory ampulla, and post-ovulatory isthmus in the side of ovulation were collected from the slaughterhouse. Frozen-thawed bull sperm were incubated with OF or phosphate-buffered saline (control) for 60 min at 38.5 °C. After protein extraction and digestion, sperm and OF samples were analyzed by nanoLC-MS/MS and label-free protein quantification. Results A quantitative comparison between proteins identified in sperm and OF samples (2333 and 2471 proteins, respectively) allowed for the identification of 245 SIPs. The highest number (187) were found in the pre-ovulatory isthmus, i.e., time and place of the sperm reservoir. In total, 41 SIPs (17%) were differentially abundant between stages in a given region or between regions at a given stage and 76 SIPs (31%) were identified in only one region × stage condition. Functional analysis of SIPs predicted roles in cell response to stress, regulation of cell motility, fertilization, and early embryo development. Conclusion This study provides a comprehensive list of SIPs in the bovine oviduct and evidences dynamic spatio-temporal changes in sperm-oviduct interactions around ovulation time. Moreover, these data provide protein candidates to improve sperm conservation and in vitro fertilization media.

Essential fatty acids (EFA) and conjugated linoleic acids (CLA) are unsaturated fatty acids with immune-modulatory effects, yet their synergistic effect is poorly understood in dairy cows. This study aimed at identifying differentially abundant proteins (DAP) and their associated pathways in dairy cows supplied with a combination of EFA and CLA during the transition from antepartum (AP) to early postpartum (PP). Sixteen Holstein cows were abomasally infused with coconut oil as a control (CTRL) or a mixture of EFA (linseed + safflower oil) and CLA (Lutalin, BASF) (EFA + CLA) from − 63 to + 63 days relative to parturition. Label-free quantitative proteomics was performed on plasma samples collected at days − 21, + 1, + 28, and + 63. During the transition time, DAP, consisting of a cluster of apolipoproteins (APO), including APOE, APOH, and APOB, along with a cluster of immune-related proteins, were related to complement and coagulation cascades, inflammatory response, and cholesterol metabolism. In response to EFA + CLA, specific APO comprising APOC3, APOA1, APOA4, and APOC4 were increased in a time-dependent manner; they were linked to triglyceride-enriched lipoprotein metabolisms and immune function. Altogether, these results provide new insights into metabolic and immune adaptation and crosstalk between them in transition dairy cows divergent in EFA + CLA status.

Background Gene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies via meta-analysis techniques has the potential to test the extensibility of conclusions based on single studies. Using the program Pointillist, we performed meta-analysis of transcription-profiling data from six independent studies of infections with mammary gland pathogens, including samples from cattle challenged in vivo with S. aureus, E. coli, and S. uberis, samples from goats challenged in vivo with S. aureus, as well as cattle macrophages and ovine dendritic cells infected in vitro with S. aureus. We combined different time points from those studies, testing different responses to mastitis infection: overall (common signature), early stage, late stage, and cattle-specific. Results Ingenuity Pathway Analysis of affected genes showed that the four meta-analysis combinations share biological functions and pathways (e.g. protein ubiquitination and polyamine regulation) which are intrinsic to the general disease response. In the overall response, pathways related to immune response and inflammation, as well as biological functions related to lipid metabolism were altered. This latter observation is consistent with the milk fat content depression commonly observed during mastitis infection. Complementarities between early and late stage responses were found, with a prominence of metabolic and stress signals in the early stage and of the immune response related to the lipid metabolism in the late stage; both mechanisms apparently modulated by few genes, including XBP1 and SREBF1. The cattle-specific response was characterized by alteration of the immune response and by modification of lipid metabolism. Comparison of E. coli and S. aureus infections in cattle in vivo revealed that affected genes showing opposite regulation had the same altered biological functions and provided evidence that E. coli caused a stronger host response. Conclusions This meta-analysis approach reinforces previous findings but also reveals several novel themes, including the involvement of genes, biological functions, and pathways that were not identified in individual studies. As such, it provides an interesting proof of principle for future studies combining information from diverse heterogeneous sources.

International audience; Studies on particle retention time in ruminants are commonly conducted utilizing chromium (Cr) and/or a lanthanide bound to feeds. Both types of markers have different chemical properties which potentially bias estimates of digesta retention--their combined use is therefore a topic of ongoing discussion. In order to evaluate the suitability of two lanthanides for studies assessing the passage kinetics of different-sized particles, we measured the mean retention time in roe deer with cerium (Ce) and lanthanum (La) labelled to the same particle length and compared it to Cr-mordanted fibre of the same size. We expected a simultaneous excretion of Ce- and La-labelled fibre, but a delayed excretion of Cr-mordanted fibre compared to the other markers. In this study, the mean retention times of Ce- and La-labelled fibre did not differ significantly, and Cr-mordanted fibre was retained on average 5 h longer than Ce and La. Despite the limitation of the small sample size, Ce and La showed the same excretion pattern and can therefore be recommended as mordants in studies assessing passage kinetics of different particle sizes.

International audience; This study aimed at investigating the synergistic effects of essential fatty acids (EFA) and conjugated linoleic acids (CLA) on the liver proteome profile of dairy cows during the transition to lactation. 16 Holstein cows were infused from 9 wk. antepartum to 9 wk. postpartum into the abomasum with either coconut oil (CTRL) or a mixture of EFA (linseed + safflower oil) and CLA (EFA + CLA). Label-free quantitative proteomics was performed in liver tissue biopsied at days -21, +1, +28, and + 63 relative to calving. Differentially abundant proteins (DAP) between treatment groups were identified at the intersection between a multivariate and a univariate analysis. In total, 1680 proteins were identified at each time point, of which between groups DAP were assigned to the metabolism of xenobiotics by cytochrome P450, drug metabolism - cytochrome P450, steroid hormone biosynthesis, glycolysis/gluconeogenesis, and glutathione metabolism. Cytochrome P450, as a central hub, enriched with specific CYP enzymes comprising: CYP51A1 (d - 21), CYP1A1 & CYP4F2 (d + 28), and CYP4V2 (d + 63). Collectively, supplementation of EFA + CLA in transition cows impacted hepatic lipid metabolism and enriched several common biological pathways at all time points that were mainly related to ω-oxidation of fatty acids through the Cytochrome p450 pathway. SIGNIFICANCE: In three aspects this manuscript is notable. First, this is among the first longitudinal proteomics studies in nutrition of dairy cows. The selected time points are critical periods around parturition with profound endocrine and metabolic adaptations. Second, our findings provided novel information on key drivers of biologically relevant pathways suggested according to previously reported performance, zootechnical, and metabolism data (already published elsewhere). Third, our results revealed the role of cytochrome P450 that is hardly investigated, and of ω-oxidation pathways in the metabolism of fatty acids with the involvement of specific enzymes.

International audience; Repeated measurements analysis of variance - simultaneous component analysis (ASCA) has been developed to handle complex longitudinal omics datasets and combine novel information with existing data. Herein, we aimed at applying ASCA to 64 liver proteomes collected at 4-time points (day -21, +1, +28, and + 63 relative to parturition) from 16 Holstein cows treated from 9 wk. antepartum to 9 wk. postpartum (PP) with coconut oil (CTRL) or a mixture of essential fatty acids (EFA) and conjugated linoleic acid (CLA) (EFA + CLA). The ASCA modeled 116, 43, and 97 differentially abundant proteins (DAP) during the transition to lactation, between CTRL and EFA + CLA, and their interaction, respectively. Time-dependent DAP were annotated to pathways related to the metabolism of carbohydrates, FA, and amino acid in the PP period. The DAP between FA and the interaction effect were annotated to the metabolism of xenobiotics by cytochrome P450, drug metabolism - cytochrome P450, retinol metabolism, and steroid hormone biosynthesis. Collectively, ASCA provided novel information on molecular markers of metabolic adaptations and their interactions with EFA + CLA supplementation. Bioinformatics analysis suggested that supplemental EFA + CLA amplified hepatic FA oxidation; cytochrome P450 was enriched to maintain metabolic homeostasis by oxidation/detoxification of endogenous compounds and xenobiotics.Significance: This report is among the first ones applying repeated measurement analysis of variance-simultaneous component analysis (ASCA) to deal with longitudinal proteomics results. ASCA separately identified differentially abundant proteins (DAP) in 'transition time', 'between fatty acid treatments', and 'their interaction'. We first identified the molecular signature of hepatic metabolic adaptations during postpartum negative energy balance; the enriched pathways were well-known pathways related to mobilizing fatty acids (FA) and amino acids to support continuous energy production through fatty acid oxidation, TCA cycle, and gluconeogenesis. Some of the DAP were not previously reported in transition dairy cows. Secondly, we provide novel information on the mechanisms by which supplemented essential FA and conjugated linoleic acids interact with hepatic metabolism. In this regard, FA amplified hepatic detoxifying and oxidation capacity through ligand activation of nuclear receptors. Finally, we briefly compared the strengths and weaknesses of the ASCA model with PLS-DA and outlined why these methods are complementary.

International audience; In contrast to exon-derived circular RNAs (exonic circRNAs), which are widely studied, much less in known on intron-derived circRNAs: when intron lariats escape degradation due to debranching failure they can become circRNA precursors. When characterizing the intronic circRNA landscape of porcine and bovine testis, liver and muscle, only a circRNA derived from a lariat of the ATXN2L gene was identified in both species. This intronic ATXN2L circRNA was always among the strongest contributors of intronic circRNAs in testes. In pubertal porcine testes, we observed a single circRNA with a uniquely highly abundant expression pattern: this was again the intronic ATXN2L circRNA. Its dominant position goes far beyond intronic circRNAs, because it is most abundant across all circRNAs in pubertal testes (7 datasets). No analogous dominating position of an exonic or intronic circRNA was found neither in the adult porcine testis, nor in pubertal bovine testis.When compiling data sets from different origins to conduct this study, we noticed that RNA preparation and sequencing protocols have a significant impact on circRNA recovery. Moreover, the comparison of porcine transcriptome of pubertal and adult testes generated with divergent protocols (at least for ribosomal sequence removal) suggested age-dependent differential expression for a large proportion of small-non-coding RNAs, so we suspect that additional non-biological effects (ribodepletion) might bias the recovery of small transcripts. This intronic ATXN2L circRNA is very small (118 nucl. in pigs) and we do not rule out that it may be partially lost by some experimental protocols.Due to its particularly high expression level at a biologically sensitive time in testis development, we strongly assume that intronic ATXN2L circRNA has a specific function, at least in the pubertal pig testis. In this tissue, we did not obtain supporting evidence for an impact of this circular transcript on the transcription of the ATXN2L gene itself. Our data suggest that we may be witnessing the emergence of a new non-coding gene in pigs.

International audience; The European Commission considers research infrastructures as key elements for the advancement of knowledge, structure the scientific community, facilitate open, interconnected, and data-driven science, and attract young people to science. PIGWEB is a Horizon 2020 project that started on March 1st, 2021. The aim of the project is to strengthen the pig research community by providing and facilitating access to research infrastructures, reinforce a culture of cooperation between the research community and industrial and societal stakeholders, and improve and integrate the services provided by the research infrastructures. The project gathers 16 partners from nine countries. Twentyeight installations provide transnational access, allowing external parties to carry out experiments in the PIGWEB installations, funded by the project for a total budget of 1.5 million euro. Transnational access is given to various housing facilities and production systems, slaughterhouses and associated equipment, experimental feed mills, and laboratories to carry out studies on pig nutrition, metabolism, physiology, behaviour, and emissions. The project also focusses on best practices for protocols, standards, and ethics in experimental pig research and on ontologies and Open Data. Joint research activities are carried out to identify and test non- and minimally invasive proxies of efficiency, health, stress, and environmental impact. Also, new methods, tools, and technologies will be developed to measure traits that are currently difficult to measure, related to welfare, behaviour, and body composition. Newly developed and available research methods and tools will be tested to carry out integrated phenotyping of pigs.

International audience; Myogenesis requires energy production for the execution of a number of regulatory and biosynthesis events. Recent studies in human have shown that mitochondria play a role in the regulation of myogenesis. Indeed, the abundance, morphology, and functional properties of mitochondria contribute to satellite stem cell fate decision during quiescence, proliferation or differentiation. Nevertheless, little attention has been paid to this process in farm animals. Understanding how mitochondria are involved in myogenesis would provide a valuable insight into the underlying mechanisms that regulate the maintenance of cellular homeostasis. The objective of the current study was to evaluate mitochondrial activity including autophagy in satellite cells (SC) during differentiation. Cells were isolated from samples of longissimus and semimembranosus muscle obtained from 4-day-old piglets. Part of the isolated cells was used to separate slow and fast proliferating SC subpopulations by Percoll gradient centrifugation. Both subpopulations were plated in growth medium, allowed to proliferate up to 80% confluence and then placed in an appropriate culture medium to differentiate into myotubes. Mitochondrial function was explored during proliferation and differentiation using Mitotracker dye in flow cytometry. Within the two subpopulations of cells, we observed two different Mitotracker staining intensity suggesting a difference in the mitochondrial membrane potential. According to two distinct peaks of fluorescence within each subpopulation, cells will be separated by cell sorting. Mitochondrial activity will be studied in myogenic cells as well their potential of differentiation. Mitochondria-related proteins expression (TOM20, MTFN1, COXIV) will be also quantified by Western blotting. This study combined with our previous results suggests that autophagy signalling pathways and mitochondria would drive muscle stem cell fate.

International audience; SmartCow project developed a common framework regarding standards, measurements, and data management to ensure high quality data production with regard to routine and experimental measurements and recordings in cattle physiology and behaviour. Experimental guidelines and protocols were published as an Open Access living handbook on PUBLISSO entitled ‘Methods in cattle physiology and behaviour research – Recommendations from the SmartCow consortium’. The book currently includes 19 chapters covering ethics in experiments on live cattle, intake and behaviour, body condition and anatomy, reproductive, stress and health assessment, rumen function, nutrient digestibility and balance studies, respiratory chamber facility and techniques to measure gas emissions (https://books. publisso.de/en/publisso_gold/publishing/books/overview/53/199). Each chapter lists specific animal traits referring to their identifiers in the Animal Trait Ontology of Livestock (ATOL) and the Environmental Ontology of Livestock (EOL). Vice versa, 92 new traits identified in the published guidelines were included in the existing ontologies. The notable new traits are: milk ketone body content, milking volume, lactation number, stage of lactation, rumen volatile fatty acid content, days of pregnancy, etc. All data providers have access for to the ontologies (http://www.atol-ontology.com/en/erter-2/). Agrimetrics authored a data management plan to set out the approach to managing data within the project, and delivered a Cloud-Based Data Platform (CBDP). The CBDP is designed to ensure the interoperability, sharing and exploitation of the data according FAIR principles. A SmartCow ontology including ATOL and ETOL represents the data and allows researchers to upload and semantically link data with that of other groups of researchers. Data that was not collected or observed at the same time can now be queried together and exported, into an environment of the user’s choice, for further analysis.

In vitro fertilization (IVF) gives rise to embryos in a number of mammalian species and is currently widely used for assisted reproduction in humans and for genetic purposes in cattle. However, the rate of polyspermy is generally higher in vitro than in vivo and IVF remains ineffective in some domestic species like pigs and horses, highlighting the importance of the female reproductive tract for gamete quality and fertilization. In this review, the way the female environment modulates sperm selective migration, survival, and acquisition of fertilizing ability in the oviduct is being considered under six aspects: (1) the utero-tubal junction that selects a sperm sub-population entering the oviduct; (2) the presence of sperm binding sites on luminal epithelial cells in the oviduct, which prolong sperm viability and plays a role in limiting polyspermic fertilization; (3) the contractions of the oviduct, which promote sperm migration toward the site of fertilization in the ampulla; (4) the regions of the oviduct, which play different roles in regulating sperm physiology and interactions with oviduct epithelial cells; (5) the time of ovulation, and (6) the steroid hormonal environment which regulates sperm release from the luminal epithelial cells and facilitates capacitation in a finely orchestrated manner., After mating or insemination, the region-specific and hormonally regulated morphology and secretions of the utero-tubal junction and oviduct lead to the selection of a limited sub-population of top quality spermatozoa at the site of fertilization.

International audience; Circular RNAs have been observed in a large number of species and tissues and are now recognized as a clear component of the transcriptome. Our study takes advantage of functional datasets produced within the FAANG consortium to investigate the pervasiveness of circular RNA transcription in farm animals. We describe here the circular transcriptional landscape in pig, sheep and bovine testicular, muscular and liver tissues using total 66 RNA-seq datasets. After an exhaustive detection of circular RNAs, we propose an annotation of exonic, intronic and sub-exonic circRNAs and comparative analyses of circRNA content to evaluate the variability between individuals, tissues and species. Despite technical bias due to the various origins of the datasets, we were able to characterize some features (i) (ruminant) liver contains more exonic circRNAs than muscle (ii) in testis, the number of exonic circRNAs seems associated with the sexual maturity of the animal. (iii) a particular class of circRNAs, sub-exonic circRNAs, are produced by a large variety of multi-exonic genes (protein-coding genes, long non-coding RNAs and pseudogenes) and mono-exonic genes (protein-coding genes from mitochondrial genome and small non-coding genes). Moreover, for multi-exonic genes there seems to be a relationship between the sub-exonic circRNAs transcription level and the linear transcription level. Finally, sub-exonic circRNAs produced by mono-exonic genes (mitochondrial protein-coding genes, ribozyme, and sno) exhibit a particular behavior. Caution has to be taken regarding the interpretation of the unannotated circRNA proportion in a given tissue/species: clusters of circRNAs without annotation were characterized in genomic regions with annotation and/or assembly problems of the respective animal genomes. This study highlights the importance of improving genome annotation to better consider candidate circRNAs and to better understand the circular transcriptome. Furthermore, it emphasizes the need for considering the relative “weight” of circRNAs/parent genes for comparative analyses of several circular transcriptomes. Although there are points of agreement in the circular transcriptome of the same tissue in two species, it will be not possible to do without the characterization of it in both species.

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18 páginas, 6 figuras, 2 tablas., Several recent studies have demonstrated the role of long non-coding RNAs (lncRNAs) in regulating the defense mechanism against parasite infections, but no studies are available that investigated their relevance for immune response to nematode infection in sheep. Thus, the aim of the current study was to (i) detect putative lncRNAs that are expressed in the abomasal lymph node of adult sheep after an experimental infection with the gastrointestinal nematode (GIN) Teladorsagia circumcincta and (ii) to elucidate their potential functional role associated with the differential host immune response. We hypothesized that putative lncRNAs differentially expressed (DE) between samples from animals that differ in resistance to infection may play a significant regulatory role in response to nematode infection in adult sheep. To obtain further support for our hypothesis, we performed co-expression and functional gene enrichment analyses with the differentially expressed lncRNAs (DE lncRNAs). In a conservative approach, we included for this predictive analysis only those lncRNAs that are confirmed and supported by documentation of expression in gastrointestinal tissues in the current sheep gene atlas. We identified 9,105 putative lncRNA transcripts corresponding to 7,124 gene loci. Of these, 457 were differentially expressed lncRNA loci (DELs) with 683 lncRNA transcripts. Based on a gene co-expression analysis via weighted gene coexpression network analysis, 12 gene network modules (GNMs) were found significantly correlated with at least one of 10 selected target DE lncRNAs. Based on the principle of “guilt-by-association,” the DE genes from each of the three most significantly correlated GNMs were subjected to a gene enrichment analysis. The significant pathways associated with DE lncRNAs included ERK5 Signaling, SAPK/JNK Signaling, RhoGDI Signaling, EIF2 Signaling, Regulation of eIF4 and p70S6K Signaling and Oxidative Phosphorylation pathways. They belong to signaling pathway categories like Cellular Growth, Proliferation and Development, Cellular Stress and Injury, Intracellular and Second Messenger Signaling and Apoptosis. Overall, this lncRNA study conducted in adult sheep after GIN infection provided first insights into the potential functional role of lncRNAs in the differential host response to nematode infection., Financial support for the experimental work of this project was received from the LE248U14 project of the Junta de Castilla and León regional government, whereas the storage and processing of the generated sequencing datasets have been funded by the RTI2018-093535-B-I00 project from the Spanish Ministry of Science and Innovation (MICINN). PC was funded by a Short-Term Scientific Missions of the Functional Annotation of Animal Genomes-European network (FAANG-Europe) COST Action CA15112 to do a short research stay at Leibniz Institute for Farm Animal Biology (FBN). MM-V was also funded by the “Ramón y Cajal” Programme (RYC-2015-18368) from MICINN.

International audience; This paper reviews existing on-farm GHG accounting models for dairy cattle systems and their ability to capture the effect of dietary strategies in GHG abatement. The focus is on methane (CH4) emissions from enteric and manure (animal excreta) sources and nitrous oxide (N2O) emissions from animal excreta. We identified three generic modelling approaches, based on the degree to which models capture diet-related characteristics: from 'none' (Type 1) to 'some' by combining key diet parameters with emission factors (EF) (Type 2) to 'many' by using process-based modelling (Type 3). Most of the selected on-farm GHG models have adopted a Type 2 approach, but a few hybrid Type 2 / Type 3 approaches have been developed recently that combine empirical modelling (through the use of CH4 and/or N2O emission factors; EF) and process-based modelling (mostly through rumen and whole tract fermentation and digestion). Empirical models comprising key dietary inputs (i.e., dry matter intake and organic matter digestibility) can predict CH4 and N2O emissions with reasonable accuracy. However, the impact of GHG mitigation strategies often needs to be assessed in a more integrated way, and Type 1 and Type 2 models frequently lack the biological foundation to do this. Only Type 3 models represent underlying mechanisms such as ruminal and total-tract digestive processes and excreta composition that can capture dietary effects on GHG emissions in a more biological manner. Overall, the better a model can simulate rumen function, the greater the opportunity to include diet characteristics in addition to commonly used variables. and thus the greater the opportunity to capture dietary mitigation strategies. The value of capturing the effect of additional animal feed characteristics on the prediction of on-farm GHG emissions needs to be carefully balanced against gains in accuracy, the need for additional input and activity data, and the variability encountered on-farm..

Background Recombination is a process by which chromosomes are broken and recombine to generate new combinations of alleles, therefore playing a major role in shaping genome variation. Recombination frequencies ($$\theta$$ θ ) between markers are used to construct genetic maps, which have important implications in genomic studies. Here, we report a recombination map for 44,696 autosomal single nucleotide polymorphisms (SNPs) according to the coordinates of the most recent bovine reference assembly. The recombination frequencies were estimated across 876 half-sib families with a minimum number of 39 and maximum number of 4236 progeny, comprising over 367 K genotyped German Holstein animals. Results Genome-wide, over 8.9 million paternal recombination events were identified by investigating adjacent markers. The recombination map spans 24.43 Morgan (M) for a chromosomal length of 2486 Mbp and an average of ~ 0.98 cM/Mbp, which concords with the available pedigree-based linkage maps. Furthermore, we identified 971 putative recombination hotspot intervals (defined as $$\theta$$ θ > 2.5 standard deviations greater than the mean). The hotspot regions were non-uniformly distributed as sharp and narrow peaks, corresponding to ~ 5.8% of the recombination that has taken place in only ~ 2.4% of the genome. We verified genetic map length by applying a likelihood-based approach for the estimation of recombination rate between all intra-chromosomal marker pairs. This resulted in a longer autosomal genetic length for male cattle (25.35 cM) and in the localization of 51 putatively misplaced SNPs in the genome assembly. Conclusions Given the fact that this map is built on the coordinates of the ARS-UCD1.2 assembly, our results provide the most updated genetic map yet available for the cattle genome.

The Food and Agriculture Organisation of the United Nations (FAO) reports that by the year 2050 the global human population is likely to reach 9.7 billion, rising to 11.2 billion by 2100 (https://population.un.org/wpp/Publications/Files/Key_Findings_WPP_2015.pdf). This population growth poses several challenges to the global food system, which will need to produce more healthy food using fewer natural resources, reducing the environmental impact, conserving biodiversity and flexibly adjusting to changing societal expectations. Meeting this demand requires environmentally sustainable improvements to farmed animal health and welfare, and of efficiency and diversification (e.g. to include a broader range of locally adapted species) [1]. The changes in breeding strategies and management practises required to meet these goals will need to build on an improved ability to accurately use genotype to predict phenotype in the world’s farmed animal species, both terrestrial and aquatic (Figure 1). Here we describe a set of research priorities to meet such present and future challenges that build on progress, successes and resources from the Functional Annotation of ANimal Genomes (FAANG) project [2]. The first stages of FAANG focused on foundational data generation to characterise expressed and regulatory genomic regions, curation and provision of annotated farmed animal genomes [2,3]. These were largely based on individual level, high depth approaches [3]. The primary challenge facing this community now is harnessing these resources to link genotype, phenotype and genetic merit in order to translate this research out of the laboratory and into industry application in the field. To achieve this effectively, we will need to generate functional genomic information for large populations of animals, rather than relying on a small number of deeply annotated individuals. Furthermore, to date, most of the datasets are from tissues consisting of heterogeneous cell populations, hindering the resolution of functional information and limiting our ability to understand the fundamental cellular and subcellular processes underlying phenotypes. Since the original FAANG white paper was published in 2015 [2], exciting new opportunities have arisen to tackle these challenges. We describe a set of research action priorities for FAANG for the next decade (Figure 2), in each of the sections below.

International audience; Most of the circRNAs reported to date originate from back splicing of a pre-mRNA, and these exonic circRNAs are termed canonical circRNAs. Our objective was to provide an overview of all other (non-canonical) circRNAs that do not originate from the junction of two exons and to characterize their common properties. Those generated through a failure of intron lariat debranching are the best known, even though studies on them are rare. These circRNAs retain the 2 '-5 ' bond derived from the intron lariat, and this feature probably explains the difficulties in obtaining efficient reverse transcription through the circular junction. Here, we provide an unprecedented overview of non-canonical circRNAs (lariat-derived intronic circRNAs, sub-exonic circRNAs, intron circles, tricRNAs), which all derive from non-coding sequences. As there are few data suggesting their involvement in cellular regulatory processes, we believe that it is early to propose a general function for circRNAs, even for lariat-derived circRNAs. We suggest that their small size and probably strong secondary structures could be major obstacles to their reliable detection. Nevertheless, we believe there are still several possible ways to advance our knowledge of this class of non-coding RNA.

International audience; The sequencing of total RNA depleted for ribosomal sequences remains the method of choice for the study of circRNAs. Our objective was to characterize non-canonical circRNAs, namely not originating from back splicing and circRNA produced by non-coding genes. To this end, we analyzed a dataset from porcine testis known to contain about 100 intron-derived circRNAs. Labelling reads containing a circular junction and originating from back splicing provided information on the very small contribution of long non-coding genes to the production of canonical circRNAs. Analyses of the other reads revealed two origins for non-canonical circRNAs: (1) Intronic sequences for lariat-derived intronic circRNAs and intron circles, (2) Mono-exonic genes (mostly non-coding) for either a new type of circRNA (including only part of the exon: sub-exonic circRNAs) or, even more rarely, mono-exonic canonical circRNAs. The most complex set of sub-exonic circRNAs was produced byRNase_MRP(ribozyme RNA). We specifically investigated the intronic circRNA ofATXN2L, which is probably an independently transcribed sisRNA (stable intronic sequence RNA). We may be witnessing the emergence of a new non-coding gene in the porcine genome. Our results are evidence that most non-canonical circRNAs originate from non-coding sequences.

In vertebrates, the carbohydrate polymer polysialic acid (polySia) is especially well known for its essential role during neuronal development, regulating the migration and proliferation of neural precursor cells, for instance. Nevertheless, sialic acid polymers seem to be regulatory elements in other physiological systems, such as the reproductive tract. Interestingly, trout fish eggs have polySia, but we know little of its cellular distribution and role during oogenesis. Therefore, we localized α2,8-linked N-acetylneuraminic acid polymers in the ovaries of Coregonus maraena by immunohistochemistry and found that prevalent clusters of oogonia showed polySia signals on their surfaces. Remarkably, the genome of this salmonid fish contains two st8sia2 genes and one st8sia4 gene, that is, three polysialyltransferases. The expression analysis revealed that for st8sia2-r2, 60 times more mRNA was present than st8sia2-r1 and st8sia4. To compare polysialylation status regarding various polySiaT configurations, we performed a comparable analysis in Sander lucioperca. The genome of this perciform fish contains only one st8sia2 and no st8sia4 gene. Here, too, clusters of oogonia showed polysialylated cell surfaces, and we detected high mRNA values for st8sia2. These results suggest that in teleosts, polySia is involved in the cellular processes of oogonia during oogenesis.

International audience; BACKGROUND A robust proxy for estimating methane (CH4) emissions of individual dairy cows would be valuable especially for selective breeding. This study aimed to improve the robustness and accuracy of prediction models that estimate daily CH4 emissions from milk Fourier transform mid-infrared (FT-MIR) spectra by (i) increasing the reference dataset and (ii) adjusting for routinely recorded phenotypic information. Prediction equations for CH4 were developed using a combined dataset including daily CH4 measurements (n = 1089; g d(-1)) collected using the SF6 tracer technique (n = 513) and measurements using respiration chambers (RC, n = 576). Furthermore, in addition to the milk FT-MIR spectra, the variables of milk yield (MY) on the test day, parity (P) and breed (B) of cows were included in the regression analysis as explanatory variables.RESULTS Models developed based on a combined RC and SF6 dataset predicted the expected pattern in CH4 values (in g d(-1)) during a lactation cycle, namely an increase during the first weeks after calving followed by a gradual decrease until the end of lactation. The model including MY, P and B information provided the best prediction results (cross-validation statistics: R-2 = 0.68 and standard error = 57 g CH4 d(-1)).CONCLUSIONS The models developed accounted for more of the observed variability in CH4 emissions than previously developed models and thus were considered more robust. This approach is suitable for large-scale studies (e.g. animal genetic evaluation) where robustness is paramount for accurate predictions across a range of animal conditions. (c) 2020 Society of Chemical Industry

Enting [1] concluded lameness, from an economic perspective, as the third most costly health disease, following mastitis and reproductive failure issues, in cattle units. Archer [2] estimated the incidence rate of lameness in the United Kingdom cattle herds roughly 50 cases/100 cows in a year; nevertheless, due to poor correlation between incidence rates and records of treatments in farms [3], the actual number seems to be higher. Surprisingly, the significance of lameness associated with cattle welfare, health and profitability of the unit has been greatly underestimated [4]. Recent works have shown a clear link between BCS and hook condition of cows with the development of lameness in these animals [5]. Lameness is a multifactorial and progressive issue where different detriments contribute to its development via complex interactions. Detection of lame cattle can be facilitated through description of the animals' gait characteristics in a numerical scaling system known as locomotion scoring [6]. The total number of visual (manual) locomotion scoring systems can reach up to 25, where differences lie mostly in the used scales, characterization of cows' gait, and posture [7]. Automated locomotion scoring tools would be a big advantage for regular monitoring of lameness in the herd. Three methods that are commonly engaged with automated systems are: kinetic, kinematic and indirect. The kinetic and kinematic approaches measure the forces, involved in locomotion, and time and distance of variables, associated to limb movement, respectively [8]. The indirect method simply exploits behavioral or production data as indicators for impaired locomotion. The automated tools/instruments that will be developed, based upon either of the aforementioned approaches, need to be validated with a ‘reference’ method. This usually is done by comparing with manual scoring; however, it is noteworthy that manual scoring systems have their own set of limitations [9].

The extent of differentiation of social relationships within groups is a means to assess social complexity, with greater differentiation indicating greater social complexity. Socio-ecological factors are likely to influence social complexity, but no attempt has been made to explain the differentiation of social relationships using multiple socio-ecological factors. Here, we propose a conceptual framework based on four components underlying multiple socio-ecological factors that influence the differentiation of social relationships: the extent of within-group contest competition to access resources, the extent to which individuals differ in their ability to provide a variety of services, the need for group-level cooperation and the constraints on social interactions. We use the framework to make predictions about the degree of relationship differentiation that can be expected within a group according to the cumulative contribution of multiple socio-ecological factors to each of the four components. The framework has broad applicability, since the four components are likely to be relevant to a wide range of animal taxa and to additional socio-ecological factors not explicitly dealt with here. Hence, the framework can be used as the basis for the development of novel and testable hypotheses about intra- and interspecific differences in relationship differentiation and social complexity.

International audience; The oviductal fluid is the first environment experienced by mammalian embryos at the very beginning of life. However, it has long been believed that the oviductal environment was not essential for proper embryonic development. Successful establishment of in vitro embryo production techniques (which completely bypass the oviduct) have reinforced this idea. Yet, it became evident that in vitro produced embryos differ markedly from their in vivo counterparts, and these differences are associated with lower pregnancy outcomes and more health issues after birth. Nowadays, researchers consider the oviduct as the most suitable microenvironment for early embryonic development and a substantial effort is made to understand its dynamic, species-specific functions. In this review, we touch on the origin and molecular components of the oviductal fluid in mammals, where recent progress has been made thanks to the wider use of mass spectrometry techniques. Some of the factors and processes known to regulate oviductal secretions, including the embryo itself, as well as ovulation, insemination, endogenous and exogenous hormones, and metabolic and heat stress, are summarized. Special emphasis is laid on farm animals because, owing to the availability of sample material and the economic importance of fertility in livestock husbandry, a large part of the work on this topic has been carried out in domestic animals used for dairy and/or meat production.

Infection and inflammation of the mammary gland, and especially prevention of mastitis, are still major challenges for the dairy industry. Different approaches have been tried to reduce the incidence of mastitis. Genetic selection of cows with lower susceptibility to mastitis promises sustainable success in this regard. Bos taurus autosome (BTA) 18, particularly the region between 43 and 59 Mb, harbors quantitative trait loci (QTL) for somatic cell score, a surrogate trait for mastitis susceptibility. Scrutinizing the molecular bases hereof, we challenged udders from half-sib heifers having inherited either favorable paternal haplotypes for somatic cell score (Q) or unfavorable haplotypes (q) with the Staphylococcus aureus pathogen. RNA sequencing was used for an in-depth analysis of challenge-related alterations in the hepatic transcriptome. Liver exerts highly relevant immune functions aside from being the key metabolic organ. Hence, a holistic approach focusing on the liver enabled us to identify challenge-related and genotype-dependent differentially expressed genes and underlying regulatory networks. In response to the S. aureus challenge, we found that heifers with Q haplotypes displayed more activated immune genes and pathways after S. aureus challenge compared with their q half-sibs. Furthermore, we found a significant enrichment of differentially expressed loci in the genomic target region on BTA18, suggesting the existence of a regionally acting regulatory element with effects on a variety of genes in this region. © 2020 American Dairy Science Association Infection and inflammation of the mammary gland, and especially prevention of mastitis, are still major challenges for the dairy industry. Different approaches have been tried to reduce the incidence of mastitis. Genetic selection of cows with lower susceptibility to mastitis promises sustainable success in this regard. Bos taurus autosome (BTA) 18, particularly the region between 43 and 59 Mb, harbors quantitative trait loci (QTL) for somatic cell score, a surrogate trait for mastitis susceptibility. Scrutinizing the molecular bases hereof, we challenged udders from half-sib heifers having inherited either favorable paternal haplotypes for somatic cell score (Q) or unfavorable haplotypes (q) with the Staphylococcus aureus pathogen. RNA sequencing was used for an in-depth analysis of challenge-related alterations in the hepatic transcriptome. Liver exerts highly relevant immune functions aside from being the key metabolic organ. Hence, a holistic approach focusing on the liver enabled us to identify challenge-related and genotype-dependent differentially expressed genes and underlying regulatory networks. In response to the S. aureus challenge, we found that heifers with Q haplotypes displayed more activated immune genes and pathways after S. aureus challenge compared with their q half-sibs. Furthermore, we found a significant enrichment of differentially expressed loci in the genomic target region on BTA18, suggesting the existence of a regionally acting regulatory element with effects on a variety of genes in this region. © 2020 American Dairy Science Association Landwirtschaftliche Rentenbank

International audience; The sustainability of cattle production relies on improved resource use efficiency, reduced GHG emissions, and improved animal health and welfare. Facing this challenge require far more complex animal traits than previously that need to be assessed under a range of conditions. It is now time to look for means to phenotype complex animal traits using smart technologies and rapid analytical methods in a standardised way applied in many contexts. The SmartCow infrastructure project (www.smartcow.eu) was selected by the European Commission for 4 years from 1st February 2018. The project will ensure that existing guidelines are adopted (e.g. ICAR guidelines) and work towards the use of unified measurement methods when no international standard is existing. The development of the cattle ontology of traits (ATOL) and the ontology of environmental conditions (EOL) will be an important step to unify research methodologies. Refining in vivo methods to evaluate feed efficiency and gas emissions will generate innovations in experimental design for more accuracy. The development of new biomarkers (proxies) that can be easily measured in milk, faeces, urine, or blood through rapid analytical methods (e.g. infrared spectroscopy) will bring new phenotyping capacities. The development of tools to generate new and improved information from animal sensors and other routinely collected data (e.g. prediction of individual cow status in terms of health and welfare) will also enable a more efficient phenotyping and genetic selection of cattle. Finally, transnational access to 11 major research infrastructures will provide access to around 2500 dairy and 1000 beef cattle and generate new phenotyping opportunities in research projects to be financed by the SmartCow project. Eleven projects have already been selected after the first call.

Behavioural and cognitive processes play important roles in mediating an individual's interactions with its environment. Yet, while there is a vast literature on repeatable individual differences in behaviour, relatively little is known about the repeatability of cognitive performance. To further our understanding of the evolution of cognition, we gathered 44 studies on individual performance of 25 species across six animal classes and used meta-analysis to assess whether cognitive performance is repeatable. We compared repeatability ( R ) in performance (1) on the same task presented at different times (temporal repeatability), and (2) on different tasks that measured the same putative cognitive ability (contextual repeatability). We also addressed whether R estimates were influenced by seven extrinsic factors (moderators): type of cognitive performance measurement, type of cognitive task, delay between tests, origin of the subjects, experimental context, taxonomic class and publication status. We found support for both temporal and contextual repeatability of cognitive performance, with mean R estimates ranging between 0.15 and 0.28. Repeatability estimates were mostly influenced by the type of cognitive performance measures and publication status. Our findings highlight the widespread occurrence of consistent inter-individual variation in cognition across a range of taxa which, like behaviour, may be associated with fitness outcomes. This article is part of the theme issue ‘Causes and consequences of individual differences in cognitive abilities’.

Although the functions of most of circular RNAs (circRNAs) are not characterized, they likely impact many biologicalprocesses. Indeed, in addition to generating a linear transcriptmany protein-coding genes produce circRNAs.By applying original strategies on seven Total-RNA-seqdatasets from testis sampled during the puberty, we detected 126 introns in 114 genes able to produce circRNAs and 5,236 exonic circRNAs produced by 2,516 genes. Comparing our RNA-seq datasets to datasets from the literature (embryonic cortex and postnatal muscle stages) revealed highly abundant intronic and exonic circRNAs in one sample each in pubertal testis and embryonic cortex, respectively.In pubertal testis with circRNAs in abundance, 24% of protein-coding genes produced linear and circular transcripts. This abundance was due to higher production of circRNA by the same genes in comparison to other testis samples, rather than the recruitment of new genes.By comparing the total-RNA-seq and mRNA-seq data, we found noglobal relationship between exoniccircRNA and mRNA productions in pubertal testis.In the list of genes with significant expression of linear transcripts, we found 84% of genes identified as able to produce ExoCirc-RNAs. The genesable to produce circRNA + mRNAwere significantly longer than the genes that only produced mRNAs.So, weshowedthat exonic circRNAs are typically produced by large genes that are also able to produce mRNAsAmong the 5,236 ExoCirc-RNAs, we noted the presence of 213 single-exon circRNAs and we showed that exons capable of constituting these single-exon circRNAs are significantly longer than those that can only be included in multi-exon circRNAs. We chose to only retain multi-exon circRNAs (5,023) to study the proximal environment of each exon involved in a circular junction. We identified single exons involved in the circular junctions of multi-exon circRNAs that we named ‘extreme exons’. For each extreme exon, we identified the two proximal exons (internal and external) and the two proximal introns. The comparison of pairs [extreme exon -external exon] showed that extreme exons are significantly smaller than their external exon counterparts. The comparison of pairs [internal intron -external intron] showed that external introns are significantly longer than internal introns. Ragan et al. (2019) showed that these features probably create preconditions for circRNA production by promoting looping interactions between flanking introns.Our data indicate that the production of circRNAs is mainly related to the structure of genes generating circRNAs.

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National audience

Ruminant production systems are important contributors to anthropogenic methane (CH4) emissions, but there are large uncertainties in national and global livestock CH4 inventories. Sources of uncertainty in enteric CH4 emissions include animal inventories, feed dry matter intake (DMI), ingredient and chemical composition of the diets, and CH4 emission factors. There is also significant uncertainty associated with enteric CH4 measurements. The most widely used techniques are respiration chambers, the sulfur hexafluoride (SF6) tracer technique, and the automated head-chamber system (GreenFeed; C-Lock Inc., Rapid City, SD). All 3 methods have been successfully used in a large number of experiments with dairy or beef cattle in various environmental conditions, although studies that compare techniques have reported inconsistent results. Although different types of models have been developed to predict enteric CH4 emissions, relatively simple empirical (statistical) models have been commonly used for inventory purposes because of their broad applicability and ease of use compared with more detailed empirical and process-based mechanistic models. However, extant empirical models used to predict enteric CH4 emissions suffer from narrow spatial focus, limited observations, and limitations of the statistical technique used. Therefore, prediction models must be developed from robust data sets that can only be generated through collaboration of scientists across the world. To achieve high prediction accuracy, these data sets should encompass a wide range of diets and production systems within regions and globally. Overall, enteric CH4 prediction models are based on various animal or feed characteristic inputs but are dominated by DMI in one form or another. As a result, accurate prediction of DMI is essential for accurate prediction of livestock CH4 emissions. Analysis of a large data set of individual dairy cattle data showed that simplified enteric CH4 prediction models based on DMI alone or DMI and limited feed- or animal-related inputs can predict average CH4 emission with a similar accuracy to more complex empirical models. These simplified models can be reliably used for emission inventory purposes.

Evaluation and mitigation of enteric methane (CH4) emissions from ruminant livestock, in particular from dairy cows, have acquired global importance for sustainable, climate-smart cattle production. Based on CH4 reference measurements obtained with the SF6 tracer technique to determine ruminal CH4 production, a current equation permits evaluation of individual daily CH4 emissions of dairy cows based on milk Fourier transform mid-infrared (FT-MIR) spectra. However, the respiration chamber (RC) technique is considered to be more accurate than SF6 to measure CH4 production from cattle. This study aimed to develop an equation that allows estimating CH4 emissions of lactating cows recorded in an RC from corresponding milk FT-MIR spectra and to challenge its robustness and relevance through validation processes and its application on a milk spectral database. This would permit confirming the conclusions drawn with the existing equation based on SF6 reference measurements regarding the potential to estimate daily CH4 emissions of dairy cows from milk FT-MIR spectra. A total of 584 RC reference CH4 measurements (mean ± standard deviation of 400 ± 72 g of CH4/d) and corresponding standardized milk mid-infrared spectra were obtained from 148 individual lactating cows between 7 and 321 d in milk in 5 European countries (Germany, Switzerland, Denmark, France, and Northern Ireland). The developed equation based on RC measurements showed calibration and cross-validation coefficients of determination of 0.65 and 0.57, respectively, which is lower than those obtained earlier by the equation based on 532 SF6 measurements (0.74 and 0.70, respectively). This means that the RC-based model is unable to explain the variability observed in the corresponding reference data as well as the SF6-based model. The standard errors of calibration and cross-validation were lower for the RC model (43 and 47 g/d vs. 66 and 70 g/d for the SF6 version, respectively), indicating that the model based on RC data was closer to actual values. The root mean squared error (RMSE) of calibration of 42 g/d represents only 10% of the overall daily CH4 production, which is 23 g/d lower than the RMSE for the SF6-based equation. During the external validation step an RMSE of 62 g/d was observed. When the RC equation was applied to a standardized spectral database of milk recordings collected in the Walloon region of Belgium between January 2012 and December 2017 (1,515,137 spectra from 132,658 lactating cows in 1,176 different herds), an average ± standard deviation of 446 ± 51 g of CH4/d was estimated, which is consistent with the range of the values measured using both RC and SF6 techniques. This study confirmed that milk FT-MIR spectra could be used as a potential proxy to estimate daily CH4 emissions from dairy cows provided that the variability to predict is covered by the model.

Enteric methane (CH) production from cattle contributes to global greenhouse gas emissions. Measurement of enteric CH is complex, expensive, and impractical at large scales; therefore, models are commonly used to predict CH production. However, building robust prediction models requires extensive data from animals under different management systems worldwide. The objectives of this study were to (1) collate a global database of enteric CH production from individual lactating dairy cattle; (2) determine the availability of key variables for predicting enteric CH production (g/day per cow), yield [g/kg dry matter intake (DMI)], and intensity (g/kg energy corrected milk) and their respective relationships; (3) develop intercontinental and regional models and cross-validate their performance; and (4) assess the trade-off between availability of on-farm inputs and CH prediction accuracy. The intercontinental database covered Europe (EU), the United States (US), and Australia (AU). A sequential approach was taken by incrementally adding key variables to develop models with increasing complexity. Methane emissions were predicted by fitting linear mixed models. Within model categories, an intercontinental model with the most available independent variables performed best with root mean square prediction error (RMSPE) as a percentage of mean observed value of 16.6%, 14.7%, and 19.8% for intercontinental, EU, and United States regions, respectively. Less complex models requiring only DMI had predictive ability comparable to complex models. Enteric CH production, yield, and intensity prediction models developed on an intercontinental basis had similar performance across regions, however, intercepts and slopes were different with implications for prediction. Revised CH emission conversion factors for specific regions are required to improve CH production estimates in national inventories. In conclusion, information on DMI is required for good prediction, and other factors such as dietary neutral detergent fiber (NDF) concentration, improve the prediction. For enteric CH yield and intensity prediction, information on milk yield and composition is required for better estimation., This study is part of the Joint Programming Initiative on Agriculture, Food Security and Climate Change (FACCE‐JPI)'s “GLOBAL NETWORK” project and the “Feeding and Nutrition Network” (http://animalscience.psu.edu/fnn) of the Livestock Research Group within the Global Research Alliance for Agricultural Greenhouse Gases (www.globalresearchalliance.org). Authors gratefully acknowledge funding for this project from: USDA National Institute of Food and Agriculture Grant no. 2014‐67003‐21979) University of California, Davis Sesnon Endowed Chair Program, USDA, and Austin Eugene Lyons Fellowship (University of California, Davis); Funding from USDA National Institute of Food and Agriculture Federal Appropriations under Project PEN 04539 and Accession number 1000803, DSM Nutritional Products (Basel, Switzerland), Pennsylvania Soybean Board (Harrisburg, PA, USA), Northeast Sustainable Agriculture Research and Education (Burlington, VT, USA), and PMI Nutritional Additives (Shoreview, MN, USA); the Ministry of Economic Affairs (the Netherlands; project BO‐20‐007‐006; Global Research Alliance on Agricultural Greenhouse Gases), the Product Board Animal Feed (Zoetermeer, the Netherlands) and the Dutch Dairy Board (Zoetermeer, the Netherlands); USDA National Institute of Food and Agriculture (Hatch Multistate NC‐1042 Project Number NH00616‐R; Project Accession Number 1001855) and the New Hampshire Agricultural Experiment Station (Durham, NH); French National Research Agency through the FACCE‐JPI program (ANR‐13‐JFAC‐0003‐01), Agricultural GHG Research Initiative for Ireland (AGRI‐I), Academy of Finland (No. 281337), Helsinki, Finland; Swiss Federal Office of Agriculture, Berne, Switzerland; the Department for Environment, Food and Rural Affairs (Defra; UK); Defra, the Scottish Government, DARD, and the Welsh Government as part of the UK's Agricultural GHG Research Platform projects (www.ghgplatform.org.uk); INIA (Spain, project MIT01‐GLOBALNET‐EEZ); German Federal Ministry of Food and Agriculture (BMBL) through the Federal Office for Agriculture and Food (BLE); Swedish Infrastructure for Ecosystem Science (SITES) at Röbäcksdalen Research Station; Comisión Nacional de Investigación Científica y Tecnológica, Fondo Nacional de Desarrollo Científico y Tecnológico (Grant Nos. 11110410 and 1151355) and Fondo Regional de Tecnología Agropecuaria (FTG/RF‐1028‐RG); European Commission through SMEthane (FP7‐SME‐262270). The authors are thankful to all colleagues who contributed data to the GLOBAL NETWORK project and especially thank Luis Moraes, Ranga Appuhamy, Henk van Lingen, James Fadel, and Roberto Sainz for their support on data analysis. All authors read and approved the final manuscript. The authors declare that they have no competing interests.

We describe an emerging initiative - the ‘Functional Analysis of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, through to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

International audience; The aim of our study was to characterize the immediate phenotypic and adaptive regulatory responses of fetuses to different in utero conditions reflecting inadequate maternal protein supply during gestation. The gilts fed high- (250% above control) or low- (50% under control) protein diets isoenergetically adjusted at the expense of carbohydrates from the day of insemination until the fetuses were collected at day 64 or 94 of gestation. We analyzed body composition, histomorphology, biochemistry, and messenger RNA (mRNA) expression of fetal skeletal muscle. Both diets had only marginal effects on body composition and muscular cellularity of fetuses including an unchanged total number of myofibers. However, mRNA expression of myogenic regulatory factors (MYOG, MRF4, P ≤ 0.1), IGF system (IGF1, IGF1R, P ≤ 0.05) and myostatin antagonist FST (P = 0.6, in males only) was reduced in the fetal muscle exposed to a maternal low-protein diet. As a result of excess protein, MYOD, MYOG, IGF1R, and IGFBP5 mRNA expression (P ≤ 0.05) was upregulated in fetal muscle. Differences in muscular mRNA expression indicate in utero regulatory adaptive responses to maternal diet. Modulation of gene expression immediately contributes to the maintenance of an appropriate fetal phenotype that would be similar to that observed in the control fetuses. Moreover, we suggest that the modified gene expression in fetal skeletal muscle can be viewed as the origin of developmental muscular plasticity involved in the concept of fetal programming.

International audience; The main aim of the present study was to examine the effects of long-term supplementing diets with saturated or unprotected polyunsaturated fatty acids from two different plant oils rich in either n-3 or n-6 fatty acids (FAs) plus docosahexaenoic acid (DHA)-rich algae on mammary gene expression and milk fat composition in lactating dairy cows. Gene expression was determined from mammary tissue and milk epithelial cells. Eighteen primiparous German Holstein dairy cows in mid-lactation were randomly assigned into three dietary treatments that consist of silage-based diets supplemented with rumen-stable fractionated palm fat (SAT; 3.1% of the basal diet dry matter, DM), or a mixture of linseed oil (2.7% of the basal diet DM) plus DHA-rich algae (LINA; 0.4% of the basal diet DM) or a mixture of sunflower oil (2.7% of the basal diet DM) plus DHA-rich algae (SUNA; 0.4% of the basal diet DM), for a period of 10 weeks. At the end of the experimental period, the cows were slaughtered and mammary tissues were collected to study the gene expression of lipogenic enzymes. During the last week, the milk yield and composition were determined, and milk was collected for FA measurements and the isolation of milk purified mammary epithelial cells (MECs). Supplementation with plant oils and DHA-rich algae resulted in milk fat depression (MFD; yield and percentage). The secretion of de novo FAs in the milk was reduced, whereas the secretion of trans-10,cis-12-CLA and DHA were increased. These changes in FA secretions were associated in mammary tissue with a joint down-regulation of mammary lipogenic enzyme gene expression (stearoyl-CoA desaturase, SCD1; FA synthase, FASN) and expression of the regulatory element binding transcription factor (SREBF1), whereas no effect was observed on lipoprotein lipase (LPL) and glycerol-3-phosphate acyltransferase 1, mitochondrial (GPAM). A positive relationship between mammary SCD1 and SREBF1 mRNA abundances was observed, suggesting a similar regulation for these genes. Such data on mammary gene expression in lactating cows presenting MFD contribute to strengthen the molecular mechanisms that govern milk fat synthesis in the mammary glands. In purified MEC, the dietary treatments had no effect on gene expressions. Differences between mammary tissue and milk purified MEC gene expression were attributed to the effect of lipid supplements on the number of milk purified MEC and its RNA quality, which are determinant factors for the analysis of gene expression using milk cells.

Gene expression profiles of bovine longissimus muscle as affected by dietary n-3 v.n-6 fatty acid (FA) intervention were analysed by microarray pre-screening of >3000 muscle biology/meat quality-related genes as well as subsequent quantitative RT-PCR gene expression validation of genes encoding lipogenesis-related transcription factors (CCAAT/enhancer-binding protein β, sterol regulatory element-binding transcription factor 1), key-lipogenic enzymes (acetyl-CoA carboxylase α (ACACA), fatty acid synthase (FASN), stearoyl-CoA desaturase (SCD)), lipid storage-associated proteins (adipose differentiation-related protein (ADFP)) and muscle biology-related proteins (cholinergic receptor, nicotinic, α1, farnesyl diphosphate farnesyl transferase 1, sema domain 3C (SEMA3C)). Down-regulation of ACACA (P = 0·00), FASN (P = 0·09) and SCD (P = 0·02) gene expression upon an n-3 FA intervention directly corresponded to reduced SFA, MUFA and total FA concentrations in longissimus muscle, whereas changes in ADFP (P = 0·00) and SEMA3C (P = 0·05) gene expression indicated improved muscle function via enhanced energy metabolism, vasculogenesis, innervation and mediator synthesis. The present study highlights the significance of dietary n-3 FA intervention on muscle development, maintenance and function, which are relevant for meat quality tailoring of bovine tissues and modulating animal production-relevant physiological processes.