16 results on '"Billon, Yvon"'
Search Results
2. Rabbit targeted genomic sequences after heterologous hybridization using human exome
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Iannuccelli, Nathalie, Sarry, Julien, Billon, Yvon, Aymard, Patrick, Helies, Virginie, Cabau, Cédric, Donnadieu, Cécile, and Demars, Julie
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- 2022
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3. Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs
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Aliakbari, Amir, Zemb, Olivier, Cauquil, Laurent, Barilly, Céline, Billon, Yvon, and Gilbert, Hélène
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- 2022
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4. Plasticity of feeding behaviour traits in response to production environment (temperate vs. tropical) in group-housed growing pigs
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Poullet, Nausicaa, Rauw, Wendy M., Renaudeau, David, Riquet, Juliette, Giorgi, Mario, Billon, Yvon, Gilbert, Hélène, and Gourdine, Jean-Luc
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- 2022
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5. Primiparous sow behaviour on the day of farrowing as one of the primary contributors to the growth of piglets in early lactation.
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Girardie, Océane, Laloë, Denis, Bonneau, Mathieu, Billon, Yvon, Bailly, Jean, David, Ingrid, and Canario, Laurianne
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PIGLETS ,LEAST squares ,MULTIVARIATE analysis ,SOWS ,SWINE - Abstract
Large White and Meishan sows differ in maternal ability and early piglet growth. We investigated the relationships between 100 maternal traits, grouped into 11 blocks according to the biological function they describe and litter growth over three successive periods after birth (D0–D1, D1–D3 and D3–D7; D0 starting at the onset of farrowing), as a measure of sow investment in early piglet production. Within- and between-breed variation was exploited to cover a maximum of the variability existing in pig maternal populations. The objective was to quantify the contribution of maternal traits, including functional traits and behavioural traits, to early litter growth. Multivariate analyses were used to depict correlations among traits. A partial least square multiblock analysis allowed quantifying the effect of maternal traits on early growth traits. Partial triadic analyses highlighted how sow behaviour changed with days, and whether it resulted in changes in litter growth. Several behavioural traits (standing activity, reactivity to different stimuli, postural activity) and functional traits (body reserves, udder quality) at farrowing contributed substantially to litter growth from D0 to D7. Sow aggression towards piglets and time spent standing at D0 were unfavourably correlated to D1–D3 litter growth. Time spent lying with udder exposed at D0 was favourably correlated to D1–D3 litter growth. The farrowing duration was negatively correlated to D0–D1 and D1–D3 litter growth. Furthermore, D3–D7 litter growth was positively correlated to feed intake in the same period. Several behavioural traits and some functional traits influence early litter growth. The contribution of sow behaviour was greater in the critical period around farrowing than in later days. [ABSTRACT FROM AUTHOR]
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- 2024
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6. Driving gut microbiota enterotypes through host genetics.
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Larzul, Catherine, Estellé, Jordi, Borey, Marion, Blanc, Fany, Lemonnier, Gaëtan, Billon, Yvon, Thiam, Mamadou Gabou, Quinquis, Benoît, Galleron, Nathalie, Jardet, Deborah, Lecardonnel, Jérôme, Plaza Oñate, Florian, and Rogel-Gaillard, Claire
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GENETICS ,ENTEROTYPES ,ANIMAL species ,POLYSACCHARIDES ,PEPTIDES ,DATABASES - Abstract
Background: Population stratification based on interindividual variability in gut microbiota composition has revealed the existence of several ecotypes named enterotypes in humans and various animal species. Enterotypes are often associated with environmental factors including diet, but knowledge of the role of host genetics remains scarce. Moreover, enterotypes harbor functionalities likely associated with varying abilities and susceptibilities of their host. Previously, we showed that under controlled conditions, 60-day-old pig populations consistently split into two enterotypes with either Prevotella and Mitsuokella (PM enterotype) or Ruminococcus and Treponema (RT enterotype) as keystone taxa. Here, our aim was to rely on pig as a model to study the influence of host genetics to assemble enterotypes, and to provide clues on enterotype functional differences and their links with growth traits. Results: We established two pig lines contrasted for abundances of the genera pairs specifying each enterotype at 60 days of age and assessed them for fecal microbiota composition and growth throughout three consecutive generations. Response to selection across three generations revealed, per line, an increase in the prevalence of the selected enterotype and in the average relative abundances of directly and indirectly selected bacterial genera. The PM enterotype was found less diverse than the RT enterotype but more efficient for piglet growth during the post-weaning period. Shotgun metagenomics revealed differentially abundant bacterial species between the two enterotypes. By using the KEGG Orthology database, we show that functions related to starch degradation and polysaccharide metabolism are enriched in the PM enterotype, whereas functions related to general nucleoside transport and peptide/nickel transport are enriched in the RT enterotype. Our results also suggest that the PM and RT enterotypes might differ in the metabolism of valine, leucin, and isoleucine, favoring their biosynthesis and degradation, respectively. Conclusion: We experimentally demonstrated that enterotypes are functional ecosystems that can be selected as a whole by exerting pressure on the host genetics. We also highlight that holobionts should be considered as units of selection in breeding programs. These results pave the way for a holistic use of host genetics, microbiota diversity, and enterotype functionalities to understand holobiont shaping and adaptation. 4B2VhAArUR-Phf8Fa7EFRX Video Abstract [ABSTRACT FROM AUTHOR]
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- 2024
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7. Divergent selection for feed efficiency in pigs altered the duodenum transcriptomic response to feed intake and its DNA methylation profiles.
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Devailly, Guillaume, Fève, Katia, Saci, Safia, Sarry, Julien, Valière, Sophie, Lluch, Jérôme, Bouchez, Olivier, Ravon, Laure, Billon, Yvon, Gilbert, Hélène, Riquet, Juliette, Beaumont, Martin, and Demars, Julie
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DNA methylation ,DUODENUM ,SWINE farms ,TRANSCRIPTOMES ,SWINE ,TIGHT junctions - Abstract
Feed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relatively low-(LRFI) and high- (HRFI) residual feed intake (RFI). Feeding behavior and metabolic differences have been previously reported between the two lines. We hypothesized that part of these differences could be related to differential sensing and absorption of nutrients in the proximal intestine. We investigated the duodenum transcriptome and DNA methylation profiles comparing overnight fasting with ad libitum feeding in LRFI and HRFI pigs (n = 24). We identified 1,106 differentially expressed genes between the two lines, notably affecting pathways of the transmembrane transport activity and related to mitosis or chromosome separation. The LRFI line showed a greater transcriptomic response to feed intake than the HRFI line. Feed intake affected genes from both anabolic and catabolic pathways in the pig duodenum, such as rRNA production and autophagy. Several nutrient transporter and tight junction genes were differentially expressed between lines and/or by short-term feed intake. We also identified 409 differentially methylated regions in the duodenum mucosa between the two lines, while this epigenetic mark was less affected by feeding. Our findings highlighted that the genetic selection for feed efficiency in pigs changed the transcriptome profiles of the duodenum, and notably its response to feed intake, suggesting key roles for this proximal gut segment in mechanisms underlying feed efficiency. [ABSTRACT FROM AUTHOR]
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- 2024
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8. Sex and fetal genome influence gene expression in pig endometrium at the end of gestation.
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Bonnet, Agnes, Bluy, Lisa, Gress, Laure, Canario, Laurianne, Ravon, Laure, Sécula, Aurelie, Billon, Yvon, and Liaubet, Laurence
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Background: A fine balance of feto-maternal resource allocation is required to support pregnancy, which depends on interactions between maternal and fetal genetic potential, maternal nutrition and environment, endometrial and placental functions. In particular, some imprinted genes have a role in regulating maternal-fetal nutrient exchange, but few have been documented in the endometrium. The aim of this study is to describe the expression of 42 genes, with parental expression, in the endometrium comparing two extreme breeds: Large White (LW); Meishan (MS) with contrasting neonatal mortality and maturity at two days of gestation (D90-D110). We investigated their potential contribution to fetal maturation exploring genes-fetal phenotypes relationships. Last, we hypothesized that the fetal genome and sex influence their endometrial expression. For this purpose, pure and reciprocally crossbred fetuses were produced using LW and MS breeds. Thus, in the same uterus, endometrial samples were associated with its purebred or crossbred fetuses. Results: Among the 22 differentially expressed genes (DEGs), 14 DEGs were differentially regulated between the two days of gestation. More gestational changes were described in LW (11 DEGs) than in MS (2 DEGs). Nine DEGs were differentially regulated between the two extreme breeds, highlighting differences in the regulation of endometrial angiogenesis, nutrient transport and energy metabolism. We identified DEGs that showed high correlations with indicators of fetal maturation, such as ponderal index at D90 and fetal blood fructose level and placental weight at D110. We pointed out for the first time the influence of fetal sex and genome on endometrial expression at D90, highlighting AMPD3, CITED1 and H19 genes. We demonstrated that fetal sex affects the expression of five imprinted genes in LW endometrium. Fetal genome influenced the expression of four genes in LW endometrium but not in MS endometrium. Interestingly, both fetal sex and fetal genome interact to influence endometrial gene expression. Conclusions: These data provide evidence for some sexual dimorphism in the pregnant endometrium and for the contribution of the fetal genome to feto-maternal interactions at the end of gestation. They suggest that the paternal genome may contribute significantly to piglet survival, especially in crossbreeding production systems. [ABSTRACT FROM AUTHOR]
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- 2024
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9. Influence of genetics and the pre-vaccination blood transcriptome on the variability of antibody levels after vaccination against Mycoplasma hyopneumoniae in pigs
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Blanc, Fany, Maroilley, Tatiana, Revilla, Manuel, Lemonnier, Gaëtan, Leplat, Jean-Jacques, Billon, Yvon, Ravon, Laure, Bouchez, Olivier, Bidanel, Jean-Pierre, Bed’Hom, Bertrand, Pinard-van der Laan, Marie-Hélène, Estellé, Jordi, and Rogel-Gaillard, Claire
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- 2021
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10. Links between fecal microbiota and the response to vaccination against influenza A virus in pigs
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Borey, Marion, Blanc, Fany, Lemonnier, Gaëtan, Leplat, Jean-Jacques, Jardet, Deborah, Rossignol, Marie-Noëlle, Ravon, Laure, Billon, Yvon, Bernard, Maria, Estellé, Jordi, and Rogel-Gaillard, Claire
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- 2021
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11. Identification of genomic regions affecting production traits in pigs divergently selected for feed efficiency
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Delpuech, Emilie, Aliakbari, Amir, Labrune, Yann, Fève, Katia, Billon, Yvon, Gilbert, Hélène, and Riquet, Juliette
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- 2021
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12. Plasma 1H-NMR metabolic and amino acid profiles of newborn piglets from two lines divergently selected for residual feed intake.
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Liaubet, Laurence, Guilmineau, Camille, Lefort, Gaëlle, Billon, Yvon, Reigner, Sébastien, Bailly, Jean, Marty-Gasset, Nathalie, Gress, Laure, Servien, Rémi, Bonnet, Agnès, Gilbert, Hélène, Vialaneix, Nathalie, and Quesnel, Hélène
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PIGLETS ,AMINO acids ,UREA ,SWINE breeding ,NEWBORN infants ,ENERGY metabolism - Abstract
Together with environmental factors, physiological maturity at birth is a major determinant for neonatal survival and postnatal development in mammalian species. Maturity at birth is the outcome of complex mechanisms of intra-uterine development and maturation during the end of gestation. In pig production, piglet preweaning mortality averages 20% of the litter and thus, maturity is a major welfare and economic concern. Here, we used both targeted and untargeted metabolomic approaches to provide a deeper understanding of the maturity in a model of lines of pigs divergently selected on residual feed intake (RFI), previously shown to have contrasted signs of maturity at birth. Analyses were conducted on plasma metabolome of piglets at birth and integrated with other phenotypic characteristics associated to maturity. We confirmed proline and myo-inositol, previously described for their association with delayed growth, as potential markers of maturity. Urea cycle and energy metabolism were found more regulated in piglets from high and low RFI lines, respectively, suggesting a better thermoregulation ability for the low RFI (with higher feed efficiency) piglets. [ABSTRACT FROM AUTHOR]
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- 2023
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13. Transcriptomic and DNA methylation response to feed intake in the duodenum in high- and low- feed efficiency pig lines
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Devailly, Guillaume, Fêve, Katia, Saci, Safia, Sarry, Julien, Valière, Sophie, Bouchez, Olivier, Ravon, Laure, Billon, Yvon, Beaumont, Martin, Gilbert, Hélène, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Expérimentale Elevages Porcins Innovants (GenESI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), French Minister of Higher Education, Research and Innovation (APAFIS#21107-2018120415595562 v10), and Devailly, Guillaume
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[SDV.MHEP.PHY] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO] ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,[SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO] ,[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] - Abstract
International audience; Feed efficiency is a complex trait of interest in animal breeding to reduce environmental impact of livestock herding and the cost of animal feed. A divergent selection on feed efficiency was carried out in pigs for more than 10 generations at an INRAE experimental unit, establishing lines of relative high- and low-feed efficiency in large white pigs. The objective of this study was to identify the molecular mechanisms underlying the divergence in feed efficiency between the two pig lines in the duodenum. We focused on the duodenum because of its sensory role in the hunger satiety pathways.Duodenum mucosal samples were collected in post-weaning pigs from the two divergent lines either after a 12 h period of feed restriction, or with a 10 h period of feed restriction followed by a 2 h period of ad libitum feed access (n = 6 per group and per line). Transcritomes and methylomes were analysed by poly-A RNA sequencing (RNA-seq) and by methylated DNA precipitation followed by sequencing (MeDP-seq), respectively. Transcriptomic reads were analysed with nf-core/rnaseq and limma-voom. MeDP-seq reads were analysed with nf-core/chipseq and the BayMeth method.A total of 962 genes were differentially expressed in the duodenum mucosa between the conditions (fasted vs fed), in contrast with 318 differentially expressed genes when comparing the divergent lines. The DNA methylome of the duodenum mucosa was unaffected by short term feed intake, but was distinct between the lines. More transcripts were affected by short term feed intake in the feed-efficient line than in the other line, including genes of the incretine secretion pathways involved in the production of GIP and GLP-1.Thus the duodenum transcriptomic response to short term feed intake was distinct in feed efficient and less efficient pig lines. These differences might in part be due to differences in DNA methylation profiles.
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- 2022
14. Heterologous hybridization using the human exome - a molecular tool to target and identify major genes
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Iannuccelli, Nathalie, Cabau, Cédric, Sarry, Julien, Bouchez, Olivier, Billon, Yvon, Riquet, Juliette, Allain, Daniel, Demars, Julie, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
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[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,human+exome+capture+sequencing+variants - Abstract
International audience; Identifying causal mutations responsible of phenotypes in a time and cost-effective manner remains a challenge still for all species. Although the portfolio of next-generation sequencing methodologies offers a broad range of opportunities nowadays, having the right and suitable molecular genetic tools in non-model organisms is often an issue. For the European rabbit (Oryctolagus cuniculus), considered as an animal model for experimental research, the OryCun2.0 reference genome was released in 2009 and the Affymetrix AxiomOrcun SNP Array was made available in 2016. This novel beadchip gives the possibility to develop conveniently genome-wide association studies (GWAS) in rabbits without however freeing itself from the subsequent steps of causal mutation characterization. Whole exome sequencing (WES) appears as a direct and suitable strategy to target and sequence variants all at once. Unfortunately, no exome enrichment tool exist for rabbits. Here, we proposed to capture the rabbit exome using the marketed human panel since human and rabbit genomes are closely related on the phylogenetic tree of species. We performed heterologous hybridization for 48 rabbits from 7 different populations and generated 2 billion sequencing reads for the whole dataset. The quality of the heterologous hybridization allowed the capture of the rabbit exome and enabled a dataset of 40,000 confident variants that specifically target both protein-coding and extended exons. This method also presents a unique opportunity to investigate both (i) the genetic diversity of different rabbits’ breeds and (ii) the mendelian determinism of specific phenotypes in rabbits without resorting to costly customized tools.
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- 2021
15. Detection of DNA methylation signatures through the lens of genomic imprinting.
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Hubert JN, Iannuccelli N, Cabau C, Jacomet E, Billon Y, Serre RF, Vandecasteele C, Donnadieu C, and Demars J
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- Animals, Swine, Epigenesis, Genetic, Gene Expression, Genome, Mammals genetics, Genomic Imprinting, DNA Methylation
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Genomic imprinting represents an original model of epigenetic regulation resulting in a parent-of-origin expression. Despite the critical role of imprinted genes in mammalian growth, metabolism and neuronal function, there is no molecular tool specifically targeting them for a systematic evaluation. We show here that enzymatic methyl-seq consistently outperforms the bisulfite-based standard in capturing 165 candidate regions for genomic imprinting in the pig. This highlights the potential for a turnkey, fully customizable and reliable capture tool of genomic regions regulated by cytosine methylation in any population of interest. For the field of genomic imprinting, it opens up the possibility of detecting multilocus imprinting variations across the genome, with implications for basic research, agrigenomics and clinical practice., (© 2024. The Author(s).)
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- 2024
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16. Analysis of image-based sow activity patterns reveals several associations with piglet survival and early growth.
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Girardie O, Bonneau M, Billon Y, Bailly J, David I, and Canario L
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An activity pattern describes variations in activities over time. The objectives of this study are to automatically predict sow activity from computer vision over 11 days peripartum and estimate how sow behavior influences piglet's performance during early lactation. The analysis of video images used the convolutional neural network (CNN) YOLO for sow detection and posture classification of 21 Large White and 22 Meishan primiparous sows housed in individual farrowing pens. A longitudinal analysis and a clustering method were combined to identify groups of sows with a similar activity pattern. Traits under study are as follows: (i) the distribution of time spent daily in different postures and (ii) different activities while standing. Six postures were included along with three classes of standing activities, i.e., eating, drinking, and other, which can be in motion or not and root-pawing or not. They correspond to a postural budget and a standing-activity budget. Groups of sows with similar changes in their budget over the period (D-3 to D-1; D0 and D1-D7) were identified with the k-means clustering method. Next, behavioral traits (time spent daily in each posture, frequency of postural changes) were used as explanatory variables in the Cox proportional hazards model for survival and in the linear model for growth. Piglet survival was influenced by sow behavior on D-1 and during the period D1-D7. Piglets born from sows that were standing and doing an activity other than drinking and eating on D-1 had a 26% lower risk of dying than other piglets. Those born from sows that changed posture more frequently on D1-D7 had a 44% lower risk of dying. The number of postural changes, which illustrate sow restlessness, influenced piglet growth in the three periods. The average daily gain of piglets born from sows that were more restless on D1-D7 and that changed posture more frequently to hide their udder on D0 decreased by 22 and 45 g/d, respectively. Conversely, those born from sows that changed posture more frequently to hide their udder during the period of D1-D7 grew faster (+71 g/d) than the other piglets. Sow restlessness at different time periods influenced piglet performance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Girardie, Bonneau, Billon, Bailly, David and Canario.)
- Published
- 2023
- Full Text
- View/download PDF
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