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International audience

This presentation describes the methodology and the first results of an experiment of genetic selection for lower piglet mortality. Young females (G1 generation) were chosen from sows (G0) reared in conventional herds. G1 females were raised from weaning in the organic pig farm from INRAE (Porganic). G0 sows were selected for high piglet survival, large number of weaned piglets, and indications from breeders about their ease of farrowing and good maternal behaviour. G0 and G1 females were inseminated with semen from boars selected for high breeding values. G1 females were conducted in batches of 12 females, half being crated around farrowing and half being loose around farrowing. Performance of G1 females after their 1st, 2nd and 3rd farrowing events are presented. These preliminary results suggest that piglet mortality is similar in both systems when calculated on the overall lactation but mortality seems to be slightly delayed in crated compared to loose-housed sows. First results also suggest that the piglet mortality is influenced by the behaviour of sows, even more in the situation of temporary crating around farrowing. These preliminary data were obtained within the Era-Net CORE Organic Cofund project (Power project: https://projects.au.dk/coreorganiccofund/core-organic-cofund-projects/power/). The experiment is continuing within the H2020 PPILOW project (https://www.ppilow.eu/).

While insemination at first estrus is not recommended, most studies agree on the benefits of early puberty, both for reproductive performance and sow longevity. In the swine population in France, sexual maturity is expected at ca. 200 days of age. Although age at puberty is crucial information, it is not recorded on farms. Since selection for low boar taint influences male puberty, it raises questions about its potential side effects on female reproductive ability. This study was carried out as part of a project that assessed impacts of selection against boar taint on the reproduction of Landrace females. The sexual maturity of 1878 gilts at ca. 200 days of age was evaluated on five farms using quantitative plasma progesterone analysis in two blood samples taken 10 days apart. Cutoff values of 2.5 or 5.0 ng/mL gave similar estimates of 19% immature gilts, with a large variation among farms (8-49%). Insemination was not performed for 4% of gilts, 9% were re-inseminated during the first cycle and 15% did not farrow. The rate of earlyreproduction difficulties varied greatly among farms. The influence of immaturity at 200 days was generally low, with a large farm effect. Further investigation is required to analyze long-term effects of late puberty.

International audience; Pig gut microbiota displays high inter-individual variability and it remains an open question to determine to what extent its taxonomic composition relies on host genetic determinism and not only on environmental conditions. We carried out a study to demonstrate coevolution of the host and its gut microbiota established one month post-weaning, by directional selection over two generations. The gut microbiota was characterized by sequencing the V3-V4 variable region of the 16S rRNA gene from fecal samples collected on 60-day-old Large White piglets. Amplicon sequence variants were inferred from amplicon data and the microbial community was further studied at the genus level. Based on the stratification of the initial population (generation G0) according to the two major pig enterotypes, characterized by relative overabundance of either Prevotella and Mitsuokella or Ruminococcus and Treponema, we used the relative abundance of these four genera as selection criteria. From the G0 population of 317 piglets, we selected 6 males and 30 females per line and produced two successive generations (G1 and G2) of approximately 130 pigs per line. We consistently confirmed a moderate heritability for each of the selected genera (h²=0.3 to 0.4). We also estimated the heritability values of the relative abundances for 64 additional bacterial genera, which ranged from 0.1 to 0.5. We showed significant differences between the two lines in the relative abundance of the four bacterial genera at G1 (P

Des odeurs désagréables, qualifiées d’odeur de verrat, peuvent se manifester lors de la cuissonde la viande de porc mâle entier. C’est en partie ce phénomène qui motive la pratiquede la castration à vif des porcelets mâles. Dans le but d’améliorer le bien-être des animauxd’élevage, la réglementation française interdit, depuis le 1er janvier 2022, cette pratique. C’estl’accumulation dans les tissus adipeux de composés tels que l’androsténone, stéroïde produitdans le testicule, qui est responsable de cette odeur désagréable. L’une des pistes pour faciliterla transition vers l’élevage de porcs non castrés est la sélection génétique d’animaux à faibleteneur en androsténone. Cette stratégie est réaliste compte tenu de l’héritabilité élevée de cecaractère. Pour préciser le déterminisme génétique de l’odeur de verrat, deux régions QTL associéesà ce caractère ont été retenues pour identifier des gènes candidats fonctionnels. Deuxméthodologies de GWAS ont été utilisées. Le QTL du SSC2 a été localisé par les deux méthodescontrairement à celui du SSC6. Les GWAS ont permis de définir une première région de 4 Mbsur le SSC2 et une région de 5 Mb sur le SSC6, très riche en gènes. Afin de mieux caractériser cesrégions, des analyses transcriptomiques par RNAseq ont été réalisées sur deux ensembles de 20verrats, sélectionnés sur la base de leurs haplotypes à ces deux QTL. Pour chaque région QTL,2 haplotypes ont été conservés, les animaux sélectionnés représentant les trois génotypes pources 2 haplotypes (homozygotes ou hétérozygotes). Pour la région située sur le chromosome 6,plusieurs gènes présentent une différence d’expression significative avec un niveau d’expressioncorrélé au génotype, extrêmes pour les homozygotes et intermédiaire pour l’hétérozygote. Nousprésenterons ces résultats et discuterons d’éventuels biais méthodologiques de cette démarche degénomique fonctionnelle.

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.

Crossbreeding in livestock can be used to increase genetic diversity. The resulting increase in variability is related to the heterozygosity of the crossbred animal. The evolution of diversity during crossbreeding can be assessed using genomic data. The objective of this study was to describe patterns of runs of homozygosity (ROH) in animals resulting from three-way crossbreeding, from parental pure lines, and in their crossbred offspring. The crossbreeding scheme consisted of a first crossbreeding Pietrain boars and Large White sows, after which the offspring of the Pietrain × Large White were crossed with Duroc boars. The offspring of the second crossbreeding are called G0, the offspring of G0 boars and G0 sows are called G1. All the animals were genotyped using the Illumina SNP60 porcine chip. After filtering, analyses were performed with 2,336 animals and 48,579 autosomal single nucleotide polymorphism (SNP). The mean ROH-based inbreeding coefficients were shown to be 0.27 ± 0.05, 0.23 ± 0.04, and 0.26 ± 0.04 for Duroc, Large White, and Pietrain, respectively. ROH were detected in the Pietrain × Large White crossbred but the homozygous segments were fewer and smaller than in their parents. Similar results were obtained in the G0 crossbred. However, in the G1 crossbreds the number and the size of ROH were higher than in G0 parents. Similar ROH hotspots were detected on SSC1, SSC4, SSC7, SSC9, SSC13, SSC14, and SSC15 in both G0 and G1 animals. Long ROH (>16 Mb) were observed in G1 animals, suggesting regions with low recombination rates. The conservation of these homozygous segments in the three crossbred populations means that some haplotypes were shared between parental breeds. Gene annotation in ROH hotspots in G0 animals identified genes related to production traits including carcass composition and reproduction. These findings advance our understanding of how to manage genetic diversity in crossbred populations.

International audience

Pig gut microbiota displays high inter-individual variability and it remains an open question to determine to what extent its taxonomic composition relies on host genetic determinism and not only on environmental conditions. We will illustrate links between host genetics and gut microbiota composition by reporting results from different experiments carried out on Large White pig cohorts. Under similar controlled feeding and environmental conditions, we have shown that the gut microbiota after weaning can be consistently classified into two enterotypes by sequencing the V3-V4 variable region of the 16S rRNA gene from fecal DNA. The two enterotypes are characterized by either an overabundance of the genera Prevotella and Mitsuokella or Ruminococcus and Treponema. We explored the contribution of host genetics to the gut microbiota composition by estimating genetic parameters and by launching a directional selection based on the enterotype assignment of 60-day-old pigs. Calculated heritabilities of the relative abundance of fecal microbiota bacteria genera and the response to selection confirmed a significant contribution of host genetics to microbiota variability. The results on this ongoing selection experiment should help to investigate coevolution of the gut microbiota with its host.

International audience

International audience

National audience; To reduce genotyping costs for genomic selection, a Low-Density SNP (LD) chip, designed in 2016, is now used routinely. This panel is composed of approximately 1100 equidistant SNPs. The relevance of this chip has been studied in French populations of the Landrace, Large White and Pietrainpig breeds. The quality of imputation was estimated by the correlation between actual and imputed genotypes and error rates. The impact of imputation on the genomic evaluations was estimatedby the correlation between the genomic values obtained for the candidates with imputed genotypes, and those obtained with the high-densitygenotypes. Average error rates of imputation estimated on all the chromosomes were 0.03, 0.11 and 0.14for Landrace, Large White and Pietrain, respectively. The estimated correlations between actual and imputed genotypes were relativelyhigh at 0.93, 0.92 and 0.88forLandrace, Large White and Pietrain populations,respectively. Correlations between genomicbreedingvalues predicted with high-density genomicdata or imputed genomic data from the LD SNP panel rangedfrom0.89-0.97 for Large White and Landrace populations for reproductivetraits. They were higher than those obtained for the Pietrain population (0.80and 0.97for production traits, respectively). In conclusion, despite the limited number of SNPs on the low-density panel used in this study, the imputation accuracyis sufficient to use the imputed genotypes in the genomic evaluations. In practice, genotyping candidates with aLD chip is a solution for selecting future breeding pigsat lower cost.

La castration des porcelets mâles a pour but de diminuer les risques de comportement agressif et d’éviter des défauts de qualité de viande. En effet, chez certains mâles entiers, l’androsténone (molécule produite dans les testicules) et le scatol (produit par les bactéries du tube digestif) s’accumulent dans le gras et donnent une odeur désagréable à la viande. Dans une perspective d’élevage de mâles entiers, une sélection contre l’accumulation d’androsténone dans le gras est envisagée, mais les éventuels effets négatifs sur la reproduction restent à analyser. L’objectif de l’étude est d’évaluer les relations entre l’accumulation d’androsténone dans le gras dorsal, la mise en place de la puberté chez les jeunes verrats, le comportement sexuel et les caractéristiques de la semence chez les verrats matures. Un phénotypage fin a été réalisé sur 114 verrats dans l’unité expérimentale INRA GenESI. Chaque verrat totalise jusqu’à 455 observations comprenant des mesures de production spermatique, des dosages d’androsténone et de scatol dans le gras dorsal et d’hormones plasmatiques (testostérone et œstradiol) à 180 jours et à 280 jours d’âge, des observations du comportement (débourrage, maintien de l’aptitude au prélèvement de semence et test de confiance vis-à-vis de l’homme) et des caractéristiques de semence. Des analyses multivariées ont été effectuées pour estimer les relations entre ces mesures. Les résultats suggèrent que l’œstradiol plasmatique peut servir de prédicteur de l’androsténone et qu’il n’y a pas de lien entre l’androsténone, les caractéristiques de la semence et le comportement sexuel des verrats., Male piglets are castrated to reduce the risk of aggressive behavior and improve meat quality. In some entire males, androstenone (from testes) and skatole (produced by the gut bacteria) accumulate in fat and give an unpleasant smell to the meat. Genetic selection against androstenone accumulation in back fat in entire males has been considered to overcome boar taint in carcasses, but possible side effects on reproductive traits have to be investigated. The objective of the study was to evaluate the relationship between androstenone accumulation in back fat, beginning of puberty, sexual behavior and semen characteristics in mature boars.To meet this objective, fine phenotyping of 114 boars was performed at the INRA GenESI experimental station. Each boar represented up to 455 observations, tests or samples, including concentrationsof androstenone and skatole in back fat, concentrations of hormones in blood at 180 and 280 days of age, behavioral observations (breaking, maintaining libido and test of confidence in humans) and semen characteristics. Multivariate analysis was performed to estimate the relationships between variables. Results suggest that plasma œstradiol may predict androstenone and that there was no relationship between androstenone, semen characteristics, and boar libido

To reduce genotyping costs for genomic selection, a Low-Density SNP (LD) chip, designed in 2016, is now used routinely. This panel is composed of approximately 1 100 equidistant SNPs. The relevance of this chip has been studied in French populations of the Landrace, Large White and Pietrain pig breeds. The quality of imputation was estimated by the correlation between actual and imputed genotypes and error rates. The impact of imputation on the genomic evaluations was estimated by the correlation between the genomic values obtained for the candidates with imputed genotypes, and those obtained with the high-density genotypes. Average error rates of imputation estimated on all the chromosomes were 0.03, 0.11 and 0.14 for Landrace, Large White and Pietrain, respectively. The estimated correlations between actual and imputed genotypes were relatively high at 0.93, 0.92 and 0.88 forLandrace, Large White and Pietrain populations, respectively. Correlations between genomic breeding values predicted with high-density genomic data or imputed genomic data from the LD SNP panel ranged from 0.89-0.97 for Large White and Landrace populations for reproductive traits. They were higher than those obtained for the Pietrain population (0.80 and 0.97 for production traits, r espectively). In conclusion, despite the limited number of SNPs on the low-density panel used in this study, the imputation accuracy is sufficient to use the imputed genotypes in the genomic evaluations. In practice, genotyping candidates with a LD chip isa solution for selecting future breeding pigs at lower cost

National audience; One of the expected benefits of crossbreeding, a common practice in the pig industry, may be the increase in genetic variability, especially in a context of creation of synthetic populations. This increase in variability, related to the heterozygous status of individuals, remains difficult to specify when only genealogical information is available. It is now possible to characterize genetic variability in pig populations at a genome scale by analyzing genotypic data. One possible approach is to detect homozygous regions along the genome to quantify genomic consanguinity in an individual. These homozygous regions can be quantified at the genome or chromosome scale. It is then possible to characterize both overall genomic consanguinity of an individual or a local one in specific areas of the genome. In this study, we used genomic information to estimate inbreeding by detecting homozygous regions in the genomes of purebred Large White dams and Pietrain sires and their crossbred offspring. All individuals were genotyped using the IlluminaSNP60 porcine chip. As expected, fewer homozygous segments were detected in crossbr ed animals than in their parental populations. In addition, the total length of these segments was lower in crossbr ed animals. These observations can be interpreted as a decrease in consanguinity; however, the conservation of homozygous segments in crossbred offspring means that some haplotypes were shared between parental populations.; Un des bénéfices attendus du croisement entre lignées, pratique répandue dans la filière porcine, peut être l’accroissement de variabilité génétique, notamment dans un contexte de création de populations synthétiques. Cette augmentation de la variabilité, liée à l’état hétérozygote des individus, reste difficile à préciser lorsque seule l’information généalogique est disponible. Il est dorénavant possible de caractériser la variabilité génétique présente dans les populations porcines à une échelle génomique via l’analyse de données de génotypage. Une des approches possibles est la détection de régions homozygotes le long du génome, qui permet de quantifier la consanguinité génomique chez un individu. La quantification de ces régions homozygotes pouvant être réalisée à l’échelle du génome ou du chromosome, elle permet de caractériser à la fois la consanguinité génomique globale d’un individu ou une consanguinité locale en des zones plus ciblées du génome. Nous proposons dans cette étude d’utiliser l’information génomique afin d’estimer la consanguinité via la détection de régions homozygotes présentes dans les génomes de reproducteurs de races pures Large White et Piétrain et de leurs produits croisés. L’ensemble des individus a été génotypé sur la puce porcine IlluminaSNP60. Comme attendu, un nombre moins important de segments homozygotes est détecté chez les animaux croisés par rapport aux deux populations parentales. De plus, la longueur totale de ces segments est plus faible chez les animaux croisés. Même si ces observations peuvent être interprétées comme une diminution de la consanguinité, la conservation de segments homozygotes chez les descendants croisés signifie que certains haplotypes sont partagés entre les populations parentales.

International audience

International audience; In pig crossbreeding programs, genetic evaluation has been based predominantly on purebred data accounting only for additive genetic effects, whereas improving crossbred performance is the ultimate goal. Theoretically, a combined crossbred and purebred selection method is advised if genetic correlation between purebred and crossbred populations differ from unity. If dominance effects are large enough, assortative mating strategies can enhance the total genetic values of the offspring. Hence, estimates of genetic parameters for purebreds and crossbreds are needed to assess the best selection crossbreeding scheme strategies. In this study, additive and dominance genetic variance components and additive and dominance genotypic correlations between a Piétrain and a Piétrain × Large White populations were estimated for backfat thickness (BFT). A total of 607 purebreds and 620 crossbred BFT records were analysed with a genotypic bivariate model that included hot carcass weight and inbreeding coefficient as covariates, an additive and a dominance genotypic effects, and a pen nested within batch random effect. Genetic parameters were estimated with EM-REML plus an additional iteration of AIREML to obtain the asymptotic standard deviations of the estimates. The additive genotypic correlation between purebreds and crossbreds was high, 0.82, indicating that the genetic progress attained in the purebreds can mostly be transferred to the crossbreds. Dominance genetic variance represented about 10% of the BFT phenotypic variance in both populations, suggesting that assortative matings could slightly enhance both purebred and crossbred performances. However, the underlying genetic mechanisms responsible for the dominance effects could differ between populations since dominance genotypic correlation was 0.49.

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International audience

International audience; The effect of divergent selection on adrenocortical activity in Large White pigs on gene expression after ACTH, LPS and social stress challenges. E. Terenina1, C. Dugué1, E. Kulikova2, D. Bazovkina2, L. Gress1, G. Lefort1, Y. Billon3, C. Larzul1 & P. Mormede1 1 GenPhySE, INRA, INPT, ENSAT, Université de Toulouse, 31326 Castanet-Tolosan, France elena.mormede@inra.fr (Corresponding Author) 2 Department of Behavioral Neurogenomics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia 3 GenESI, INRA, Le Magneraud, 17700 Surgères, France The objective of the present experiment is to analyze the expression of candidate genes related to HPA axis and stress in the third generation of selection of two lines of pigs divergently selected on the basis of plasma cortisol levels measured one hour after injection of ACTH. This test allows to objectify the activity level of the hypothalamic-pituitary-adrenal (HPA) axis, a major neuroendocrine system of the stress response. The kinetics of the blood transcriptomic responses to adrenocorticotropic hormone (ACTH), lipopolysaccharide (LPS) and social stress were measured at 4 time points (0, 1h, 4h, and 24h after the challenge). Our results suggest that the responses to these different challenges are not affected in the same way by HPA axis activity. We found 22 differentially expressed genes for the inflammatory stress, 2 genes specific to the response to ACTH injection and 12 genes for the social stress. The expression of studied candidate genes did not differ according to the line. Four genes (MEGF9, S100A9, CERS4 and PSAP) were found to be differentially expressed in the three tests and could therefore be used for the overall study of stress response. With the financial support of the Agence Nationale de la Recherche, program ANR BIOADAPT, project SUSoSTRESS (ANR-12-ADAP-0008).

Notice à Reprendre avec Recueil des Proceedings; This experiment had the goal to analyze responses to various sources of stress (weaning, exposure to heat and pre-slaughter mixing) in the third generation of selection of two lines of pigs genetically selected on the basis of plasma cortisol levels (“high” or “low”) measured one hour after injection of adrenocorticotropin. This test assesses the activity of the adrenocortical axis, a major endocrine system of the stress response. Results show that the high line had a significantly lower post-weaning growth rate. However, its growth rate was higher in the late fattening period, so that the two lines had the same overall growth rate throughout their productive lives. Prolonged exposure to heat (29.9°C vs 26.1°C) during the late fattening period (D133-D158) reduced the growth rate of animals to the same extent in both lines. Group-mixing stress prior to slaughter increased cortisol levels measured in urine collected from the bladder as well as skin lesions on carcasses, and increased muscle pH measured 24h after slaughter. These consequences of pre-slaughter mixing, however, did not differ between lines. These results show that responses to different sources of stress are affected in different ways by the level of adrenocortical activity. Associated with production data, they will allow evaluation of the relevance of this selection criterion for increasing animal robustness.

International audience; This experiment had the objective to analyze responses to various breeding challenges in the third generation of selection of two lines of pigs genetically selected on the basis of plasma cortisol levels measured one hour after injection of ACTH. This test allows to objectify the activity level of the hypothalamic-pituitary-adrenal (HPA) axis, a major neuroendocrine system of the stress response. The results presented here show that the post-weaning growth rate was significantly lower in the high line, although the two lines had the same overall growth rate throughout their productive lives. The effects of a prolonged exposure to high temperature (30°C) and of group mixing stress prior to slaughter did not differ between the lines. These results show that the responses to different challenges are not affected in the same way by the HPA axis activity. These results, together with production data, will allow to evaluate the relevance of this criterion of selection to increase the robustness of animals. With the financial support of the Agence Nationale de la Recherche, program ANR BIOADAPT, project SUSoSTRESS (ANR-12-ADAP-0008). Keywords: genetic selection, cortisol, stress, robustness, heat stress, weaning stress, mixing stress, pig.

International audience; Boar taint in the pork meat from entire male pigs results from the presence of two molecules: androstenone and skatole. The genetic determinism of androstenone and skatole has been studied for a few decades. It is well known that the heritability values are moderate to high and the genetic correlation between both levels is moderately positive. Nevertheless, application of selecting against boar taint has been limited in breeding schemes to obtain low boar taint lines. An important topic is the relationships between boar taint risk and other trait of economic interest. The genetic correlations with production traits such as growth rate, feed efficiency or carcass quality are mostly favourable, and selection applied in sire lines should tend to decrease boar taint. In dam lines, the genetic relationships with reproductive traits still need to be further explored. Some studies showed low correlations between boar taint risk and litter traits or fertility, but other evidences led to the conclusion that selection against boar taint would unfavourably impact female reproductive traits. Several issues have been addressed regarding potential criteria to predict boar taint at slaughter. One of the most promising has been human nose scoring at slaughter house, but relevant predictors are still needed that can directly be measured on live animals. New instrumental methods have to be developed for breeding purposes. In that respect, genomic information and a better understanding of genes involved in boar taint metabolism will provide useful tools for breeding entire males.

International audience

International audience; The overall objective of the COST action IPEMA is to find and disseminate general, region-specific or chain-specific solutions for the development of alternatives to surgical castration of male pigs: entire male production (EM) and immunocastration (IC). IPEMA is looking for integrated solutions taking into account meat quality (boar taint, water holding capacity, tenderness, fat quantity and quality), animal welfare, breeding, nutrition and economy. IPEMA aims to coordinate research between national programmes and fill knowledge gaps between different areas in Europe and between science and relevant stakeholders. The specific objectives are (1) to guide breeding programmes for pork production systems with EM (boar taint, other meat quality traits, behaviour), (2) to develop nutritional concepts for EM and IC (requirements, boar taint, fat quantity and quality), (3) to define EM specific housing, management, transport and slaughter conditions, (4) to evaluate innovations in grading and meat quality control systems (boar taint, other meat quality traits), (5) to assist innovations in the processing industry to adapt products to EM and IC characteristics and to valorise tainted meat, (6) to develop specific information strategies for European countries and export markets and harmonise sensory studies on boar taint. IPEMA started in October 2016 and will finish in September 2020. IPEMA membership currently includes institutions from 22 European countries. IPEMA wants to extend its membership by including more members from (1) the Eastern part of Europe, neighbouring countries and other international partners and (2) all levels of the pig chains: organisation representing the farmers as well as upstream and downstream industry. The IPEMA consortium acknowledges the financial support of the EU, COSTaction CA15215