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International audience; We evaluated the economic and environmental impacts of strategies that incorporated selection for pig feed:gain and dietary optimization based on a single or multiple objectives tailored to meet the population’s nutritional requirements, with the goal to optimize sustainable farm feed efficiency. The economic and environmental features of the strategy were evaluated using life cycle assessment (LCA) and bio-economic models. An individual trait-based LCA model was applied to evaluate global warming potential (GWP), terrestrial acidification potential (AP), freshwater eutrophication potential (EP), and land occupation (LO) of the combined genetics and nutrition optimization to produce 1kg of live pig weighing 120kg at the farm gate. A parametric individual trait-based bio-economic model was developed and applied to determine the cost breakdown, revenue and profit to be gained from a 120kg live pig at the farm gate. Applying the combined genetics and nutrition optimization, the individual performance traits of pigs from two genetic lines with contrasted levels of feed efficiency were simulated with InraPorc in response to diets formulated for least cost, least environmental impacts, or minimum combination of cost and environmental impacts objectives, and accounting for the nutritional requirements of each line. Significant differences in the environmental impacts (P < 0.0001) and profit (P < 0.05) between lines predicted the same reference diet showed that selection for feed efficiency (residual feed intake, RFI) in pigs improves pig production sustainability. When pig responses were simulated with their line optimized diets, except for EP, all the line environmental impacts were less (P < 0.05) than with the reference diet. The high correlations of feed conversion ratio (FCR) with the environmental impacts (> 0.82) and the profit (< -0.88) in both lines underline the importance of feed efficiency as a lever for the sustainability of pig production systems. Implementing combined genetics and nutrition optimization, the inherent profit and environmental differences between the genetic lines was predicted to be reduced from 23.4% with the reference diet to 7.6% with the diet optimized jointly for economic and environmental objectives (joint diet). Consequently, for increased pig sustainability, diet optimization for sustainability objectives should be applied to cover the specific nutritional requirements arising in the herd from the pigs’ genetic level.

International audience; Purpose Use a holistic individual life cycle assessment (LCA) to investigate possible mitigation of environmental impacts through optimisation of overall farm feed efciency by combining animal selection for feed efciency and formulation of diets with minimum environmental impacts tailored to pig nutritional requirements.Methods A linear multi-objective optimisation method was used to combine diet optimisation tailored to meet the representative nutritional requirements of genetic lines with environmental optimisation of the environmental impacts of the diet. Environmental optimisation was obtained by weighting the environmental impacts of the diet in a single environmental impact score. An individual trait-based LCA model with a cradle-to-farm-gate system boundary and functional unit of 1 kg live pig at the farm gate was applied to genetic lines selected for high (LRFI, high feed efcient line) and low (HRFI, low feed efcient line) feed efciency data. The production traits of each individual animal in response to the optimised diets were simulated with InraPorc® and imported into the individual LCA model to assess global warming potential (GWP), terrestrial acidifcation potential (AP), freshwater eutrophication potential (EP), and land occupation (LO) of the overall farm feed efciency approach.Results and discussion Integrating selection for feed efciency, nutritional requirements of genetic lines (HRFI and LRFI) and environmental diet optimisation resulted in overall mitigation of environmental impacts. Compared to the conventional diet, the environmental score of the optimised tailored diets was reduced by 5.8% and 5.2% for LRFI and HRFI lines, respectively. At the general production system level, the environmental impacts decreased by an average of 4.2% for LRFI and 3.8% for HRFI lines compared to environmental impacts of the lines fed the conventional diet (P < 0.05). The HRFI line with its optimised tailored diet had fewer impacts than the LRFI line with the conventional diet, except for EP. Individual LCA revealed high correlations between environmental impacts and feed efciency and protein deposition traits.Conclusions Implementation of overall farm feed efciency would efectively mitigate environmental impacts. A holistic economic evaluation of the resulting trade-of between diet costs and pig performances is now needed

Eberle, U., Smetana, S., Bos, U. (Eds.); International audience; Purpose. European pig production aims at reducing its environmental impacts with various mitigation strategies. Among them, the replacement of Brazilian soybean meal (BSM) associated to deforestation with European protein sources (EPS) combined with the genetic improvement of feedefficiency was tested in the H2020 Feed-A-Gene project. The goal was to estimate the environmental impacts of pig production resulting from incorporating EPS in fattening feeds.Methods. Four EPS were examined: fine fraction of rapeseed meal, partly defatted soybean meals obtained from crushing of dehulled or non-dehulled soybeans, and protein paste extracted from biomass. Environmental impacts per ton of protein for feedstuffs and per kilogram of pig at the farm gate were estimated using life cycle assessment. Benefits were calculated by comparing each EPS scenario with a reference using BSM and traditional protein sources. Least cost formulation defined feed compositions. For current feedstuffs, prices come from four European countries for four contrasting years. Prices of BSM and EPS were considered zero respectively in reference and innovative scenarios in order to maximize their incorporation. Improved genetic was assessed thanks to the comparison of two lines respectively with low and high feed efficiency.Results and discussion. At feedstuff level, the EPS reduce climate change impact more than twice compared to BSM but other impacts could be increased as acidification, eutrophication and land occupation. At pig level, the average incorporation of BSM in the reference fattening diet was 13%. Compared to this baseline, EPS scenarios reduce climate change impacts (by 8-9% for the European soybean meal and by 3-4% for the protein paste and the fine fraction of rapeseed meal) but still with a transfer of impact to land use (increase of 13%). With an additional improved genetic, the reduction on climate change with EPS rises 12-16% and limits the increase of land occupation below 5%. Theseresults show a potential interest of EPS.Conclusions. EPS can’t be considered competitive as a replacement for BSM in the current context in which less than 5% of BSM was currently used in fattening diets due to the relative prices of protein sources. EPS seem interesting for climate change in a context economically favorable to BSM. But because of the transfer of impacts, there is a need for more macroscopic analyses to capture indirect land use effects.

International audience; The objective of Feed-a-Gene (H2020 grant agreement 633531) was to adapt the feed, the animal and the feeding techniques to improve the efficiency and sustainability of monogastric livestock production systems. Efficiency is a complex trait affecting the components of sustainability. Imported soybean meal is a high-quality protein source, but its use can have environmental and social impacts. Technological treatments applied to European-grown protein sources (i.e. soybean meal, rapeseed meal, and green biomass) allow to obtain fractions with different nutritional characteristics that can be fed to different livestock species. Replacing Brazilian soybean meal with locally-produced protein sources reduced energy cost and impact on climate change, but resulted in a transfer of land-use and in more arable land use. Novel traits indicative for feed efficiency were developed and tested (e.g. individual feed intake in broilers, genomic information on nitrogen efficiency, large-scale measurements of digestibility in individual pigs, blood metabolites, and behavioural traits). These traits can be used in livestock management strategies, and digestibility, microbiota, and blood biomarkers appeared promising for genetic selection. Different mathematic models were developed to assess digestive and metabolic efficiency, animal robustness, and variation among animals. A userfriendly tool was developed allowing users to work with these models. Prototypes of precision feeding systems were developed for broilers, growing pigs, and sows. These systems adjust the type of feed to the daily changing nutritional requirements of individual or groups of animals. Precision feeding in pigs reduced key environmental impacts and increased profitability compared to conventional feeding systems.

International audience; Despite major advances, it is estimated that a large part of melanoma predisposing genes remains to be discovered. Animal models of spontaneous diseases are valuable tools and experimental crosses can be used to identify and fine-map new susceptibility loci associated with melanoma. We performed a Genome-Wide Association Study (GWAS) of melanoma occurrence and progression (clinical ulceration and presence of metastasis) in a porcine model of spontaneous melanoma, the MeLiM pig. Five loci on chromosomes 2, 5, 7, 8 and 16 showed genome-wide significant associations ( p < 5 × 10 –6 ) with either one of these phenotypes. Suggestive associations ( p < 5 × 10 –5 ) were also found at 16 additional loci. Moreover, comparison of the porcine results to those reported by human melanoma GWAS indicated shared association signals notably at CDKAL1 and TERT loci but also nearby CCND1 , FTO, PLA2G6 and TMEM 38B-RAD23B loci. Extensive search of the literature revealed a potential key role of genes at the identified porcine loci in tumor invasion ( DST , PLEKHA5, CBY1 , LIMK2 and ETV5 ) and immune response modulation ( ETV5 , HERC3 and DICER1 ) of the progression phenotypes. These biological processes are consistent with the clinico-pathological features of MeLiM tumors and can open new routes for future melanoma research in humans.

International audience; To appoint proper strategy for prospective feed efficient pig farming it is wise to shed light on ongoing selection scenarios. Selection based on residual feed intake (RFI) has been proposed to improve feed efficiency, and potentially reduce the environmental impacts accordingly. Data were collected for pigs from the 5th generation of lines divergently selected for RFI (low line, more efficient pigs, LRFI; high line, less efficient pigs HRFI). Individual records for daily feed intake, body weights and body composition were available for about 60 pigs per line. The averages of feed conversion ratio and daily feed intake in the LRFI pigs were 7% lower than the average of the HRFI pigs according to the records. To compare the effects of the difference in feed efficiency on environmental impacts, a parametric model for life cycle assessment (LCA) was developed based on the net energy fluxes. A nutritional growth pig tool, InraPorc® was integrated as a module into the model to embed the flexibility for change in feed, traits and housing conditions, along with simulating individual pig performance. The comparative LCA showed 6% lower environmental impacts for LRFI on average relative to HRFI, considering climate change (CC), acidification potential (AP), eutrophication potential (EP), land occupation (LO) and water depletion (WD). Impacts of CC, AP,EP, LO and WD for 1 kg live weight of pig as the functional unit were 2.61 kg CO2-eq, 44.8 g SO2-eq, 3.37 g PO4-eq, 4.208 m3, 0.0448 m3 for LRFI, and 2.76 kg CO2-eq, 48 g SO2-eq, 3.62 g PO4-eq, 4.44 m3, 0.047 m3 for HRFI,respectively. Parallel Monte Carlo simulation on input parameters demonstrated that LRFI pigs would have a lower environmental impact than HRFI pigs in more than 70% of the calculations, except for water depletion (55% of the calculations). A once-at-a-time sensitivity analysis revealed that environmental impacts are highly sensitive toprotein content of the body and protein deposition. This correspondence between improvement of feed efficiencyand reduction of environmental impacts is very promising for prospective sustainable breeding objectives.

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.

International audience; The majority of genomic predictions use a unique population split between a reference and a validation set. However, a genomic evaluation using genetically different reference and validation sets could provide more flexibility for the choice of reference sets in small populations. The aim of our study was to investigate the potential of genomic evaluation for feed efficiency related traits using a reference set that combines two different lines. Data came from two lines divergently selected for residual feed intake during 9 generations. Genomic breeding values (GBVs) of animals for five production traits were predicted using the single-step genomic BLUP method with six scenarios. All scenarios aimed to predict GBVs of pigs of the three last generations (~ 400 pigs, G7 to G9) in one or in the other line (validation line). To compare the scenarios prediction accuracy, a first scenario (control) had a reference set with animals from G1 to G6 (~ 400 pigs) of the validation line. In scenario 2, in addition to those of the control scenario, the reference set included about 600 pigs from G4 to G9 of the alternate line. Scenario 3 had ~ 800 pigs in the reference set, by excluding animals from G4 to G6 of the alternate line from the reference set compared to scenario 2. For the last three scenarios, fewer animals from the validation line were included in the reference set (~200 pigs from G4 to G6). In scenario 4, G4 to G9 animals from the alternate line (~600 pigs, as in scenario 2) were included in the reference set. In scenario 5, only ~400 pigs from G7 to G9, and in scenario 6 ~200 pigs from G9, were used. In scenarios 2, 3 and 4, genotyping 400 to 600 additional individuals from the alternate line provided on average limited improvement the prediction accuracies for the five traits (

International audience; To appoint proper strategy for prospective feed efficient pig farming it is wise to shed light on ongoing selection scenarios. Selection based on residual feed intake (RFI) has been proposed to improve feed efficiency, and potentially reduce the environmental impacts accordingly. Data were collected for pigs from the 5th generation of lines divergently selected for RFI (low line, more efficient pigs, LRFI; high line, less efficient pigs HRFI). Individual records for daily feed intake, body weights and body composition were available for about 60 pigs per line. The averages of feed conversion ratio and daily feed intake in the LRFI pigs were 7% lower than the average of the HRFI pigs according to the records. To compare the effects of the difference in feed efficiency on environmental impacts, a parametric model for life cycle assessment (LCA) was developed based on the net energy fluxes. A nutritional growth pig tool, InraPorc® was integrated as a module into the model to embed the flexibility for change in feed, traits and housing conditions, along with simulating individual pig performance. The comparative LCA showed 6% lower environmental impacts for LRFI on average relative to HRFI, considering climate change (CC), acidification potential (AP), eutrophication potential (EP), land occupation (LO) and water depletion (WD). Impacts of CC, AP,EP, LO and WD for 1 kg live weight of pig as the functional unit were 2.61 kg CO2-eq, 44.8 g SO2-eq, 3.37 g PO4-eq, 4.208 m3, 0.0448 m3 for LRFI, and 2.76 kg CO2-eq, 48 g SO2-eq, 3.62 g PO4-eq, 4.44 m3, 0.047 m3 for HRFI,respectively. Parallel Monte Carlo simulation on input parameters demonstrated that LRFI pigs would have a lower environmental impact than HRFI pigs in more than 70% of the calculations, except for water depletion (55% of the calculations). A once-at-a-time sensitivity analysis revealed that environmental impacts are highly sensitive toprotein content of the body and protein deposition. This correspondence between improvement of feed efficiencyand reduction of environmental impacts is very promising for prospective sustainable breeding objectives.

International audience; Genetic improvement of feed efficiency is a major challenge for the sustainability of monogastric animal productions. It also has positive consequences on the environmental impact of livestock, through the reduction of excretion. Two divergent lines are conducted at INRA considering Residual Feed Intake (RFI) as a criterion for selection. In each generation, first parity males were tested during growth to select the 6 boars with the lowest (LRFI line) or highest (HRFI line) RFI. A second parity was produced to evaluate the correlated responses to selection on production and carcass traits on females and castrated males. In total, data comprised records from 1,632 sires and dams (parents from generation G0 to G9), and 2,426 response animals. Dams had no phenotypic records. Genotyping was completed on sires and dams with the Illumina PorcineSNP60 (MD) beadchip (n = 1,632). In addition, the 32 G0 animals most contributing to the pedigree (12 boars and 20 dams) were genotyped using the Illumina high-density (HD) porcine SNP chip. Using the FIMPUTE software (v-2.2), HD genotypes were imputed to all the parents of the design using linkage disequilibrium and pedigree information. Imputation accuracy was assessed based on the correlation between the true and the imputed genotypes, per animal (r = 0.982) and per SNP (r = 0.946). In a second step, genotypes for the 570,440 SNP of the HD SNP chip were imputed to the progeny with phenotypic records and no genotypes (second parity), using the average genotype of the 2 parents. Genome-wide association studies (GWAS) were then performed on those animals for 24 traits (RFI, related traits as average daily gain (ADG), backfat thickness (BFT), and FCR, together with traits related to carcass composition and meat quality). Results from GWAS revealed 198 associations with the traits, including 9 regions associated with RFI. GWAS performed separately in each line revealed significant associations in different genomic regions, indicating that different metabolic pathways were mobilized during the selection. Fine mapping of the detected regions will provide new insights into the genetic basis of feed efficiency in pigs.

International audience

The present study aimed at investigating the impact of heat challenges on gut microbiota composition in growing pigs and its relationship with pigs’ performance and thermoregulation responses. From a total of 10 F1 sire families, 558 and 564 backcross Large White × Créole pigs were raised and phenotyped from 11 to 23 wk of age in temperate (TEMP) and in tropical (TROP) climates, respectively. In TEMP, all pigs were subjected to an acute heat challenge (3 wk at 29 °C) from 23 to 26 wk of age. Feces samples were collected at 23 wk of age both in TEMP and TROP climate (TEMP23 and TROP23 samples, respectively) and at 26 wk of age in TEMP climate (TEMP26 samples) for 16S rRNA analyses of fecal microbiota composition. The fecal microbiota composition significantly differed between the 3 environments. Using a generalized linear model on microbiota composition, 182 operational taxonomic units (OTU) and 2 pathways were differentially abundant between TEMP23 and TEMP26, and 1,296 OTU and 20 pathways between TEMP23 and TROP23. Using fecal samples collected at 23 wk of age, pigs raised under the 2 climates were discriminated with 36 OTU using a sparse partial least square discriminant analysis that had a mean classification error-rate of 1.7%. In contrast, pigs in TEMP before the acute heat challenge could be discriminated from the pigs in TEMP after the heat challenge with 32 OTU and 9.3% error rate. The microbiota can be used as biomarker of heat stress exposition. Microbiota composition revealed that pigs were separated into 2 enterotypes. The enterotypes were represented in both climates. Whatever the climate, animals belonging to the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype were 3.3 kg heavier (P < 0.05) at 11 wk of age than those belonging to the Lactobacillus-dominated enterotype. This latter enterotype was related to a 0.3 °C lower skin temperature (P < 0.05) at 23 wk of age. Following the acute heat challenge in TEMP, this enterotype had a less-stable rectal temperature (0.34 vs. 0.25 °C variation between weeks 23 and 24, P < 0.05) without affecting growth performance (P > 0.05). Instability of the enterotypes was observed in 34% of the pigs, switching from an enterotype to another between 23 and 26 wk of age after heat stress. Despite a lower microbial diversity, the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype was better adapted to heat stress conditions with lower thermoregulation variations.

International audience; Part of the variability of performances in animal production is due to the genetic variation in the level of a trait between animals; that is the keystone of all genetic improvement programs and has to be maintained to guarantee the long-term sustainability of the selection progress. Another part of the performance variability comes from the individual variation of responses to various environmental conditions, called environmental sensitivity, which can have a highly negative impact on the final profitability of the production. Joint estimations of breeding values (EBV) and genetic parameters of the individual environmental sensitivity of a trait can be obtained along with those of the level of the trait. Moreover, use of these two kinds of EBV in genetic programs partly depends on their correlations as well as their genetic relationships with other traits. In pigs, homogeneity of litter size is desired and in many cases its mean level should not decrease. Similar relationships between objectives exist for the birth weight components (mean and variability); homogeneity is desired to ensure good perinatal viability and subsequent growth, but the mean birth weight should also not decrease. The genetic parameters and relationships between components (mean and variability) of birth weight and litter size in pigs will be presented along with similar parameters estimated in a mice experiment. Furthermore, similar estimations were obtained for production traits, such as residual feed intake and growth, which will be discussed in the perspective of producing more efficient and robust animals.

International audience; Finisher pigs tend to be 3-way crossbreds kept in pens of 8-15 in Europe and 20-30 in the Americas, with many exceptions. In theory it is possible to feed finisher pigs individually, but costs and management requirements of automatic feeding systems, and availability of easy to handle decision making software limit their use on commercial farms. Management unit is, therefore, the pen, even though there is still a lot of variation among individual animals (among others, mendelian sampling). In addition, there is phenotypic variation, since piglets differ in birth weight (which is a maternal trait), in colostrum intake and in establishment of gut microbiome coming from their (foster) dam, and later depend on their pen mates influence (activity, hierarchy) and farm ambient conditions. Measuring feed efficiency, and predicting it to feed animals according to requirements given a certain environmental condition, thus remains a challenge, but yet animal sorting options are being put into practice to optimize feeding on a pen level. Alternatives to individual electronic feeder measurements are also tested to produce individual measurements, including on-farm identification of drivers of the biological basis of feed efficiency (genomic and bio-markers) and measurements of components of feed efficiency (body composition, activity, gut microbiome composition). Feed efficiency is (still) mainly energy efficiency, and it has been the main driver of selection until now. However, energy requirements are now most often properly covered, protein efficiency is coming up and other efficiencies (vitamins, minerals) are being explored that might become of interest. In addition, by feeding animals high quality easy to digest feed, feed efficiency is essentially metabolic efficiency, but the increasing diversity of feed resources, including industry byproducts with higher dietary fibre contents, questions the opportunity to now focus on the genetic variability of digestive efficiency.

International audience; Hypothermia is a factor of piglet neonatal mortality. This study used Infra-Red Thermography (IRT) to assess thermoregulation abilities of piglets from two lines divergent for residual feed intake (RFI). At birth, body weight and rectal temperature were recorded from piglets of the 11th generation of the low RFI (LRFI, more efficient; n=34) and the high RFI (HRFI, less efficient; n=28). IRT images were taken at 8, 15, 30 and 60 min post-partum. Temperatures of the ear base and tip, and minimum, maximum and average temperatures of the back (i.e. shoulders to rumps) were extracted with Thermacam Researcher Pro 2.0, and analysed with linear mixed models (SAS 9.4). All temperatures increased overtime. The rectal temperature of piglets at birth was correlated with the initial temperature of the ear base and the maximum back temperature (0.36 and 0.35, respectively, P

International audience; Gut microbiota plays a central role in health and nutrient digestion and would help the host for better coping with environmental perturbations. In tropical conditions or in temperate countries during Summer, elevated ambient temperatures can cause economic losses to the pig industry. During heat stress (HS), the reduction in voluntary feed intake is the main adaptation response for reducing heat production. This lower feed intake has subsequent negative effects on pig performance. The main purpose of this study was to investigate the relationships between HS and gut microbiota composition. A better understanding of the microbiota response to HS could allow the selection for animals well adapted to HS. Genetically related pigs were raised under temperate or tropical farm conditions with mean thermal humidity indexes respectively 23 and 25.5 from 11 to 23 weeks of age. In temperate conditions, pigs were submitted to a 3-week HS challenge at 30 °C. Faecal samples were collected in all pigs at 23 weeks of age in both environments (n=1,200 samples) and at 26 weeks of age in the temperate environment (n=600). Therefore, it was possible to compare microbiota from pigs raised in a temperate environment, a tropical climate, and exposed to HS. Microbiota extracted from pigs under temperate and tropical climate had different compositions whereas pigs exposed to heat challenge or raised in tropical conditions tended to share a common microbiota. HS challenge drastically modified gut microbiota and the groups before and after the challenge could be predicted in a multilevel sparse partial least square discriminant analysis with 30 OTUs and a mean classification error rate of 14%. Our experiment suggests that microbiota can be used as biomarkers of HS exposition.

Dietary fiber content and composition affect microbial composition and activity in the gut, which in turn influence energetic contribution of fermentation products to the metabolic energy supply in pigs. This may affect feed efficiency (FE) in pigs. The present study investigated the relationship between the fecal microbial composition and FE in individual growing-finishing pigs. In addition, the effects of diet composition and sex on the fecal microbiome were studied. Fecal samples were collected of 154 grower-finisher pigs (3-way crossbreeds) the day before slaughter. Pigs were either fed a diet based on corn/soybean meal (CS) or a diet based on wheat/barley/by-products (WB). Fecal microbiome was characterized by 16S ribosomal DNA sequencing, clustered by operational taxonomic unit (OTU), and results were subjected to a discriminant approach combined with principal component analysis to discriminate diets, sexes, and FE extreme groups (10 high and 10 low FE pigs for each diet by sex-combination). Pigs on different diets and males vs. females had a very distinct fecal microbiome, needing only 2 OTU for diet (P = 0.020) and 18 OTU for sex (P = 0.040) to separate the groups. The 2 most important OTU for diet, and the most important OTU for sex, were taxonomically classified as the same bacterium. In pigs fed the CS diet, there was no significant association between FE and fecal microbiota composition based on OTU (P > 0.05), but in pigs fed the WB diet differences in FE were associated with 17 OTU in males (P = 0.018) and to 7 OTU in females (P = 0.010), with 3 OTU in common for both sexes. In conclusion, our results showed a diet and sex-dependent relationship between FE and the fecal microbial composition at slaughter weight in grower-finisher pigs.

International audience; This study aims at assessing the contribution of the additive and dominance genomic variances to the phenotypic expression of several purebred Piétrain and crossbred (Piétrain × Large White) pig performances. A total of 636 purebred and 720 crossbred male piglets were phenotyped for 22 traits that can be classified into the trait groups growth rate and feed efficiency, carcass composition, meat quality, behaviour, boar taint and puberty. Additive and dominance variances estimated in univariate genotypic models including additive and dominance genotypic effects and a genomic inbreeding covariate allowed us to retrieve the additive and dominance SNP variances for purebred and crossbred performances. These estimated variances were used, together with the allelic frequencies of the parental populations, to obtain additive and dominance variances in terms of genomic breeding values and dominance deviations. Estimates of additive genetic variances across traits were consistent with previous results without dominance indicating that additive and dominance genetic effects were non-confounded. Some traits showed a relevant amount of dominance genetic variance in both populations (i.e. growth rate 8%, feed conversion ratio 9-12%, backfat thickness 14-12%, lean meat 10-8%, carcass lesions 9%, in purebreds and crossbreds, respectively) or increased amounts in crossbreds (i.e. ham cut 8-13%, loin 7-16%, pH semimembranosus 13-18%, pH Longissimus dorsi 9-14%, dressing yield 5-15%, androstenone 5-13% and estradiol 6-11%). Results suggest that accounting for dominance in the models of these traits could lead to an increased GEBV accuracy and that using crossbred information can be beneficial to evaluate purebred candidates to selection for crossbred performance. Further research will compare additive and dominance marker effects between crossbred and purebred performances.

International audience; Feed efficiency (FE) is an important trait in the pig industry, as feed costs are responsible for the major part of production costs. Availability in the market and cost of feed ingredients dictate changes in feed composition. As a result, fibre level and composition can vary between pig diets. Microbiota in the gastrointestinal tract play an important role in fibre digestion, because they produce enzymes that break down fibre structures and deliver volatile fatty acids (VFA) to the pig. These VFA can be used as metabolic energy sources. As such, microbial fermentation could influence FE in pigs. The aim of this study was to investigate the association between FE and faecal microbiome in commercial grower-finisher pigs. Three-way crossbreed grower-finisher pigs (154) were either fed a diet based on corn/soybean meal (CS) or a diet based on wheat/barley/by-products (WB). Faecal samples were collected on the day before slaughter (mean body weight 122 kg), and sequenced for the V3-V4 16S ribosomal DNA regions. Sequences we clustered according to operational taxonomic units (OTU) for each individual. A partial least square regression was applied to the dataset, together with a discriminant analysis using principal components of FE extreme groups (10 high and 10 low FE animals for each diet by sex-combination). Pigs on different diets and males vs females had a very distinct microbiome, needing only two OTUs for diet (P=0.018) and 18 OTUs for sex (P=0.002) to separate the groups. Faecal microbiome was not related to FE groups fed the CS diet, but there were sex specific OTUs related to FE in male and female pigs in the groups fed the WB diet. In conclusion, our results show a diet and sex dependent relationship between the faecal microbial composition and FE in grower-finisher pigs at slaughter weight. This study is part of the Feed-a-Gene project and received funding from the European Union’s H2020 program under grant agreement no. 633531.

International audience

Background Animal’s efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI). Results Pigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age. Transcriptomics data were generated from longissimus muscle, liver and two adipose tissues using a porcine microarray and analyzed for the line effect (n = 24 pigs per line). The most apparent effect of the line was seen in muscle, whereas subcutaneous adipose tissue was the less affected tissue. Molecular data were analyzed by bioinformatics and subjected to multidimensional statistics to identify common biological processes across tissues and key genes participating to differences in the genetics of feed efficiency. Immune response, response to oxidative stress and protein metabolism were the main biological pathways shared by the four tissues that distinguished pigs from the low or high RFI lines. Many immune genes were under-expressed in the four tissues of the most efficient pigs. The main genes contributing to difference between pigs from the low vs high RFI lines were CD40, CTSC and NTN1. Different genes associated with energy use were modulated in a tissue-specific manner between the two lines. The gene expression program related to glycogen utilization was specifically up-regulated in muscle of pigs from the low RFI line (more efficient). Genes involved in fatty acid oxidation were down-regulated in muscle but were promoted in adipose tissues of the same pigs when compared with pigs from the high RFI line (less efficient). This underlined opposite line-associated strategies for energy use in skeletal muscle and adipose tissue. Genes related to cholesterol synthesis and efflux in liver and perirenal fat were also differentially regulated in pigs from the low vs high RFI lines. Conclusions Non-productive functions such as immunity, defense against pathogens and oxidative stress contribute likely to inter-individual variations in feed efficiency. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3639-0) contains supplementary material, which is available to authorized users.

International audience

International audience; The objective of the present study was to compare a random regression model, usually used in genetic analyses of longitudinal data, with the structured antedependence (SAD) model to study the longitudinal feed conversion ratio (FCR) in growing Large White pigs and to propose criteria for animal selection when used for genetic evaluation. The study was based on data from 11,790 weekly FCR measures collected on 1,186 Large White male growing pigs. Random regression (RR) using orthogonal polynomial Legendre and SAD models was used to estimate genetic parameters and predict FCR-based EBV for each of the 10 wk of the test. The results demonstrated that the best SAD model (1 order of antedependence of degree 2 and a polynomial of degree 2 for the innovation variance for the genetic and permanent environmental effects, i.e., 12 parameters) provided a better fit for the data than RR with a quadratic function for the genetic and permanent environmental effects (13 parameters), with Bayesian information criteria values of -10,060 and -9,838, respectively. Heritabilities with the SAD model were higher than those of RR over the first 7 wk of the test. Genetic correlations between weeks were higher than 0.68 for short intervals between weeks and decreased to 0.08 for the SAD model and -0.39 for RR for the longest intervals. These differences in genetic parameters showed that, contrary to the RR approach, the SAD model does not suffer from border effect problems and can handle genetic correlations that tend to 0. Summarized breeding values were proposed for each approach as linear combinations of the individual weekly EBV weighted by the coefficients of the first or second eigenvector computed from the genetic covariance matrix of the additive genetic effects. These summarized breeding values isolated EBV trajectories over time, capturing either the average general value or the slope of the trajectory. Finally, applying the SAD model over a reduced period of time suggested that similar selection choices would result from the use of the records from the first 8 wk of the test. To conclude, the SAD model performed well for the genetic evaluation of longitudinal phenotypes.

Gompertz model improves breeding value prediction for feed conversion ratio for incomplete weights. 67. Annual Meeting of the European Association for Animal Production (EAAP)

Responses to weaning in two pig lines divergently selected on residual feed intake depending on diet. 67. Annual Meeting of the European Federation of Animal Science (EAAP)

International audience; Selection for residual feed intake (RFI), which is used to select animals for feed efficiency, also influences nutrient partitioning between growth and maintenance functions. This study was designed to investigate if selection for reduced RFI can alter the trade-off between growth and immunity and contributes to differences in metabolic responses to an inflammatory challenge. Piglets from 2 lines divergently selected on RFI (low: RFI−, n = 10, and high: RFI+, n = 11) were challenged at 55 d of age (on d 0) with complete Freund’s adjuvant (CFA) to induce a noninfectious pneumonia. Plasma haptoglobin and nutrient concentrations (in fasted state and 2 h after feeding) were determined from d −1 to d 7, and tissue protein metabolism was determined on d 8. Haptoglobin concentrations were greater from d 1 to d 7 relative to d −1 (P < 0.01). Feed intake was less on d 1 than on the other days (P < 0.001), as was total AA plasma concentrations at fasted state (P < 0.05). Fasted concentrations of His (P = 0.06) and Trp (P = 0.05) tended to be less, those of Val were less (P < 0.05), and fed concentrations of Lys were increased (P < 0.05) on d 7 compared to d −1. Uremia was less on d 7 than on d −1 at fasted state (P < 0.05), whereas it did not vary at fed state (P > 0.1). Fasted glucose and insulin plasma concentrations were stable across days (P > 0.1). In the fed state and in only RFI+ pigs, glucose concentration was greater on d 1 than on d 3, 5, and 7 (P < 0.05). Total AA, Gln, Ile, Leu, Pro (P < 0.05), and hydroxyproline (P = 0.07) were less in RFI− than RFI+ pigs at fed state, whereas Ala and Gly were less in RFI− pigs at fasted and fed states (P < 0.05). Citrulline (P < 0.05) and Met (P < 0.01) concentrations were greater in RFI− than RFI+ pigs in the fasted state, whereas Asp was greater in RFI− pigs in both fasted and fed states (P < 0.05). On d 8, liver and LM protein synthesis tended to be lower (P = 0.07 and 0.09, respectively) and liver calpain activity was greater (P = 0.07) in RFI− than RFI+ pigs. Liver and LM proteasome did not differ between lines (P > 0.1). The metabolic differences between lines were not associated with differences in feed intake, ADG between d −1 and d 8, and haptoglobin concentration (P > 0.1). Thus, it seems that that, using different metabolic strategies, both lines coped similarly with the CFA challenge. Contrary to our hypothesis, this experiment showed, in young pigs, no advantage of RFI+ animals in response to an inflammatory challenge.

International audience; Selection for residual feed intake (RFI), which is used to select animals for feed efficiency, also influences nutrient partitioning between growth and maintenance functions. This study was designed to investigate if selection for reduced RFI can alter the trade-off between growth and immunity and contributes to differences in metabolic responses to an inflammatory challenge. Piglets from 2 lines divergently selected on RFI (low: RFI−, n = 10, and high: RFI+, n = 11) were challenged at 55 d of age (on d 0) with complete Freund’s adjuvant (CFA) to induce a noninfectious pneumonia. Plasma haptoglobin and nutrient concentrations (in fasted state and 2 h after feeding) were determined from d −1 to d 7, and tissue protein metabolism was determined on d 8. Haptoglobin concentrations were greater from d 1 to d 7 relative to d −1 (P < 0.01). Feed intake was less on d 1 than on the other days (P < 0.001), as was total AA plasma concentrations at fasted state (P < 0.05). Fasted concentrations of His (P = 0.06) and Trp (P = 0.05) tended to be less, those of Val were less (P < 0.05), and fed concentrations of Lys were increased (P < 0.05) on d 7 compared to d −1. Uremia was less on d 7 than on d −1 at fasted state (P < 0.05), whereas it did not vary at fed state (P > 0.1). Fasted glucose and insulin plasma concentrations were stable across days (P > 0.1). In the fed state and in only RFI+ pigs, glucose concentration was greater on d 1 than on d 3, 5, and 7 (P < 0.05). Total AA, Gln, Ile, Leu, Pro (P < 0.05), and hydroxyproline (P = 0.07) were less in RFI− than RFI+ pigs at fed state, whereas Ala and Gly were less in RFI− pigs at fasted and fed states (P < 0.05). Citrulline (P < 0.05) and Met (P < 0.01) concentrations were greater in RFI− than RFI+ pigs in the fasted state, whereas Asp was greater in RFI− pigs in both fasted and fed states (P < 0.05). On d 8, liver and LM protein synthesis tended to be lower (P = 0.07 and 0.09, respectively) and liver calpain activity was greater (P = 0.07) in RFI− than RFI+ pigs. Liver and LM proteasome did not differ between lines (P > 0.1). The metabolic differences between lines were not associated with differences in feed intake, ADG between d −1 and d 8, and haptoglobin concentration (P > 0.1). Thus, it seems that that, using different metabolic strategies, both lines coped similarly with the CFA challenge. Contrary to our hypothesis, this experiment showed, in young pigs, no advantage of RFI+ animals in response to an inflammatory challenge.

Adipose tissue is a primary sensor for nutrient availability and regulates many functions including feed intake and energy homeostasis. This study was undertaken to determine the molecular responses of adipose tissue to differences in feed intake and feed efficiency. Subcutaneous adipose tissue was collected from two lines of pigs divergently selected for residual feed intake (RFI), a measure of feed efficiency defined as the difference between actual and expected feed intake, and from a subset of high-RFI pigs that were feed-restricted at the level of the voluntary feed intake of low-RFI pigs during the growing-finishing period. Transcriptomics analyses indicated that the number of genes that were differentially expressed (P < 0.01) between low- and high-RFI pigs (n = 8 per group at each stage) in adipose tissue was much lower when pigs were considered at 19 kg (postweaning) than at 115 kg BW (market weight). Extended investigations were performed at 115 kg BW to compare low-RFI (n =8), high-RFI (n = 8), and feed-restricted high-RFI (n =8) pigs. They included in silico pathway analyses of the differentially expressed (DE) genes (P < 0.01) and a complementary proteomic investigation to list adipose proteins with a differential abundance (P < 0.10). Only 23% of the DE genes were affected by both RFI and feed restriction. This indicates that the responses of adipose tissue to RFI difference shared only some common mechanisms with feed intake modulation, notably the regulation of cell cycle (including IGF2) and transferase activity pathway. Two carboxylesterase genes (CES1, CES3) involved in lipolysis, were among the most overexpressed genes in the low-RFI pigs; they were also affected by feed restriction within the high-RFI line. About 60% of the molecular changes between low- and high-RFI pigs were specific to genetic divergence in feed efficiency, independently of feed intake. Different genes and proteins known to be associated with mitochondrial oxidative metabolism were overexpressed in adipose tissue of low-RFI pigs compared with high-RFI pigs; other proteins participating in the generation of energy were also affected by feed restriction within the high-RFI line. Finally, mitochondrial antioxidant genes were upregulated in low-RFI pigs vs. high-RFI pigs. Altogether, increased oxidative and antioxidant processes in adipose tissue might be associated with improved feed efficiency.

In crossbreeding schemes, within-line selection of purebred lines mainly aims at improving performance of crossbred progeny in field conditions. The genetic correlation between purebred and crossbred performance is an important parameter to be assessed to ascertain that purebred performance is a good predictor of crossbred performance. With the availability of high density markers, feasibility of using crossbred information for evaluating purebred candidates can be reevaluated. This study implements and applies to real data a single-step terminal-cross model to estimate genetic parameters of several production traits in Pietrain and Pietrain x Large White pigs.Piglets were recorded for growth rate between 35 and 110 kg. Animals were genotyped using the 60K SNP chip. For each trait, purebred and crossbred performances were jointly analyzed. The purebred animals were evaluated through an animal model, whereas the additive genetic effect of a crossbred individual was decomposed into its purebred sire and dam allelic contribution effects. Piétrain genotypes were introduced in genetic evaluation in a single-step procedure. The same model but only accounting for pedigree information was compared to the genomic model in terms of breeding value accuracies obtained from the mixed model equations. Genetic correlation between purebreds and sire allelic contribution to crossbred performance was high (0.84 and 0.79 for the genomic and the pedigree model, respectively). Breeding value accuracies of the genotyped animals obtained with the genomic model outperformed the pedigree model.

The aim of the study was to evaluate the effects of two environment (temperate TEMP vs tropical humid TROP) on production trait and thermoregulatory response of genetically linked growing pigs. Large white (LW) pigs were crossed with tropical pigs from the Creole breed (CR), which is less productive but more thermotolerant than LW. A total of 1,296 half-sib backcross, from 10 (LW x CR) boars and about 65 LW sows in each environment were reared in TROP (n=667) and in TEMP (n=629). TROP was characterized by an average daily ambient temperature (T) of 26.0±0.3 °C and an a'erage daily relative humidity (RH) of 84.5±0.5%. The corresponding values for TEMP were 25.1±0.6 °C and 61.2±3.8% respectively. Live body weight (BW) was measured at the beginning of test (week 11), at weeks 19 and 21, and at the end of test (week 23). Backfat thickness (BT) and cutaneous temperature (CT) were measured at weeks 19 and 23. Rectal temperature (RT) was recorded at weeks 19, 21 and 23. Under TROP, the average daily gain (ADG) during the test and BT were lower than under TEMP (718 vs 813 g/d and 14 vs 18 mm, P

International audience

Heat stress (HS) in pig production is a critical problem intemperate countries during summer but also in tropical areaswhere pig production dramatically increased over the past 2decades. Physiological and metabolic adjustments resultingfrom the thermoregulatory responses to HS have negative consequenceson pig productivity and health. The objectives of thisexperiment were to improve knowledge on the mechanismsunderlining heat tolerance by comparing thermoregulatoryresponses in 3 different pig genotypes (G). This experimentwas performed on a total of 36 castrated male pigs: 1 genotypesensitive to HS (Large White [LW]), 1 genotype tolerant toHS (Créole [CR]), and a cross between LW and CR pigs. Pigswere housed at 24°C for 10 d and thereafter at 32°C for 5 d.The temperature (T) transition from 24 to 32°C occurred on d0 at a constant rate of 2°C/h. Pigs had free access to water andfeed. Body T and respiratory rate were measured on d –7, –4,and –3 at 24°C and on d 1, 2, 3, 4, and 5 at 32°C. Eighteen pigs(6 per G) were slaughtered on d –2 (before the T transition) andon d 5. At slaughter, blood and 3 tissue samples (backfat [BF],longissimus dorsi [LD], and liver [LI]) were collected. A transcriptomeanalysis was performed on blood and tissues usinga semicustom 60K microarray (GPL16524). Blood hormonesand metabolites were also measured. The T × G interactionwas not significant (P > 0.05) for feed intake and thermoregulatoryresponses (except for skin T). Whatever the G, HS hada significant negative effect on voluntary feed intake (–200 g/don average). The T increase resulted in an increased rectal andskin T and respiratory rate within the first 24 to 72 h of exposureand in a subsequent recovery phase characterized bya rapid decrease of these thermoregulatory responses. Plasmaglucose, lactate, glycerol, and albumin concentrations weresignificantly reduced under HS but creatine concentration increasedat 32°C. Thyroid hormone (triiodothyronine and thyroxine)concentrations were reduced at 32°C. Irrespective tothe G, a considerable number of differentially expressed genes(false discovery rate < 0.05) were found by comparing blood(13,807), LD (6,261), BF (5,236), and LI (435) samples collectedat 24°C with those collected at 32°C. A first functionalanalysis revealed that most of the significantly differentiallyexpressed genes especially in BF and LD were involved in theregulation of the oxidative phosphorylation pathway.

National audience

Improving feed efficiency is a relevant strategy to reduce feed cost and environmental waste in livestock production. Selection experiments on residual feed intake (RFI), a measure of feed efficiency, previously indicated that low RFI was associated with lower feed intake, similar growth rate, and greater lean meat content compared with high RFI. To gain insights into the molecular mechanisms underlying these differences, 24 Large White females from 2 lines divergently selected for RFI were examined. Pigs from a low-RFI (“efficient”) and high-RFI (“inefficient”) line were individually fed ad libitum from 67 d of age (27 kg BW) to slaughter at 115 kg BW (n = 8 per group). Additional pigs of the high-RFI line were feed restricted to the daily feed intake of the ad libitum low-RFI pigs (n = 8) to investigate the impact of selection independently of feed intake. Global gene and protein expression profiles were assessed in the LM collected at slaughter. The analyses involved a porcine commercial microarray and 2-dimensional gel electrophoresis. About 1,000 probes were differentially expressed (P < 0.01) between RFI lines. Only 10% of those probes were also affected by feed restriction. Gene functional classification indicated a greater expression of genes involved in protein synthesis and a lower expression of genes associated with mitochondrial energy metabolism in the low-RFI pigs compared with the high-RFI pigs. At the protein level, 11 unique identified proteins exhibited a differential abundance (P < 0.05) between RFI lines. Differentially expressed proteins were generally not significantly affected by feed restriction. Mitochondrial oxidative proteins such as aconitase hydratase, ATP synthase subunit α, and creatine kinase S-type had a lower abundance in the low-RFI pigs, whereas fructose-biphosphate aldolase A and glyceraldehyde-3-phosphate dehydrogenase, 2 proteins involved in glycolysis, had a greater abundance in those pigs compared with high-RFI pigs. Antioxidant proteins such as superoxide dismutase and glutathione peroxidase 3 at the mRNA level and peroxiredoxin-6 at the protein level were also less expressed in LM of the most efficient pigs, likely related to lower oxidative molecule production. Collectively, both the transcriptomic and proteomic approaches revealed a lower oxidative metabolism in muscle of the low-RFI pigs and all these modifications were largely independent of differences in feed intake.

Chantier qualité GA; Residual feed intake (RFI) has been explored as an alternative selection criterion to feed conversion ratio to capture the fraction of feed intake not explained by expected production and maintenance requirements. Selection experiments have found that low RFI in the growing pig is genetically correlated with reduced fatness and feed intake. Selection for feed conversion ratio also reduces sow appetite and fatness, which, together with increased prolificacy, has been seen as a hindrance for sow lifetime performance. The aims of our study were to derive equations for sow RFI during lactation (SRFI) and to evaluate the effect of selection for RFI during growth on sow traits during lactation. Data were obtained on 2 divergent lines selected for 7 generations for low and high RFI during growth in purebred Large Whites. The RFI was measured on candidates for selection (1,065 pigs), and sow performance data were available for 480 sows having from 1 to 3 parities (1,071 parities). Traits measured were sow daily feed intake (SDFI); sow BW and body composition before farrowing and at weaning (28.4 +/- 1.7d); number of piglets born total, born alive, and surviving at weaning; and litter weight, average piglet BW, and within-litter SD of piglet BW at birth, 21 d of age (when creep feeding was available), and weaning. Sow RFI was defined as the difference between observed SDFI and SDFI predicted for sow maintenance and production. Daily production requirements were quantified by litter size and daily litter BW gain as well as daily changes in sow body reserves. The SRFI represented 24% of the phenotypic variability of SDFI. Heritability estimates for RFI and SRFI were both 0.14. The genetic correlation between RFI and SRFI was 0.29 +/- 0.23. Genetic correlations of RFI with sow traits were low to moderate, consistent with responses to selection; selection for low RFI during growth reduced SDFI and increased number of piglets and litter growth, but also increased mobilization of body reserves. No effect on rebreeding performance was found. Metabolic changes previously observed during growth in response to selection might explain part of the better efficiency of the low-RFI sows, decreasing basal metabolism and favoring rapid allocation of resources to lactation. We propose to consider SRFI as an alternative to SDFI to select for efficient sows with reduced input demands during lactation.

International audience

The aim of the study was to evaluate the consequences of a divergent selection for residual feed intake (RFI) during growth in a temperate environment (TEMP) on sow performance in a tropical environment (TROP). Sows came from a selection experiment conducted at INRA in which 2 lines were selected for larger (RFI(+)) or smaller (RFI(─)) feed intake than predicted from performance. In the first analysis, a subsample of data obtained in TROP conditions (49 lactations) was compared to those obtained in TEMP on their sibs mated with the same boars (54 lactations). In the second analysis, data obtained in the TROP environment (82 lactations) were analyzed for testing the effect of season (warm vs. hot) and line on sow performance. Except for the lactation length, the interaction between line and climatic environment was not significant for the others traits (P > 0.05). The ADFI expressed per kilogram of litter BW gain tended to be higher in the RFI(+) line bred in the TROP environment (P = 0.080), together with piglet BW at weaning, which tended to be lower (P = 0.080). The ADFI was lower in TROP than in TEMP (4.56 vs. 5.86 kg/d; P = 0.003), with negative consequence on litter BW gain and maternal BW loss. The RFI(-) sows tended to eat less feed than RFI(+) sows during lactation (4.55 vs. 5.86 kg/d; P = 0.099). Litter BW at weaning was higher in the RFI(─) line. The RFI(─) sows ate significantly less feed to produce 1 kg of litter than the RFI(+) sows and tended to lose a larger amount of BW during lactation than the RFI(+) sows (2.40 vs. 3.02 kg/kg and -0.66 vs. -0.39 kg/d, respectively, P < 0.10). Whatever the line, ADFI was reduced by about 21% in the hot season (P < 0.05). Litter BW gain was depressed (P < 0.05) in the hot season (1.72 vs. 2.08 kg/d in the warm season; P = 0.023). Lactation maternal BW loss tended to increase in the hot season (1.10 vs. 0.71 kg/d in the warm season; P = 0.016), but back fat loss remained constant (P = 0.295). In the TROP environment, the amount of feed required to produce 1 kg of litter was not influenced by the line in the warm season (2.53 kg/kg on average; P = 0.99), but it tended to be lower in the RFI(─) line when compared to the RFI(+) line in the hot season (2.06 vs. 3.45 kg/kg; P = 0.050). This higher apparent efficiency in RFI(─) sows was mainly related to greater maternal body reserve mobilization (i.e., BW and back fat losses). In conclusion, selection for low RFI during growth in a TEMP environment did not impair sow and litter performance in tropical conditions.

National audience

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"Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access "; il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : REPORT; The climate is changing and according to the recent estimates from the IPCC, the likelihood of heatwave events is expected to increase both in number and in intensity. Temperature is projected toincrease from 1.8 to 4.0°C from 1980-1999 to 2090-2099. Hence, heat stress-related costs in pigproduction will be amplified in the future, both in temperate areas (summer heat waves) and tropicalareas (hot and humid environment). Meanwhile, world pig production is moving rapidly to tropicaland subtropical regions reaching now more than 50% of the total production. The world developmentof pig production has been achieved through improvement of animal genetics and management intemperate countries. However, selection performed in optimally controlled conditions has increasedthe sensitivity of animals to high ambient temperature. Heat stressed pigs reduce their feed intakewhich impair their growth or reproduction performances. Management solutions are available toattenuate the effect of heat stress on pigs, such as environmental solutions (water or feedingmanagement). However, these solutions are technically and economically difficult to implement. Thegenetic selection for improving environmental adaptation in pig production is the most promising longterm option. The PigHeaT project aims 1) at identifying QTLs for heat adaptation, by examining directresponses to find genes involved in metabolic ways, indirect responses to find genes affecting growthor robustness to environmental variations, 2) at better understanding the physiological mechanismsunderlying heat adaptation. It will provide tools for improving breeding strategies to face theupcoming global warming, and knowledge to better comprehend the physiological reactions ofanimals submitted to short and long term heat stress. The PigHeaT project is based on originalbiological resources and original experimental facilities. The studied population will be a backcrossbetween Large White pigs, productive but poorly thermotolerant breed, and Creole pigs, lowproductive but highly thermotolerant breed. The progeny issued from this backcross will express allpossible levels of thermal tolerance and production performances when submitted to heat stress,depending on the alleles received from their parents. High throughput phenotyping, metabolomics onall the progeny, and transcriptomics on a subset of extreme pigs selected on thermal toleranceresponse, will be applied. It will allow to refine the phenotypes and to achieve a high level of accuracyin QTL detection in the frame of the PigHeaT project. Additionally, the design will benefit from theunique combination of experimental facilities available at INRA: the first part of the project will relyon the backcross population raised in the experimental facilities located in the West Indies(Guadeloupe, tropical environment). The concomitant production of the same population in theexperimental facilities available in temperate France (Charente Maritime) will allow the detection ofgenetic by environment (GxE) effects for the QTL detected in Guadeloupe. Moreover, a heat wavephenomenon will be systematically simulated in the temperate environment at the end of the growingperiod. As a result, chromosomal regions robust or susceptible to GxE interactions will be identified,GxE being either tropical vs temperate, or tropical vs heat wave. Finally, an integrated analysis of the(fine) phenotypes and QTL will be proposed to better understand the metabolic pathways involved inheat stress responses. The respective use of the QTL and biological knowledge in further breedingstrategies will finally be considered.

Chantier qualité GA; Previous selection experiments using residual feed intake (RFI) to select pigs with a high feed efficiency have reported that a low RFI was associated with a reduced body fat content and a greater muscle glycogen content. In the current study, growing Large White female piglets from 2 lines divergently selected for RFI were used to determine the changes in energy and protein metabolisms in key tissues and their cross talks in response to selection. Pigs of low RFI (RFI(-); n = 26) or high RFI (RFI(+); n = 36) selection lines were offered free access to feed during postweaning and growing periods. Pigs of each line were then slaughtered at 19 kg (n = 8 per line) or 115 kg BW (n = 14 to 18 per line). A third group of pigs of the RFI(+) line was offered feed at the same level per metabolic BW (BW0.60) as RFI- pigs (group RFI+R, n = 14). Regardless of the growth period considered, G:F was less in RFI(+) pigs than in RFI(-) pigs. At 19 kg BW, RFI(+) and RFI(-) pigs had a similar body composition and tissue lipid content. The fractional rate of protein synthesis and proteasome activity were decreased (P < 0.090) in the livers of RFI(+) pigs compared with RFI(-) pigs whereas activities of energy catabolic enzymes did not differ in the liver and LM samples. Plasma insulin was conversely greater (P = 0.049) in RFI(+) pigs at this stage. At 115 kg BW, enzyme activities of protein catabolism in the liver and in the LM did not differ (P > 0.10) between RFI(+) pigs and RFI(-) pigs. Both lactate dehydrogenase activity participating in glucose metabolism and hydroxylacylCoA dehydrogenase activity involved in fatty acid oxidation were greater (P < 0.05) in the liver and LM of RFI(+) pigs compared with RFI(-) pigs. In the liver, contrary to the LM, those differences in enzyme activities were directly associated with selection on RFI regardless of ADFI. Increased backfat depth and content and greater lipid content and adipocyte hypertrophy (P < 0.05) in subcutaneous adipose tissue were reported in RFI(+) pigs compared with RFI(-) pigs at 115 kg BW without marked changes in key lipogenic enzyme activities; these changes were directly associated with ADFI. In conclusion, the present study shows an increase of catabolic pathway activities in the liver and muscle of RFI(+) pigs at market weight that is likely to generate more ATP compared with RFI(-) pigs.

Chantier qualité GA; A QTL analysis of female reproductive data from a 3-generation experimental cross between Meishan and Large White pig breeds is presented. Six F1 boars and 23 F1 sows, progeny of 6 Large White boars and 6 Meishan sows, produced 502 F2 gilts whose reproductive tract was collected after slaughter at 30 d of gestation. Five traits [i.e., the total weight of the reproductive tract, of the empty uterine horns, of the ovaries (WOV), and of the embryos], as well as the length of uterine horns (LUH), were measured and analyzed with and without adjustment for litter size. Animals were genotyped for a total of 137 markers covering the entire porcine genome. Analyses were carried out based on interval mapping methods, using a line-cross regression and a half-full sib maximum likelihood test. A total of 18 genome-wide significant (P < 0.05) QTL were detected on 9 different chromosomes (i.e., SSC 1, 5, 6, 7, 9, 12, 13, 18, and X). Five genome-wide significant QTL were detected for LUH, 4 for weight of the empty uterine horns and WOV, 2 for total weight of the reproductive tract, and 1 for weight of the embryos. Twenty-two additional suggestive QTL were also detected. The largest effects were obtained for LUH and WOV on SSC13 (9.2 and 7.0% of trait phenotypic variance, respectively). Meishan alleles had both positive (e.g., on SSC7) and negative effects (e.g., on SSC13) on the traits investigated. Moreover, the QTL were generally not fixed in founder breeds, and opposite effects were in some cases obtained in different families. Although reproductive tract characteristics had only a moderate correlation with reproductive performances, most of the major QTL detected in this study were previously reported as affecting female reproduction, generally with reduced significance levels. This study thus shows that focusing on traits with high heritability might help to detect loci involved in low heritability major traits for breeding.

Chantier qualité GA; Data were collected in the course of a divergent selection experiment for residual feed intake (RFI) of Large White growing pigs. This data set was used to estimate (i) heritability for RFI and genetic correlations of RFI with growth and carcass traits within the three sexes (male, castrate and female) and (ii) genetic correlations between sexes for these traits. Individual feed intake of animals raised in collective pens was measured by single-place electronic feeders on 1121 males (candidates for selection), 508 females and 535 castrates (sibs of candidates). Variance components were estimated using the REML methodology applied to a multitrait animal model. Estimates of heritability for RFI were 0.16 ± 0.04, 0.16 ± 0.08 and 0.23 ± 0.10 for males, females and castrates, respectively. Estimates of genetic correlations between sexes for homologous traits were not significantly different from 1 (0.88 to 0.99 for RFI, 0.79 to 0.99 for growth traits and 0.65 to 0.99 for carcass composition traits). The relatively low genetic correlations between castrates and males or females for backfat thickness (0.65 and 0.69, respectively) suggest the presence of genotype by sex interactions for this trait.

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An F2 cross between Duroc and Large White pigs was carried out in order to detect quantitative trait loci (QTL) for 11 meat quality traits (L*, a* and b* Minolta coordinates and water-holding capacity (WHC) of two ham muscles, ultimate pH of two ham and one loin muscles), 13 production traits (birth weight, average daily gain during post-weaning and fattening periods, carcass fat depths at three locations, estimated lean meat content, carcass length and weights of five carcass cuts) and three stress hormone-level traits (cortisol, adrenaline and noradrenaline). Animals from the three generations of the experimental design (including 456 F2 pigs) were genotyped for 91 microsatellite markers covering all the autosomes. A total of 56 QTL were detected: 49 reached the chromosome-wide level (suggestive QTL with a maximal probability of 0.05) and seven were significant at the genome-wide level (with a probability varying from 631024 to 331023). Twenty suggestive QTL were identified for ultimate pH, colour measurements and WHC on chromosome (SSC) 5, 6, 7, 8, 9, 11, 13, 14, 15 and 17. For production traits, 33 QTL were detected on all autosomes except SSC6, 8 and 9. Seven of these QTL, located on SSC2, 3, 10, 13, 16 and 17, exceeded the genome-wide significance threshold. Finally, three QTL were identified for levels of stress hormones: a QTL for cortisol level on SSC7 in the cortisol-binding globulin gene region, a QTL for adrenaline level on SSC10 and a QTL for noradrenaline level on SSC13. Among all the detected QTL, seven are described for the first time: a QTL for ultimate pH measurement on SSC5, two QTL affecting birth weight on SSC2 and 10, two QTL for growth rate on SSC15 (during fattening) and 17 (during post-weaning) and two QTL affecting the adrenaline and noradrenaline levels. For each QTL, only one to five of the six F1 sires were found to be heterozygous. It means that all QTL are segregating in at least one of the founder populations used in this study. These results suggest that both meat quality and production traits can be improved in purebred Duroc and Large White pigs through markerassisted selection. It is of particular interest for meat quality traits, which are difficult to include in classical selection programmes.