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Background: It is now widespread in livestock and plant breeding to use genotyping data to predict phenotypes with genomic prediction models. In parallel, genomic annotations related to a variety of traits are increasing in number and granularity, providing valuable insight into potentially important positions in the genome. The BayesRC model integrates this prior biological information by factorizing the genome according to disjoint annotation categories, in some cases enabling improved prediction of heritable traits. However, BayesRC is not adapted to cases where markers may have multiple annotations. Results: We propose two novel Bayesian approaches to account for multi-annotated markers through a cumulative (BayesRC+) or preferential (BayesRC π ) model of the contribution of multiple annotation categories. We illustrate their performance on simulated data with various genetic architectures and types of annotations. We also explore their use on data from a backcross population of growing pigs in conjunction with annotations constructed using the PigQTLdb. In both simulated and real data, we observed a modest improvement in prediction quality with our models when used with informative annotations. In addition, our results show that BayesRC+ successfully prioritizes multi-annotated markers according to their posterior variance, while BayesRC π provides a useful interpretation of informative annotations for multi-annotated markers. Finally, we explore several strategies for constructing annotations from a public database, highlighting the importance of careful consideration of this step. Conclusion: When used with annotations that are relevant to the trait under study, BayesRC π and BayesRC+ allow for improved prediction and prioritization of multi-annotated markers, and can provide useful biological insight into the genetic architecture of traits. [ABSTRACT FROM AUTHOR]

Breeding efficient pigs is a way to reduce dietary costs and environmental waste. However, optimization of feed efficiency must not be linked to a decrease of the ability of animals to cope with stress, such as the weaning. This study characterizes the response after weaning of pigs from two lines divergently selected for residual feed intake (RFI) during growth. Animals of the low (L) RFI line are more efficient than animals from the high (H) RFI line. Thirty‐six piglets from each line weaned at 28 days of age were individually housed and fed a conventional dietary sequence. Their performance, behaviour, health and oxidative status, immune and nutritional parameters were followed during three weeks. Daily feed intake and growth rate of pigs from the LRFI line were 35% and 40% lower compared with HRFI (p < 0.001). Pigs from the LRFI‐line had lower total tract apparent digestibility (−6% for OM) and suffered more from undernutrition with a 167 and 55% higher plasmatic concentration of NEFA and urea compared with HRFI (p < 0.01). In the first week after the weaning, they had more diarrhoea and had a higher inflammatory status with concentration of haptoglobin 52% higher (p < 0.001). These piglets then seemed to adapt to the weaning conditions and to recover during the second and third weeks. Both lines had similar zootechnical performance and physiological characteristics at the end of the post‐weaning period. To conclude, the physiological responses to the weaning differed between lines. Pigs from the LRFI line, selected for greater feed efficiency, were more sensitive to the weaning stress. They were also more resilient as they finally adapted to the new condition and recovered to show similar performance results as pigs of the HRFI line. [ABSTRACT FROM AUTHOR]

Weaning is a stress every piglet has to face. It is a main cause of antibiotic uses due to digestive disorders. In this study, response to weaning was analyzed in pigs from two lines divergently selected for residual feed intake (RFI) during growth. A total of 132 pigs from each line, housed per line and diet in conventional postweaning units of 12 castrated males and 12 females, were fed either a conventional control (two successive diets) or a complex (three successive diets) dietary sequence during the postweaning period (4 to 10 wk of age). BWs were recorded at weaning (days 0 and 28 of age), days 1, 2, 6, 12, 19, 26, and 42 (10 wk of age), and at 23 wk of age. Feces texture was examined before weaning (day −1), at day 1, 2, 6, 12, and 19. Feed intake was recorded at pen level from days 0 to 42 after weaning, and individually thereafter. Plasma was collected after blood samplings at days −1, 6, 19, and 42 on half of the piglets: all piglets of a given sex in each pen were sampled, to achieve a balanced number across factors. Pigs of the low RFI (LRFI) line were heavier at weaning, had greater glucose concentration, and lower levels of diarrhea at days 1 and 2 than pigs from the high RFI (HRFI) line (P < 0.01). At day 42, there was no BW difference between lines, and G:F ratio did not differ between lines (P = 0.40). The LRFI pigs had lower feed intake and growth rate from day 0 to day 19 (P < 0.005), and greater plasma concentration of non-esterified fatty acid (P < 0.001), indicating an increased mobilization of body lipids and proteins immediately after weaning compared with HRFI pigs. They also had greater levels of diarrhea at day 6 (22% for LRFI vs. 14% for HRFI, P = 0.002), but the concentration of plasma haptoglobin did not indicate acute inflammation. The complex diet sequence improved feed intake and growth, and reduced diarrhea, mainly in the LRFI line (P < 0.001). To conclude, pigs from the LRFI line were more negatively affected by weaning stress, but managed to recover afterwards. The complex diet sequence ameliorated some of the negative effects that weaning had on the LRFI pigs, but limited effects of nursery period feeding sequence on growth performance were observed during the growing-finishing period. [ABSTRACT FROM AUTHOR]

Recently, a Haley–Knott-type regression method using combined linkage disequilibrium and linkage analyses (LDLA) was proposed to map quantitative trait loci (QTLs). Chromosome of 5 and 25 cM with 0·25 and 0·05 cM, respectively, between markers were simulated. The differences between the LDLA approaches with regard to QTL position accuracy were very limited, with a significantly better mean square error (MSE) with the LDLA regression (LDLA_reg) in sparse map cases; the contrary was observed, but not significantly, in dense map situations. The computing time required for the LDLA variance components (LDLA_vc) model was much higher than the LDLA_reg model. The precision of QTL position estimation was compared for four numbers of half-sib families, four different family sizes and two experimental designs (half-sibs, and full- and half-sibs). Regarding the number of families, MSE values were lowest for 15 or 50 half-sib families, differences not being significant. We observed that the greater the number of progenies per sire, the more accurate the QTL position. However, for a fixed population size, reducing the number of families (e.g. using a small number of large full-sib families) could lead to less accuracy of estimated QTL position. [ABSTRACT FROM AUTHOR]

Background: In previous studies, a major QTL affecting fatness and growth has been mapped to pig chromosome 1q (SSC1q) using Large White - Meishan intercrosses. A higher fat depth and a larger growth rate have been reported for the allele of MS origin. Additionally the LW allele showed partial dominance effects over the MS allele for both traits. In order to refine the QTL mapping interval, advanced backcross generations were produced. Recombinant heterozygous sires were mated to LW sows in order to progeny test the sire segregation of the QTL and refine the QTL localisation. However due to the partial dominance of the LW allele, BC scheme using LW as the receiving population was not optimal. Results: To overcome the difficulties related to the dominance of the LW QTL allele, a population of dams locally homozygous for the MS haplotype in the QTL region, but with an overall 29/32 LW genetic background, has been set up. Progeny testing results, using these receiver dams, were much more significant than those previously obtained with LW dams, and the SSC1 QTL interval was refined to 8 cM. Considering the results obtained, a powerful experimental design for farm animals is proposed, mimicking locally genetically identical strains used in mouse for QTL fine mapping. Conclusions: We have further characterized the fatness QTL on pig chromosome 1 and refined its map position from a 30 cM interval to a 8 cM interval, using a locally congenic BC design. We have obtained highly significant results and overcome difficulties due to the dominance of the LW allele. This design will be used to produce additional, advanced BC families to further refine this QTL localization. [ABSTRACT FROM AUTHOR]

A multivariate QTL detection was carried out on fatness and carcass composition traits on porcine chromosome 7 (SSC7). Single-trait QTLs have already been detected in the SLA region, and multivariate approaches have been used to exploit the correlations between the traits to obtain more information on their pattern: almost 500 measurements were recorded for backfat thickness (BFT1, BFT2), backfat weight (BFW) and leaf fat weight (LFW) but only about half that number for intramuscular fat content (IMF), affecting the detection. First, groups of traits were selected using a backward selection procedure: traits were selected based on their contribution to the linear combination of traits discriminating the putative QTL haplotypes. Three groups of traits could be distinguished based on successive discriminant analyses: external fat (BFT1, BFT2), internal fat (LFW, IMF) and BFW. At least four regions were distinguished, preferentially affecting one or the other group, with the SLA region always influencing all the traits. Meishan alleles decreased all trait values except IMF, confirming an opportunity for marker-assisted selection to improve meat quality with maintenance of carcass composition based on Meishan alleles. [ABSTRACT FROM AUTHOR]

Feed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relatively low-(LRFI) and high- (HRFI) residual feed intake (RFI). Feeding behavior and metabolic differences have been previously reported between the two lines. We hypothesized that part of these differences could be related to differential sensing and absorption of nutrients in the proximal intestine. We investigated the duodenum transcriptome and DNA methylation profiles comparing overnight fasting with ad libitum feeding in LRFI and HRFI pigs (n = 24). We identified 1,106 differentially expressed genes between the two lines, notably affecting pathways of the transmembrane transport activity and related to mitosis or chromosome separation. The LRFI line showed a greater transcriptomic response to feed intake than the HRFI line. Feed intake affected genes from both anabolic and catabolic pathways in the pig duodenum, such as rRNA production and autophagy. Several nutrient transporter and tight junction genes were differentially expressed between lines and/or by short-term feed intake. We also identified 409 differentially methylated regions in the duodenum mucosa between the two lines, while this epigenetic mark was less affected by feeding. Our findings highlighted that the genetic selection for feed efficiency in pigs changed the transcriptome profiles of the duodenum, and notably its response to feed intake, suggesting key roles for this proximal gut segment in mechanisms underlying feed efficiency. [ABSTRACT FROM AUTHOR]

The present research has estimated the additive and dominance genetic variances of genic and intergenic segments for average daily gain (ADG), backfat thickness (BFT) and pH of the semimembranosus dorsi muscle (PHS). Further, the predictive performance using additive and additive dominance models in a purebred Piétrain (PB) and a crossbred (Piétrain × Large White, CB) pig population was assessed. All genomic regions contributed equally to the additive and dominance genetic variations and lead to the same predictive ability that did not improve with the inclusion of dominance genetic effect and inbreeding in the models. Using all SNPs available, additive genotypic correlations between PB and CB performances for the three traits were high and positive (> 0.83) and dominance genotypic correlation was very inaccurate. Estimates of dominance genotypic correlations between all pairs of traits in both populations were imprecise but positive for ADG-BFT in CB and BFT-PHS in PB and CB with a high probability (> 0.98). Additive and dominance genotypic correlations between BFT and PHS were of different sign in both populations, which could indicate that genes contributing to the additive genetic progress in both traits would have an antagonistic effect when used for exploiting dominance effects in planned matings. [ABSTRACT FROM AUTHOR]

Trade‐offs between life history traits are expected to occur due to the limited amount of resources that organisms can obtain and share among biological functions, but are of least concern for selection responses in nutrient‐rich or benign environments. In domestic animals, selection limits have not yet been reached despite strong selection for higher meat, milk or egg yields. Yet, negative genetic correlations between productivity traits and health or fertility traits have often been reported, supporting the view that trade‐offs do occur in the context of nonlimiting resources. The importance of allocation mechanisms in limiting genetic changes can thus be questioned when animals are mostly constrained by their time to acquire and process energy rather than by feed availability. Selection for high productivity traits early in life should promote a fast metabolism with less energy allocated to self‐maintenance (contributing to soma preservation and repair). Consequently, the capacity to breed shortly after an intensive period of production or to remain healthy should be compromised. We assessed those predictions in mammalian and avian livestock and related laboratory model species. First, we surveyed studies that compared energy allocation to maintenance between breeds or lines of contrasting productivity but found little support for the occurrence of an energy allocation trade‐off. Second, selection experiments for lower feed intake per unit of product (i.e. higher feed efficiency) generally resulted in reduced allocation to maintenance, but this did not entail fitness costs in terms of survival or future reproduction. These findings indicate that the consequences of a particular selection in domestic animals are much more difficult to predict than one could anticipate from the energy allocation framework alone. Future developments to predict the contribution of time constraints and trade‐offs to selection limits will be insightful to breed livestock in increasingly challenging environments. [ABSTRACT FROM AUTHOR]

We evaluated the economic and environmental impacts of strategies that incorporated selection for pig feed efficiency and dietary optimization based on a single or multiple objectives tailored to meet the population 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, terrestrial acidification potential, freshwater eutrophication potential (EP), and land occupation of the combined genetics and nutrition optimization to produce 1 kg of live pig weighing 120 kg 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 120-kg live pig at the farm gate. Data from two genetic lines with contrasted levels of feed efficiency were used to apply the combined genetics and nutrition optimization: accounting for the average nutritional requirements for each line, the individual pig responses to diets formulated for least cost, least environmental impacts, or minimum combination of costs and environmental impacts objectives were predicted with INRAPorc. Significant differences in the environmental impacts (P < 0.0001) and profit (P < 0.05) between lines predicted with the same reference diet showed that selection for feed efficiency (residual feed intake) 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 lower (P < 0.05) than with the reference diet. The high correlations of feed conversion ratio with the environmental impacts (> 0.82) and the profit (< −0.88) in both lines underlined 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 were 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. [ABSTRACT FROM AUTHOR]

The aim of this experiment was to evaluate the significance of neonatal environment on feed efficiency. For that purpose, rabbits from a line selected for residual feed intake (RFI) during 10 generations (G10 kits) were cross‐fostered with non‐selected control does (i.e., G0 line), and reciprocally. In parallel, sibs were fostered by mothers from their original line. Nine hundred animals were raised in individual (N = 456) or collective (N = 320) cages. Traits analysed in this study were body weight at 32 days and at 63 days, average daily gain (ADG), feed intake between weaning and 63 days (FI), feed conversion ratio (FCR) and RFI. The maternal environment offered by does from the line selected for RFI deteriorated the FCR of the kits, independently of their line of origin, during fattening (+0.08 ± 0.02) compared to FCR of kits nursed by G0 does. The line, the type of housing and the batch were significant effects for all the measured traits: G10 kits were lighter than their G0 counterparts at 32 days (−82.9 ± 9 g, p < 0.0001) and at 63 days (−161 ± 16 g, p < 0.0001). They also had a lower ADG (−2.36 ± 0.36 g/day, p < 0.0001), RFI (−521 ± 24 g/day, p < 0.0001) and a lower FI (−855 ± 31 g, p < 0.0001), resulting in a more desirable feed efficiency (FCR: −0.35 ± 0.02). There was no significant difference in the contrast of G10 and G0 performances between collective and individual/digestive cages (p > 0.22): −2.35 g/day versus 2.94 g/day for ADG, −0.39 versus −0.40 for FCR, −577 g versus −565 g for RFI and −879 g versus −859 g for FI, respectively). Thus, no genotype‐by‐environment (housing) interaction is expected at the commercial level, that is, no re‐ranking of the animals due to collective housing. [ABSTRACT FROM AUTHOR]

Together with environmental factors, physiological maturity at birth is a major determinant for neonatal survival and postnatal development in mammalian species. Maturity at birth is the outcome of complex mechanisms of intra-uterine development and maturation during the end of gestation. In pig production, piglet preweaning mortality averages 20% of the litter and thus, maturity is a major welfare and economic concern. Here, we used both targeted and untargeted metabolomic approaches to provide a deeper understanding of the maturity in a model of lines of pigs divergently selected on residual feed intake (RFI), previously shown to have contrasted signs of maturity at birth. Analyses were conducted on plasma metabolome of piglets at birth and integrated with other phenotypic characteristics associated to maturity. We confirmed proline and myo-inositol, previously described for their association with delayed growth, as potential markers of maturity. Urea cycle and energy metabolism were found more regulated in piglets from high and low RFI lines, respectively, suggesting a better thermoregulation ability for the low RFI (with higher feed efficiency) piglets. [ABSTRACT FROM AUTHOR]

Heat stress affects pig metabolism, health and welfare, resulting in reduced growth and important economic losses. The present experiment aimed to evaluate the effects of two climatic environments [temperate (TEMP) vs. tropical humid (TROP)] on feeding behaviour in growing pigs. The feeding behaviour traits were measured with automated feeders and included: daily feed intake, daily eating time, feeding rate, daily number of meals, feed intake per meal, and feeding time per meal. Pigs came from a backcross population between Large White (LW, heat sensitive) and Creole (CR, heat tolerant) pigs. The same 10 F1 LW × CR boars (sire families [SF]) were mated with related LW sows in each environment. Feeding behaviour was recorded for a total of 1,296 pigs (n = 634 pigs for TEMP and n = 662 pigs for TROP) between 11 and 23 weeks of age. Growth performance and thermoregulatory responses (rectal and skin temperatures) were also measured. Results show that TROP conditions affect feeding behaviour traits: animals had more meals per day but these meals were smaller both in duration and in size, resulting in lower daily feed intake and less time eating per day. Significant SF by environment (GxE) interactions were found for all feeding behaviour traits. When SF were distributed into robust and sensitive groups (previously defined according to performance and thermoregulatory traits), results showed group by environment interactions for all feeding traits, except meal frequency. Moreover, a significant difference in feeding rate between robust and sensitive group was detected in TEMP, suggesting that feeding rate may be a good candidate to evaluate heat tolerance. [ABSTRACT FROM AUTHOR]

Background: Improving feed efficiency (FE) is an important goal due to its economic and environmental significance for farm animal production. The FE phenotype is complex and based on the measurements of the individual feed consumption and average daily gain during a test period, which is costly and time-consuming. The identification of reliable predictors of FE is a strategy to reduce phenotyping efforts. Results: Gene expression data of the whole blood from three independent experiments were combined and analyzed by machine learning algorithms to propose molecular biomarkers of FE traits in growing pigs. These datasets included Large White pigs from two lines divergently selected for residual feed intake (RFI), a measure of net FE, and in which individual feed conversion ratio (FCR) and blood microarray data were available. Merging the three datasets allowed considering FCR values (Mean = 2.85; Min = 1.92; Max = 5.00) for a total of n = 148 pigs, with a large range of body weight (15 to 115 kg) and different test period duration (2 to 9 weeks). Random forest (RF) and gradient tree boosting (GTB) were applied on the whole blood transcripts (26,687 annotated molecular probes) to identify the most important variables for binary classification on RFI groups and a quantitative prediction of FCR, respectively. The dataset was split into learning (n = 74) and validation sets (n = 74). With iterative steps for variable selection, about three hundred's (328 to 391) molecular probes participating in various biological pathways, were identified as important predictors of RFI or FCR. With the GTB algorithm, simpler models were proposed combining 34 expressed unique genes to classify pigs into RFI groups (100% of success), and 25 expressed unique genes to predict FCR values (R2 = 0.80, RMSE = 8%). The accuracy performance of RF models was slightly lower in classification and markedly lower in regression. Conclusion: From small subsets of genes expressed in the whole blood, it is possible to predict the binary class and the individual value of feed efficiency. These predictive models offer good perspectives to identify animals with higher feed efficiency in precision farming applications. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the genetic relationship between faecal microbial composition and five feed efficiency (FE) and production traits, residual feed intake (RFI), feed conversion ratio (FCR), daily feed intake (DFI), average daily gain (ADG) and backfat thickness (BFT). A total of 588 samples from two experimental pig lines developed by divergent selection for RFI were sequenced for the 16 rRNA hypervariable V3‐V4 region. The 75 genera with less than 20% zero values (97% of the counts) and two α‐diversity indexes were analysed. Line comparison of the microbiota traits and estimations of heritability (h2) and genetic correlations (rg) were analysed. A non‐metric multidimensional scaling showed line differences between genera. The α‐diversity indexes were higher in the LRFI line than in the HRFI line (p <.01), with h2 estimates of 0.19 ± 0.08 (Shannon) and 0.12 ± 0.06 (Simpson). Forty‐eight genera had a significant h2 (>0.125). The rg of the α‐diversities indexes with production traits were negative. Some rg of genera belonging to the Lachnospiraceae, Ruminococcaceae, Prevotellaceae, Lactobacillaceae, Streptococcaceae, Rikenellaceae and Desulfovibrionaceae families significantly differed from zero (p <.05) with FE traits, RFI (3), DFI (7) and BFT (11). These results suggest that a sizable part of the variability of the gut microbial community is under genetic control and has genetic relationships with FE, including diversity indicators. It offers promising perspectives for selection for feed efficiency using gut microbiome composition in pigs. [ABSTRACT FROM AUTHOR]

The use of diets with increased dietary fibre content (HF) from alternative feedstuffs is a solution to limit the impact of increased feed costs on pig production. This study aimed at determining the impact of an alternative HF diet on pig digestibility and at estimating genetic parameters of this trait. Digestibility coefficients (DC) of energy, organic matter and nitrogen were predicted from faecal samples analysed with near infrared spectrometry for 1,242 samples, and it represented 654 Large White pigs fed a conventional (CO) diet and 588 fed a HF diet. Growth and feed efficiency traits, carcass composition and meat quality traits were recorded. Pigs fed the HF diet had significantly lower DC than pigs fed the CO diet (−4.5 to 6.0 points). The DC were moderately to highly heritable (about 0.26 ± 0.12 and 0.54 ± 0.15 in the CO and the HF diet, respectively). Genetic correlations were favourable with feed conversion ratio, daily feed intake and residual feed intake, but unfavourable with average daily gain (ADG) and carcass yield (CY). To conclude, DC could be an interesting trait to include in future breeding objectives if pigs were fed diet with HF diets, but adverse genetic trends with ADG and CY would have to be taken into account. [ABSTRACT FROM AUTHOR]

Non‐genetic information (epigenetic, microbiota, behaviour) that results in different phenotypes in animals can be transmitted from one generation to the next and thus is potentially involved in the inheritance of traits. However, in livestock species, animals are selected based on genetic inheritance only. The objective of the present study was to determine whether non‐genetic inherited effects play a role in the inheritance of residual feed intake (RFI) in two species: pigs and rabbits. If so, the path coefficients of the information transmitted from sire and dam to offspring would differ from the expected transmission factor of 0.5 that occurs if inherited information is of genetic origin only. Two pigs (pig1, pig2) and two rabbits (rabbit1, rabbit2) datasets were used in this study (1,603, 3,901, 5,213 and 4,584 records, respectively). The test of the path coefficients to 0.5 was performed for each dataset using likelihood ratio tests (null model: transmissibility model with both path coefficients equal to 0.5, full model: unconstrained transmissibility model). The path coefficients differed significantly from 0.5 for one of the pig datasets (pig2). Although not significant, we observed, as a general trend, that sire path coefficients of transmission were lower than dam path coefficients in three of the datasets (0.46 vs 0.53 for pig1, 0.39 vs 0.44 for pig2 and 0.38 vs 0.50 for rabbit1). These results suggest that phenomena other than genetic sources of inheritance explain the phenotypic resemblance between relatives for RFI, with a higher transmission from the dam's side than from the sire's side. [ABSTRACT FROM AUTHOR]

Pig production systems provide multiple benefits to humans. However, the global increase in meat consumption has profound consequences for our earth. This perspective describes two alternative scenarios for improving the sustainability of future pig production systems. The first scenario is a high input–high output system based on sustainable intensification, maximizing animal protein production efficiency on a limited land surface at the same time as minimizing environmental impacts. The second scenario is a reduced input–reduced output system based on selecting animals that are more robust to climate change and are better adapted to transform low quality feed (local feeds, feedstuff co‐products, food waste) into meat. However, in contrast to the first scenario, the latter scenario results in reduced predicted yields, reduced production efficiency and possibly increased costs to the consumer. National evaluation of the availability of local feed and feedstuff co‐product alternatives, determination of limits to feed sourced from international markets, available land for crop and livestock production, desired production levels, and a willingness to politically enforce policies through subsidies and/or penalties are some of the considerations to combine these two scenarios. Given future novel sustainable alternatives to livestock animal protein, it may become reasonable to move towards an added general premium price on 'protein from livestock animals' to the benefit of promoting higher incomes to farmers at the same time as covering the extra costs of, politically enforced, welfare of livestock animals in sustainable production systems. © 2020 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Heat stress affects pig health, welfare, and production, and thus the economic viability of the pig sector in many countries. Breeding for heat tolerance is a complex issue, increasingly important due to climate change and the development of pig production in tropical areas. Characterizing genetic determinism of heat tolerance would help building selection schemes dedicated to high performance in tropical areas. The main objective of our study was to estimate the genetic parameters for production and thermoregulation traits in two highly related growing pig populations reared in temperate (TEMP) or tropical humid (TROP) environment. Pigs came from a backcross population between Large White (LW , heat sensitive) and Creole (CR , heat tolerant) pigs. Phenotypic data were obtained on a total of 1,297 pigs using the same procedures in both environments, for body weight (BW, at weeks 11 and 23), daily feed intake (ADFI), backfat thickness (BFT , at weeks 19 and 23), cutaneous temperature (CT , at weeks 19 and 23), and rectal temperature (RT , at weeks 19, 21, and 23). Feed conversion ratio (FCR) and residual feed intake (RFI) were computed for the whole test period (11 to 23 wk). Criteria comparing the fits to the data revealed genotype × environment (G × E) interactions for most traits but not for FCR. The variance components were obtained using two different methods, a restricted maximum likelihood method and a Bayesian Markov chain Monte Carlo method, considering that traits are either similar or different in each environment. Regardless of the method, heritability estimates for production traits were moderate to high, except for FCR (lower than 0.18). Heritability estimates for RT were low to moderate, ranging from 0.04 to 0.34. The genetic correlations of each trait between environments generally differed from 1, except for FCR and ADG. For most thermoregulation traits, they also did not differ significantly from zero, suggesting that the main genetic bases of heat tolerance may vary in different environment. Within environments, the unfavorable genetic correlations between production traits and RT suggest an antagonism between the ability to maintain inner temperature and the ability to increase ADFI and ADG. However, greater RT were also associated to leaner pigs and better feed efficiency. Nevertheless, due to large inaccuracies of these estimations, larger cohorts would be needed to decide about the best breeding schemes to choose for tropical pig production. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The negative impact of heat stress (HS) on the production performances in pig faming is of particular concern. Novel diagnostic methods are needed to predict the robustness of pigs to HS. Our study aimed to assess the reliability of blood metabolome to predict the sensitivity to chronic HS of 10 F1 (Large White × Creole) sire families (SF) reared in temperate (TEMP) and in tropical (TROP) regions (n = 56±5 offsprings/region/SF). Live body weight (BW) and rectal temperature (RT) were recorded at 23 weeks of age. Average daily feed intake (AFDI) and average daily gain were calculated from weeks 11 to 23 of age, together with feed conversion ratio. Plasma blood metabolome profiles were obtained by Nuclear Magnetic Resonance spectroscopy (1HNMR) from blood samples collected at week 23 in TEMP. The sensitivity to hot climatic conditions of each SF was estimated by computing a composite index of sensitivity (Isens) derived from a linear combination of t statistics applied to familial BW, ADFI and RT in TEMP and TROP climates. A model of prediction of sensitivity was established with sparse Partial Least Square Discriminant Analysis (sPLS-DA) between the two most robust SF (n = 102) and the two most sensitive ones (n = 121) using individual metabolomic profiles measured in TEMP. The sPLS-DA selected 29 buckets that enabled 78% of prediction accuracy by cross-validation. On the basis of this training, we predicted the proportion of sensitive pigs within the 6 remaining families (n = 337). This proportion was defined as the predicted membership of families to the sensitive category. The positive correlation between this proportion and Isens (r = 0.97, P < 0.01) suggests that plasma metabolome can be used to predict the sensitivity of pigs to hot climate. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The molecular mechanisms underlying feed efficiency need to be better understood to improve animal efficiency, a research priority to support a competitive and sustainable livestock production. This study was undertaken to determine whether pig blood transcriptome was affected by differences in feed efficiency and by ingested nutrients. Growing pigs from two lines divergently selected for residual feed intake (RFI) and fed isoproteic and isocaloric diets contrasted in energy source and nutrients were considered. Between 74 and 132 days of age, pigs (n = 12 by diet and by line) received a regular diet rich in cereals and low in fat (LF) or a diet where cereals where partially substituted by lipids and fibers (HF). At the end of the feeding trial, the total number of white blood cells was not affected by the line or by the diet, whereas the red blood cell number was higher (P<0.001) in low RFI than in high RFI pigs. Analysis of the whole blood transcriptome using a porcine microarray reveals a higher number of probes differentially expressed (DE) between RFI lines than between diets (2,154 versus 92 probes DE, P<0.01). This corresponds to 528 overexpressed genes and 477 underexpressed genes in low RFI pigs compared with high RFI pigs, respectively. Overexpressed genes were predominantly associated with translational elongation. Underexpressed genes were mainly involved in the immune response, regulation of inflammatory response, anti-apoptosis process, and cell organization. These findings suggest that selection for RFI has affected the immune status and defense mechanisms of pigs. Genes DE between diets were mainly related to the immune system and lipid metabolism. Altogether, this study demonstrates the usefulness of the blood transcriptome to identify the main biological processes affected by genetic selection and feeding strategies. [ABSTRACT FROM AUTHOR]

Deciphering the molecular architecture of coat coloration for a better understanding of the biological mechanisms underlying pigmentation still remains a challenge. We took advantage of a rabbit French experimental population in which both a pattern and a gradient of coloration from white to brown segregated within the himalayan phenotype. The whole experimental design was genotyped using the high density Affymetrix® AxiomOrcun™ SNP Array and phenotyped into 6 different groups ordered from the lighter to the darker. Genome-wide association analyses pinpointed an oligogenic determinism, under recessive and additive inheritance, involving genes already known in melanogenesis (ASIP , KIT , MC1R , TYR), and likely processed pseudogenes linked to ribosomal function, RPS20 and RPS14. We also identified (i) gene-gene interactions through ASIP:MC1R affecting light cream/beige phenotypes while KIT : RPS responsible of dark chocolate/brown colors and (ii) a genome-wide epistatic network involving several others coloration genes such as POT1 or HPS5. Finally, we determined the recessive inheritance of the English spotting phenotype likely involving a copy number variation affecting at least the end of the coding sequence of the KIT gene. Our analyses of coloration as a continuous trait allowed us to go beyond much of the established knowledge through the detection of additional genes and gene-gene interactions that may contribute to the molecular architecture of the coloration phenotype. • Deciphering the molecular architecture of coat coloration still remains a challenge. • Gene-gene interactions contribute to the coloration of body extremities. • RPS processed pseudogenes are likely involved in the coloration of body extremities. • A CNV affecting the KIT gene is likely involved in the English spotting phenotype. [ABSTRACT FROM AUTHOR]

The objective of this study was to evaluate the performance and thermoregulatory responses during acclimation to high ambient temperature (Ta) of pigs from two lines selected for high (RFI) or low (RFI) residual feed intake with the hypothesis that RFI pigs producing less heat would better tolerate high Ta. Pigs (50 kg initial body weight; 17 per line among which 10 of them were catheterized) were individually housed in a climatic-controlled room where Ta was maintained at 24.2 ± 0.4 °C during 7 days and thereafter at 30.4 ± 0.7 °C during 14 days. Irrespective of Ta, RFI pigs had lower feed intake (ADFI) and similar average daily gain (ADG) than RFI pigs. Whatever the line, ADFI, ADG, and feed efficiency decreased with increased Ta. Overall, the Ta increase resulted in an increase in rectal temperature (RT), skin temperature (ST), and respiratory rate (RR) within the first 24-48 h and, subsequently, in a decrease followed by stabilization. The RT decrease during acclimation occurred 24 h earlier in RFI pigs than in RFI. Thyroid hormones and cortisol decreased at high Ta and it was similar in both lines. Based on performance and RT, ST, and RR responses, it seems that selection for low RFI tends to ameliorate pigs' tolerance to high Ta. Nevertheless, this selection does not induce significant differences between lines in endocrine and metabolite responses during thermal stress. [ABSTRACT FROM AUTHOR]

Some sheep breeds are naturally prolific, and they are very informative for the studies of reproductive genetics and physiology. Major genes increasing litter size (LS) and ovulation rate (OR) were suspected in the French Grivette and the Polish Olkuska sheep populations, respectively. To identify genetic variants responsible for the highly prolific phenotype in these two breeds, genome-wide association studies (GWAS) followed by complementary genetic and functional analyses were performed. Highly prolific ewes (cases) and normal prolific ewes (controls) from each breed were genotyped using the Illumina OvineSNP50 Genotyping Beadchip. In both populations, an X chromosome region, close to the BMP15 gene, harbored clusters of markers with suggestive evidence of association at significance levels between 1E-05 and 1E-07. The BMP15 candidate gene was then sequenced, and two novel non-conservative mutations called FecXGr and FecXO were identified in the Grivette and Olkuska breeds, respectively. The two mutations were associated with the highly prolific phenotype (pFecXGr = 5.98E-06 and pFecXo = 2.55E-08). Homozygous ewes for the mutated allele showed a significantly increased prolificacy (FecXGr/FecXGr, LS = 2.50±0.65 versus FecX+r/FecXGr, LS = 1.93±0.42, p<1E-03 and FecXO/ FecXO, OR = 3.286±.85 versus FecX+/FecXO, OR = 2.02±0.47, p,1E-03). Both mutations are located in very well conserved motifs of the protein and altered the BMP15 signaling activity in vitro using a BMP-responsive luciferase test in COV434 granulosa cells. Thus, we have identified two novel mutations in the BMP15 gene associated with increased LS and OR. Notably, homozygous FecXGr/ FecXGr Grivette and homozygous FecXO/ FecXO Olkuska ewes are hyperprolific in striking contrast with the sterility exhibited by all other known homozygous BMP15 mutations. Our results bring new insights into the key role played by the BMP15 protein in ovarian function and could contribute to a better understanding of the pathogenesis of women9s fertility disorders. [ABSTRACT FROM AUTHOR]

Cutaneous melanoma arises from transformed melanocytes and is caused mainly by environmental effects such as ultraviolet radiation and to a lesser extent by predisposing genetic variants. Only a few susceptibility genes for cutaneous melanoma have been identified so far in human; therefore, animal models represent a valuable alternative for genetic studies of this disease. In a previous quantitative trait locus (QTL) study, several susceptibility regions were identified in a swine biomedical model, the MeLiM (Melanoblastoma-bearing Libechov minipig) pigs. This article details the fine-mapping of a QTL located on SSC13 ( Sus scrofa chromosome 13) through an increase in marker density. New microsatellites were used to confirm the results of the first analysis, and MITF (microphthalmia-associated transcription factor) was selected as a candidate gene for melanoma development. A single-marker association analysis was performed with single-nucleotide polymorphisms (SNPs) spread over the locus, but it did not reveal a significant association with diverse melanoma-related traits. In parallel, MITF alternative transcripts were characterized and their expression was investigated in different porcine tissues. The obtained results showed a complex transcriptional regulation concordant with the one present in other mammals. Notably, the ratio between MITF+ and MITF− isoforms in melanoma samples followed the same pattern as in human tumors, which highlights the adequacy of the MeLiM pig as a model for human melanoma. In conclusion, although MITF does not seem to be the causal gene of the QTL initially observed, we do not exclude a prominent role of its transcription and function in the outbreak and evolution of the tumors observed in pigs. [ABSTRACT FROM AUTHOR]

Background: Improving feed efficiency (FE) is a major challenge in pig production. This complex trait is characterized by a high variability. Therefore, the identification of predictors of FE may be a relevant strategy to reduce phenotyping efforts in breeding and selection programs. The aim of this study was to investigate the suitability of expressed muscle genes in prediction of FE traits in growing pigs. The approach considered different transcriptomics experiments to cover a large range of FE values and identify reliable predictors. Results: Microarrays data were obtained from longissimus muscles of two lines divergently selected for residual feed intake (RFI). Pigs (n = 71) from three experiments belonged to generations 6 to 8 of selection, were fed either a diet with a standard composition or a diet rich in fiber and lipids, received feed ad libitum or at restricted level, and weighed between 80 and 115 kg at slaughter. For each pig, breeding value for RFI was estimated (RFI-BV), and feed conversion ratio (FCR) and energy-based feed conversion ratio (FCRe) were calculated during the test periods. Gradient boosting algorithms were used on the merged muscle transcriptomes to identify very important predictors of FE traits. About 20,405 annotated molecular probes were commonly expressed in longissimus muscle across experiments. Six to 267 expressed muscle genes covering a variety of biological processes were found as important predictors for RFI-BV (R2 = 0.63–0.65), FCR (R2 = 0.61–0.70) and FCRe (R2 = 0.49–0.52). The error of prediction was less than 8% for FCR. Altogether, 56 predictors were common to RFI-BV and FCR. Expression levels of 24 target genes were further measured by qPCR. Linear regression confirmed the good accuracy of combining mRNA levels of these genes to fit FE traits (RFI-BV: R2 = 0.73, FRC: R2 = 0.76; FCRe: R2 = 0.75). Stepwise regression procedure highlighted 10 genes (FKBP5, MUM1, AKAP12, FYN, TMED3, PHKB, TGF, SOCS6, ILR4, and FRAS1) in a linear combination predicting FCR and FCRe. In addition, FKBP5 and expression levels of five other genes (IGF2, SERINC3, CSRNP3, EZR and RPL16) significantly contributed to RFI-BV. Conclusion: It was possible to identify few genes expressed in muscle that might be reliable predictors of feed efficiency. [ABSTRACT FROM AUTHOR]

A correction to the article "Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex" by Lisanne M.G. Verschuren and colleagues that was published in the April 2018 issue is presented.

A letter to the editor is presented that discusses the prompt and safe retrieval of discarded needles as an effective approach in preventing community-acquired needle-stick injuries.