Social interactions among individuals are ubiquitous both in animals and in plants, and in natural as well as domestic populations. These interactions affect both the direction and the magnitude of responses to selection and are a key factor in evolutionary success of species and in the design of breeding schemes in agriculture. At present, however, very little is known of the contribution of social effects to heritable variance in trait values. Here we present estimates of the direct and social genetic variance in growth rate, feed intake, back fat thickness, and muscle depth in a population of 14,032 domestic pigs with known pedigree. Results show that social effects contribute the vast majority of heritable variance in growth rate and feed intake in this population. Total heritable variance expressed relative to phenotypic variance was 71% for growth rate and 70% for feed intake. These values clearly exceed the usual range of heritability for those traits. Back fat thickness and muscle depth showed no heritable variance due to social effects. Our results suggest that genetic improvement in agriculture can be substantially advanced by redirecting breeding schemes, so as to capture heritable variance due to social effects. S OCIAL interactions among individuals are ubiquitous both in animals and in plants, and in natural as well as domestic populations. These interactions affect both the direction and the magnitude of responses to artificial and natural selection (e.g., Wilham 1963;Hamilton 1964;Griffing 1967;Wade 1977;Frank 1998;Wolf et al. 1998). Social interactions, therefore, are a key factor in the design of artificial breeding programs in domestic species (Denison et al. 2003;Muir 2005) and for the outcome of evolutionary processes in natural populations (e.g., Hamilton 1964;Queller 1992;Frank 1998;Keller 1999;Clutton-Brock 2002).In agriculture, reduction of competitive behaviors is critical for improving animal well-being and productivity in confined high-intensity rearing conditions (Craig and Muir 1996;Kestemont et al. 2003;Muir 2005). Both theoretical and empirical work has shown that the relatedness among interacting individuals and the distribution of selection pressure over the individual and group levels are key factors for response to selection

The increased productivity of sows increases the risk of a more pronounced negative energy balance during lactation. One possibility to prevent this is to increase the lactation efficiency (LE) genetically and thereby increase milk output for a given feed intake and mobilization of body tissue. The benefits of selection for LE depend on its heritability and the relationships with other traits of interest. The objectives of this study were to estimate genetic parameters for LE, its underlying traits, and to predict the consequences of current selection strategies in dam lines. Data from 4 farms were available to estimate genetic parameters. Heritabilities were estimated by using a univariate repeatability model, and genetic correlations were estimated bivariately. Selection index theory was used to predict the genetic progress by 3 alternative breeding programs: 1) a breeding program that aimed at balanced progress in the total number of piglets born, piglet mortality, and percent prolonged interval from weaning to estrus; 2) extension of this breeding goal with LE; and 3) a breeding goal that included only one selection criterion, litter weight gain, to demonstrate the effect of indirect selection for milk production. The heritability for LE was low (0.12). Body fat mass (0.52) and BW (0.45) of sows at the beginning of lactation showed the greatest heritabilities. Protein mass at the beginning of lactation, protein loss, weight loss, and ad libitum feed intake during lactation showed moderate heritabilities (0.39, 0.21, 0.20, and 0.30, respectively). Low to moderate heritabilities were found for litter weight at birth, within-litter SD in the birth weight of piglets, litter weight gain, fat loss, and restricted feed intake during lactation (0.19, 0.09, 0.18, 0.05, and 0.14, respectively). Within-litter SD in the weaning weight of piglets showed no genetic variability. It was predicted that a breeding goal for dam lines with an emphasis on the total number of piglets born, piglet mortality, and percent prolonged interval from weaning to estrus would not dramatically change BW or body composition at the beginning of lactation, or mobilization of body tissue and feed intake during lactation. Inclusion of LE in the breeding goal will improve stayability, as defined by the first-litter survival of sows and LE itself, without negative consequences for other economically important traits. Nevertheless, it might be worthwhile to design a breeding goal in which LE increases and feed intake remains unchanged.

BackgroundGenomic prediction of purebred animals for crossbred performance can be based on a model that estimates effects of single nucleotide polymorphisms (SNPs) in purebreds on crossbred performance. For crossbred performance, SNP effects might be breed-specific due to differences between breeds in allele frequencies and linkage disequilibrium patterns between SNPs and quantitative trait loci. Accurately tracing the breed-of-origin of alleles (BOA) in three-way crosses is possible with a recently developed procedure called BOA. A model that accounts for breed-specific SNP effects (BOA model), has never been tested empirically on a three-way crossbreeding scheme. Therefore, the objectives of this study were to evaluate the estimates of variance components and the predictive accuracy of the BOA model compared to models in which SNP effects for crossbred performance were assumed to be the same across breeds, using either breed-specific allele frequencies ( model) or allele frequencies averaged across breeds ( model). In this study, we used data from purebred and three-way crossbred pigs on average daily gain (ADG), back fat thickness (BF), and loin depth (LD).ResultsEstimates of variance components for crossbred performance from the BOA model were mostly similar to estimates from models and . Heritabilities for crossbred performance ranged from 0.24 to 0.46 between traits. Genetic correlations between purebred and crossbred performance () across breeds ranged from 0.30 to 0.62 for ADG and from 0.53 to 0.74 for BF and LD. For ADG, prediction accuracies of the BOA model were higher than those of the and models, with significantly higher accuracies only for one maternal breed. For BF and LD, prediction accuracies of models and were higher than those of the BOA model, with no significant differences. Across all traits, models and yielded similar predictions.ConclusionsThe BOA model yielded a higher prediction accuracy for ADG in one maternal breed, which had the lowest (0.30). Using the BOA model was especially relevant for traits with a low . In all other cases, the use of crossbred information in models and , does not jeopardize predictions and these models are more easily implemented than the BOA model.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-017-0350-1) contains supplementary material, which is available to authorized users.

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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.