Thirty pelleted diets were given to broiler chickens (eight birds per diet; 21 to 35 days of age) for individual in vivo measurements of dietary net energy (NE) value, using three trials with 10 diets/trial. Amino acid formulation of diets was done on the basis of ratios to CP. NE was measured according to the body analysis method. The basal metabolism component of NE values was calculated on the basis of mean metabolic weight using a coefficient obtained in a previous experiment. Information about apparent metabolisable energy (AME) value of diets, AME corrected to zero nitrogen retention (AMEn) and digestibilities of proteins, lipids, starch and sugars was available from a previous publication. In each trial, mean NE/AME ratios of diets varied by about 6%. From the multiple regressions (n=30) expressing NE and AMEn values as functions of digestible component contents, it was deduced that the NE/AMEn ratios assigned to dietary components were 0.760, 0.862, 0.806, 0.690 and 0.602 for CP, lipids, starch, (sucrose+glucose) and fermentable sugars (α-galacto-oligosaccharides and lactose), respectively. The NE/AME ratio of CP was 0.680. Regression calculations showed that the NE values assigned to individual birds (n=240) could also be predicted with diet AMEn values (NE=0.80 AMEn; R 2=0.770) or with an equation combining AMEn value and CP/AMEn ratio (R 2=0.773). The latter ratio was found to be the only additional parameter that was significant when added in the NE regression scheme based on AMEn.

Piglet survival is a major problem, especially during the first 3 days after birth. Piglets are born deficient of energy, but at the same time they have a very high energy requirement because of high physical activity, high need for thermoregulation (because of their lean body with low insulation) and high heat production in muscle tissues. To be able to survive, newborn piglets may rely upon three different sources of energy, namely, glycogen, colostrum and transient milk, which orchestrate to cover their energy requirements. Piglets are born with limited amounts of energy in glycogen depots in the liver and muscle tissues and these depots are sufficient for normal activity for ∼16 h. Intake and oxidation of fat and lactose from colostrum must supply sufficient amount of energy to cover at least another 18 h until transient milk becomes available in the sow udder ∼34 h after the first piglet is born. Selection for large litters during the last two decades has challenged piglets even further during the critical neonatal phase because the selection programs indirectly decreased birth weight of piglets and because increased litter size has increased the competition between littermates. Different attempts have been made to increase the short-term survival of piglets, that is, survival until day 3 of lactation, by focusing on improving transfer of vital maternal energy to the offspring, either in utero or via mammary secretions. Thus, the present review addresses how sow nutrition in late gestation may favor survival of newborn piglets by increasing glycogen depots, improving colostrum yield or colostrum composition, or by increasing production of transient milk.

Enteric Escherichia coli infections are a highly relevant cause of disease and death in young pigs. Breeding genetically resistant pigs is an economical and sustainable method of prevention. Resistant pigs are protected against colonization of the intestine through the absence of receptors for the bacterial fimbriae, which mediate adhesion to the intestinal surface. The present work aimed at elucidation of the mode of inheritance of the F4ad receptor which according to former investigations appeared quite confusing. Intestines of 489 pigs of an experimental herd were examined by a microscopic adhesion test modified in such a manner that four small intestinal sites instead of one were tested for adhesion of the fimbrial variant F4ad. Segregation analysis revealed that the mixed inheritance model explained our data best. The heritability of the F4ad phenotype was estimated to be 0.7±0.1. There are no relations to the strong receptors for variants F4ab and F4ac. Targeted matings allowed the discrimination between two F4ad receptors, that is, a fully adhesive receptor (F4adRFA) expressed on all enterocytes and at all small intestinal sites, and a partially adhesive receptor (F4adRPA) variably expressed at different sites and often leading to partial bacterial adhesion. In pigs with both F4ad receptors, the F4adRPA receptor is masked by the F4adRFA. The hypothesis that F4adRFA must be encoded by at least two complementary or epistatic dominant genes is supported by the Hardy–Weinberg equilibrium statistics. The F4adRPA receptor is inherited as a monogenetic dominant trait. A comparable partially adhesive receptor for variant F4ab (F4abRPA) was also observed but the limited data did not allow a prediction of the mode of inheritance. Pigs were therefore classified into one of eight receptor phenotypes: A1 (F4abRFA/F4acR+/F4adRFA); A2 (F4abRFA/F4acR+/F4adRPA); B (F4abRFA/F4acR+/F4adR−); C1 (F4abRPA/F4acR−/F4adRFA); C2 (F4abRPA/F4acR−/F4adRPA); D1 (F4abR−/F4acR−/F4adRFA); D2 (F4abR−/F4acR−/F4adRPA); E (F4abR−/F4acR−/F4adR−).

The aim of this study was to estimate genetic parameters for feed intake recorded as farmers’ perception of young sows’ appetite for the first 3 weeks of lactation (APP) and feed intake recorded for one day in the 3rd week of lactation (FEED), litter weight (LW) at 3 weeks, sow body condition at weaning (BC) and the following five reproduction traits: weaning-to-service interval of 1 to 7 days (WSI7), weaning-to-service interval of 1 to 50 days (WSI50), delayed service or not (DELAYED), pregnant on first service or not (PREGNANT) and litter size in 2nd parity (NBT2). The analyses included data on 4606 Norwegian Landrace 1st-parity sows and their litters. The Gibbs sampling method was used. The traits DELAYED and PREGNANT were analysed as threshold traits and APP, FEED, LW, BC, WSI7, WSI50 and NBT2 were analysed as linear traits. The heritability estimates for APP and FEED were low (<0.1), whereas the estimates for DELAYED and PREGNANT were rather high (0.4 and 0.3). The heritability estimate for BC was 0.2. The genetic correlations confirmed the complexity of breeding for sow performance; selection for heavy 1st litters may lead to lower body condition at weaning, which in turn leads to lower reproductive performance and smaller litters in 2nd parity. Selection for higher sow feed intake would improve body condition, but the simple way of measuring feed intake tested in this study (APP and FEED) cannot be recommended because of the low heritability obtained for these traits.

An experiment of a 2×2 full diallelic cross between two contemporary Iberian pig strains (Retinto: RR, and Torbiscal: TT) was conducted to estimate the crossbreeding effects for growth and carcass traits. Phenotypic records were obtained under intensive management and consisted of two different data sets. The first set comprised growth traits until weaning and was collected at two different farms (6236 and 1208 records, respectively). Specific data included individual piglet weight at birth and at weaning at 28 days and average daily gain from birth to weaning at 28 days (ADG28) for both RR and TT and their reciprocal crosses. The second set comprised growth data from birth to slaughter (~340 days and ~160 kg) and carcass traits from 349 individuals (randomly) sampled at weaning from the first dataset. Data were analyzed through a Bayesian analysis by using a reparameterization of Dickerson’s model that allowed estimation of the posterior distributions of the following crossbreeding effects: average maternal breed effect (gM), average paternal breed effect (gP) and individual heterosis (hI). Results showed that the relative magnitude of crossbreeding effects depends on the trait analyzed. Crosses where Torbiscal strain was used as mother (RT and TT) achieved the greatest performance for all growth traits at weaning, leading to remarkable gM effects. The most outstanding example is the case of ADG28 where the probability of relevance was one. In contrast, TR cross showed the greatest differences from RR cross for all growth at slaughter and carcass traits. These differences were mainly due to hI and gP crossbreeding parameters. In particular, the posterior mean of hI was more noticeable for live weight at slaughter, average daily gain at slaughter and carcass length, while gP was more relevant for hams (kg) and loins (kg) representing from 3% to10% of average performance of traits. Hence, growth traits at weaning did not reveal any notable advantage of the crossbreeding scheme because of the superiority of the Torbiscal strain with respect to its mothering ability and the small hI. However, results from growth and carcass traits at slaughter would support the implementation of a TR crossbred system. It would allow exploitation of both the gP of the Torbiscal strain and the hI between these two Iberian pig strains. Additionally, gP estimates and phenotypic differences between reciprocal crosses might suggest signs of the presence of paternal genetic imprinting in primal cuts traits.

In livestock, many studies have reported the results of imputation to 50k single nucleotide polymorphism (SNP) genotypes for animals that are genotyped with low-density SNP panels. The objective of this paper is to review different measures of correctness of imputation, and to evaluate their utility depending on the purpose of the imputed genotypes. Across studies, imputation accuracy, computed as the correlation between true and imputed genotypes, and imputation error rates, that counts the number of incorrectly imputed alleles, are commonly used measures of imputation correctness. Based on the nature of both measures and results reported in the literature, imputation accuracy appears to be a more useful measure of the correctness of imputation than imputation error rates, because imputation accuracy does not depend on minor allele frequency (MAF), whereas imputation error rate depends on MAF. Therefore imputation accuracy can be better compared across loci with different MAF. Imputation accuracy depends on the ability of identifying the correct haplotype of a SNP, but many other factors have been identified as well, including the number of genotyped immediate ancestors, the number of animals with genotypes at the high-density panel, the SNP density on the low- and high-density panel, the MAF of the imputed SNP and whether imputed SNP are located at the end of a chromosome or not. Some of these factors directly contribute to the linkage disequilibrium between imputed SNP and SNP on the low-density panel. When imputation accuracy is assessed as a predictor for the accuracy of subsequent genomic prediction, we recommend that: (1) individual-specific imputation accuracies should be used that are computed after centring and scaling both true and imputed genotypes; and (2) imputation of gene dosage is preferred over imputation of the most likely genotype, as this increases accuracy and reduces bias of the imputed genotypes and the subsequent genomic predictions.

Crib-biting in horses is a stereotypic oral behaviour. Genetic susceptibility has been suggested on a causal basis, together with environmental factors such as stress, gastric discomfort and frustration caused by stall restrictions. This study aimed to test the associations of known or suspected stereotypic genes with equine crib-biting, including Ghrelin, Ghrelin receptor, Leptin, Dopamine receptor, μ-opioid receptor, N-cadherin, Serotonin receptor and Semaphorin. We conducted a candidate gene study with a case–control design, including 98 crib-biting and 135 control horses of two breeds, Finnhorses and half-breds. Detailed phenotypic information on crib-biting behaviour was surveyed through an owner-completed questionnaire. Control horses were more than 10 years old and without a history of crib-biting. Single nucleotide polymorphisms flanking the candidate genes were genotyped using either Sanger sequencing or Taqman assays. According to the survey, the affected horses started crib-biting at a young age, had exhibited crib-biting for more than a year, and expressed the behaviour after feeding or when stressed. Comparison of allele frequencies between the cases and controls for each breed separately did not provide evidence of an association at any of the tested loci. These results suggest that the previously known stereotypic genes are not major risk factors for crib-biting in horses, and further genome-wide studies are warranted on larger sample cohorts.

Feed is a major component of variable costs associated with dairy systems and is therefore an important consideration for breeding objectives. As a result, measures of feed efficiency are becoming popular traits for genetic analyses. Already, several countries account for feed efficiency in their breeding objectives by approximating the amount of energy required for milk production, maintenance, etc. However, variation in actual feed intake is currently not captured in dairy selection objectives, although this could be possible by evaluating traits such as residual feed intake (RFI), defined as the difference between actual and predicted feed (or energy) intake. As feed intake is expensive to accurately measure on large numbers of cows, phenotypes derived from it are obvious candidates for genomic selection provided that: (1) the trait is heritable; (2) the reliability of genomic predictions are acceptable to those using the breeding values; and (3) if breeding values are estimated for heifers, rather than cows then the heifer and cow traits need to be correlated. The accuracy of genomic prediction of dry matter intake (DMI) and RFI has been estimated to be around 0.4 in beef and dairy cattle studies. There are opportunities to increase the accuracy of prediction, for example, pooling data from three research herds (in Australia and Europe) has been shown to increase the accuracy of genomic prediction of DMI from 0.33 within country to 0.35 using a three-country reference population. Before including RFI as a selection objective, genetic correlations with other traits need to be estimated. Weak unfavourable genetic correlations between RFI and fertility have been published. This could be because RFI is mathematically similar to the calculation of energy balance and failure to account for mobilisation of body reserves correctly may result in selection for a trait that is similar to selecting for reduced (or negative) energy balance. So, if RFI is to become a selection objective, then including it in an overall multi-trait selection index where the breeding objective is net profit is sensible, as this would allow genetic correlations with other traits to be properly accounted for. If genetic parameters are accurately estimated then RFI is a logical breeding objective. If there is uncertainty in these, then DMI may be preferable.

An a posteriori granddaughter design was applied to estimate quantitative trait loci genotypes of sires with many sons in the US Holstein population. The results of this analysis can be used to determine concordance between specific polymorphisms and segregating quantitative trait loci. Determination of the actual polymorphisms responsible for observed genetic variation should increase the accuracy of genomic evaluations and rates of genetic gain. A total of 52 grandsire families, each with ⩾100 genotyped sons with genetic evaluations based on progeny tests, were analyzed for 33 traits (milk, fat and protein yields; fat and protein percentages; somatic cell score (SCS); productive life; daughter pregnancy rate; heifer and cow conception rates; service-sire and daughter calving ease; service-sire and daughter stillbirth rates; 18 conformation traits; and net merit). Of 617 haplotype segments spanning the entire bovine genome and each including ~5×106 bp, 5 cM and 50 genes, 608 autosomal segments were analyzed. A total of 19 335 unique haplotypes were found among the 52 grandsires. There were a total of 133 chromosomal segment-by-trait combinations, for which the nominal probability of significance for the haplotype effect was <10−8, which corresponds to genome-wide significance of <10−4. The number of chromosomal regions that met this criterion by trait ranged from one for rear legs (rear view) to seven for net merit. For each of the putative quantitative trait loci, at least one grandsire family had a within-family contrast with a t-value of >3. Confidence intervals (CIs) were estimated by the nonparametric bootstrap for the largest effect for each of nine traits. The bootstrap distribution generated by 100 samples was bimodal only for net merit, which had the widest 90% CI (eight haplotype segments). This may be due to the fact that net merit is a composite trait. For all other chromosomes, the CI spanned less than a third of the chromosome. The narrowest CI (a single haplotype segment) was found for SCS. It is likely that analysis by more advanced methods could further reduce CIs at least by half. These results can be used as a first step to determine the actual polymorphisms responsible for observed quantitative variation in dairy cattle.

The use of molecular genetic information in the evaluation of livestock has become more common. This study looks at the efficacy of using such information to improve the genetic evaluation of a rare breed of dual-purpose cattle. Data were available in the form of pedigree information on the Gloucester cattle breed in the United Kingdom and recorded milk and beef performance on a small number of animals. In addition, molecular genetic information in the form of multi-marker, multiple regression results converted to a 1 to 10 score (Igenity scores) and 123 single nucleotide polymorphism (SNP) genotypes for 199 non-recorded animals were available. Appropriate mixed-animal models were explored for the recorded traits and these were used to calculate estimated breeding values (EBV), and their accuracies, for 6527 animals in the breed’s pedigree file. Various ways to improve the accuracy of these EBV were explored. This involved using multivariate BLUP analyses, genomic estimated breeding values (GEBV) and combining Igenity scores with recorded traits in a series of bivariate genetic analyses. Using the milk recording traits as an example, the accuracy of a number of traits could be improved using multivariate analyses by up to 14%, depending on the combination of traits used. The level of increase in accuracy largely corresponded to the absolute difference between the genetic and residual correlations between two traits, but this was not always symmetrical. The use of GEBV did not increase the accuracy of milk trait EBV owing to the low proportion of variance explained by the 101 SNPs used. Using Igenity scores in bivariate analyses with the recorded data was more successful in increasing EBV accuracy. The largest increases were found in genotyped animals with no recorded performance (e.g. a 58% increase in fat weight in milk); however, the size of the increase depended on the level of the genetic correlation between the recorded trait and the Igenity score for that trait. Lower levels of improvements in accuracy were seen in animals that were recoded but not genotyped, and ancestors which were neither genotyped nor recorded. This study demonstrated that it was possible to improve the accuracy of EBV estimation by including Igenity score information in genetic analyses but it also concluded that increasing the level of performance recording in the breed would be beneficial.

This study assessed the long-term effects of feeding diets containing either a gelling fibre (alginate (ALG)), or a fermentable fibre (resistant starch (RS)), or both, on feeding patterns, behaviour and growth performance of growing pigs fed ad libitum for 12 weeks. The experiment was set up as a 2×2 factorial arrangement: inclusion of ALG (yes or no) and inclusion of RS (yes or no) in the control diet, resulting in four dietary treatments, that is, ALG−RS− (control), ALG+RS−, ALG−RS+, and ALG+RS+. Both ALG and RS were exchanged for pregelatinized potato starch. A total of 240 pigs in 40 pens were used. From all visits to an electronic feeding station, feed intake and detailed feeding patterns were calculated. Apparent total tract digestibility of energy, dry matter (DM), and CP was determined in week 6. Pigs’ postures and behaviours were scored from live observations in weeks 7 and 12. Dietary treatments did not affect final BW and average daily gain (ADG). ALG reduced energy and DM digestibility (P<0.01). Moreover, ALG increased average daily DM intake, and reduced backfat thickness and carcass gain : digestible energy (DE) intake (P<0.05). RS increased feed intake per meal, meal duration (P<0.05) and inter-meal intervals (P=0.05), and reduced the number of meals per day (P<0.01), but did not affect daily DM intake. Moreover, RS reduced energy, DM and CP digestibility (P<0.01). Average daily DE intake was reduced (P<0.05), and gain : DE intake tended to be increased (P=0.07), whereas carcass gain : DE intake was not affected by RS. In week 12, ALG+RS− increased standing and walking, aggressive, feeder-directed, and drinking behaviours compared with ALG+RS+ (ALG×RS interaction, P<0.05), with ALG−RS− and ALG−RS+ in between. No other ALG×RS interactions were found. In conclusion, pigs fed ALG compensated for the reduced dietary DE content by increasing their feed intake, achieving similar DE intake and ADG as control pigs. Backfat thickness and carcass efficiency were reduced in pigs fed ALG, which also showed increased physical activity. Pigs fed RS changed feeding patterns, but did not increase their feed intake. Despite a lower DE intake, pigs fed RS achieved similar ADG as control pigs by increasing efficiency in DE use. This indicates that the energy utilization of RS in pigs with ad libitum access to feed is close to that of enzymatically digestible starch.

Resistant starch (RS) has been suggested to prolong satiety in adult pigs. The present study investigated RS-induced changes in behaviour, satiety-related hormones and metabolites in catheterized growing pigs to explore possible underlying mechanisms for RS-induced satiety. In a cross-over design with two 14-day periods, 10 pigs (initial BW: 58 kg) were assigned to two treatments comprising diets containing either 35% pregelatinized starch (PS) or 34% retrograded starch (RS). Diets were isoenergetic on gross energy. Pigs were fed at 2.8× maintenance. Postprandial plasma response of satiety-related hormones and metabolites was measured at the end of each period using frequent blood sampling. Faecal and urinary energy losses were measured at the end of each period. Behaviour was scored 24 h from video recordings using scan sampling. Energy digestibility and metabolizability were ~6% lower in RS compared with PS diet (P<0.001), and metabolizable energy (ME) intake was ~3% lower in RS-fed than in PS-fed pigs (P<0.001). RS-fed pigs showed less feeder-directed (P=0.001) and drinking (P=0.10) behaviours than PS-fed pigs throughout the day. Postprandial peripheral short-chain fatty acid (SCFA) levels were higher in RS-fed than in PS-fed pigs (P<0.001). Postprandial glucose and insulin responses were lower in RS-fed than in PS-fed pigs (P<0.001). Triglyceride levels were higher in RS-fed than in PS-fed pigs (P<0.01), and non-esterified fatty acid levels did not differ between diets (P=0.90). Glucagon-like peptide-1 (GLP-1) levels were lower in RS-fed than in PS-fed pigs (P<0.001), and peptide tyrosine tyrosine (PYY) levels did not differ between diets (P=0.90). Blood serotonin levels were lower (P<0.001), whereas monoamine oxidase activity (P<0.05) and tryptophan (P<0.01) levels were higher in RS-fed than in PS-fed pigs. Despite a lower ME intake, RS seemed to prolong satiety, based on behavioural observations. Possible underlying mechanisms for RS-induced satiety include increased 24 h plasma SCFA levels, and decreased postprandial glucose and insulin responses. GLP-1 and PYY seemed not to play a role in RS-induced satiety. Low blood serotonin levels in RS-fed pigs suggested a difference in intestinal serotonin release between treatments. Increased postprandial plasma triglyceride levels corresponded with increased SCFA levels, but it is unclear whether triglycerides may have signalled satiety in RS-fed pigs.

Genetic parameters and environmental factors were estimated for foaling ease (FE) and stillbirths (SBs) in four breeds of draft horses based on 11 229, 38 877, 35 764 and 13 274 FE and SB scores recorded between 1998 and 2010 for Ardennais (A), Breton (B), Comtois (C) and Percheron (P), respectively. Incidences for the three FE categories were: easy or without help 91.0% (A) to 95.4% (B), difficult 3.4% (B) to 7.1% (A) and intervention of a veterinarian 1.1% (B) to 1.9% (A). The frequency of SB ranged between 5.4% (B) and 9.4% (A). A multiple-trait threshold animal model was used that included the effects of sex of foal, region, month, year of foaling, combined maternal age and parity, direct genetic, maternal genetic and permanent environments. Estimates were obtained using Markov Chain Monte Carlo Gibbs sampling. The most unfavourable effect was first parity, which decreased the probability of easy foaling to 78.6% for A and 88.3% for B. Interaction with age showed that the risk for first foaling for mares aged 3 years was higher than at 4 or 5 to 9 years. This was also observed for SB with an increased probability of SB at first foaling of 17.9% (A) or 9.6% (B). The most unfavourable month was found to be the most frequent month for foaling (April) and not the most demanding months weather-wise (winter). For FE, direct heritabilities were A 0.27 (0.06), B 0.14 (0.03), C 0.18 (0.03) and P 0.18 (0.04), and maternal heritabilities were A 0.25 (0.06), B 0.19 (0.04), C 0.12 (0.03) and P 0.21 (0.06). Genetic correlations between direct and maternal genetic effects were A −0.29 (0.14), B −0.39 (0.12), C −0.09 (0.14) and P −0.54 (0.17). For SB, direct heritabilities were A 0.52 (0.09), B 0.42 (0.04), C 0.28 (0.04) and P 0.39 (0.05), and maternal heritabilities were A 0.25 (0.05), B 0.10 (0.02), C 0.07 (0.02) and P 0.14 (0.02). Genetic correlations between direct and maternal genetic effects were A −0.85 (0.06), B −0.63 (0.06), C −0.64 (0.11) and P −0.69 (0.06). Direct genetic correlations between FE and SB traits were A 0.60 (0.10), B 0.58 (0.10), C 0.36 (0.10) and P 0.29 (0.15). Maternal genetic correlations between FE and SB traits were A 0.67 (0.10), B 0.47 (0.13), C 0.28 (0.15) and P 0.39 (0.15). These estimates are posterior means of the Gibbs samples and are within the upper limits of comparable results reported in cattle.

The impact of nutrition and energy reserves on the fertility of ruminants has been extensively described. However, the metabolic factors and the molecular mechanisms involved in the interactions between nutrition and ovarian function are still poorly understood. These factors could be hormonal (either reproductive and/or metabolic) and/or dietary and metabolic (glucose, amino acids and fatty acids). In this review, we briefly summarize the impact of those nutrients (fatty acids, glucose and amino acids) and metabolic hormones (insulin/IGF-I, growth hormone, T3/4, ghrelin, apelin and the adipokines (leptin, adiponectin and resistin)) implicated in the development of ovarian follicles, oocytes and embryos in ruminants. We then discuss the current hypotheses on the mechanisms of action of these factors on ovarian function. We particularly describe the role of some energy sensors including adenosine monophosphate-activated kinase and peroxisome proliferator-activated receptors in the ovarian cells.

Selection of Quarter Horses for different purposes has led to the formation of lines, including racing and cutting horses. The objective of this study was to identify genomic regions divergently selected in racing line of Quarter Horses in relation to cutting line applying relative extended haplotype homozygosity (REHH) analysis, an extension of extended haplotype homozygosity (EHH) analysis, and the fixation index (F ST) statistic. A total of 188 horses of both sexes, born between 1985 and 2009 and registered at the Brazilian Association of Quarter Horse Breeders, including 120 of the racing line and 68 of the cutting line, were genotyped using single nucleotide polymorphism arrays. On the basis of 27 genomic regions identified as selection signatures by REHH and F ST statistics, functional annotations of genes were made in order to identify those that could have been important during formation of the racing line and that could be used subsequently for the development of selection tools. Genes involved in muscle growth (n=8), skeletal growth (n=10), muscle energy metabolism (n=15), cardiovascular system (n=14) and nervous system (n=23) were identified, including the FKTN, INSR, GYS1, CLCN1, MYLK, SYK, ANG, CNTFR and HTR2B.

The horse’s hindgut bacterial ecosystem has often been studied using faecal samples. However few studies compared both bacterial ecosystems and the validity of using faecal samples may be questionable. Hence, the present study aimed to compare the structure of the equine bacterial community in the hindgut (caecum, right ventral colon) and faeces using a fingerprint technique known as Automated Ribosomal Intergenic Spacer Analysis (ARISA). Two DNA extraction methods were also assessed. Intestinal contents and faeces were sampled 3 h after the morning meal on four adult fistulated horses fed meadow hay and pelleted concentrate. Irrespective of the intestinal segment, Principal Component Analysis of ARISA profiles showed a strong individual effect (P<0.0001). However, across the study, faecal bacterial community structure significantly (P<0.001) differed from those of the caecum and colon, while there was no difference between the two hindgut communities. The use of a QIAamp® DNA Stool Mini kit increased the quality of DNA extracted irrespective of sample type. The differences observed between faecal and hindgut bacterial communities challenge the use of faeces as a representative for hindgut activity. Further investigations are necessary to compare bacterial activity between the hindgut and faeces in order to understand the validity of using faecal samples.

The breeding scheme of a Swiss sire line was modeled to compare different target traits and information sources for selection against boar taint. The impact of selection against boar taint on production traits was assessed for different economic weights of boar taint compounds. Genetic gain and breeding costs were evaluated using ZPlan+, a software based on selection index theory, gene flow method and economic modeling. Scenario I reflected the currently practiced breeding strategy as a reference scenario without selection against boar taint. Scenario II incorporated selection against the chemical compounds of boar taint, androstenone (AND), skatole (SKA) and indole (IND) with economic weights of −2.74, −1.69 and −0.99 Euro per unit of the log transformed trait, respectively. As information sources, biopsy-based performance testing of live boars (BPT) was compared with genomic selection (GS) and a combination of both. Scenario III included selection against the subjectively assessed human nose score (HNS) of boar taint. Information sources were either station testing of full and half sibs of the selection candidate or GS against HNS of boar taint compounds. In scenario I, annual genetic gain of log-transformed AND (SKA; IND) was 0.06 (0.09; 0.02) Euro, which was because of favorable genetic correlations with lean meat percentage and meat surface. In scenario II, genetic gain increased to 0.28 (0.20; 0.09) Euro per year when conducting BPT. Compared with BPT, genetic gain was smaller with GS. A combination of BPT and GS only marginally increased annual genetic gain, whereas variable costs per selection candidate augmented from 230 Euro (BPT) to 330 Euro (GS) or 380 Euro (both). The potential of GS was found to be higher when selecting against HNS, which has a low heritability. Annual genetic gain from GS was higher than from station testing of 4 full sibs and 76 half sibs with one or two measurements. The most effective strategy to reduce HNS was selecting against chemical compounds by conducting BPT. Because of heritabilities higher than 0.45 for AND, SKA and IND and high genetic correlations to HNS, the (correlated) response in units of the trait could be increased by 62% compared with scenario III with GS and even by 79% compared with scenario III, with station testing of siblings with two measurements. Increasing the economic weights of boar taint compounds amplified negative effects on average daily gain, drip loss and intramuscular fat percentage.

The development of integrated crop–livestock systems (ICLS) is a major challenge for the ecological modernisation of agriculture but appears difficult to implement at a large scale. A participatory method for ICLS design has been developed and implemented in 15 case studies across Europe, representing a range of production systems, challenges, constraints and resources for innovation. Local stakeholders, primarily farmers, but also cooperatives, environmental-association representatives and natural-resource managers, were involved in the identification of challenges and existing initiatives of crop-livestock integration; in the design of new options at field, farm and territory levels; and then in qualitative multicriteria assessment of these options. A conceptual framework based on a conceptual model (crops, grasslands, animals) was developed to act as a boundary object in the design step and invite innovative thinking in ‘metabolic’ and ‘ecosystemic’ approaches. A diversity of crops and grasslands interacting with animals appeared central for designing sustainable farming systems at the territory level, providing and benefitting from ecosystem services. Within this diversity, we define three types of integrated systems according to their degrees of spatial and temporal coordination: complementarity, local synergy, territorial synergy. Moreover, the options for cooperation and collective organisation between farmers and other stakeholders in territories to organise and manage this diversity of land use revealed opportunities for smart social innovation. The qualitative multicriteria assessment identified farmer workload as the main issue of concern while demonstrating expected benefits of ICLS simultaneously for economic, agronomic, environmental and social criteria. This study concludes that participatory design of ICLS based on a generic multi-level and multi-domain framework and a methodology to deal with a local context can identify new systems to be tested. Further assessment and redesign work will be performed in later stages of the European FP7 CANTOGETHER project.