The effect of raising pigs outdoors or conventionally in a barren environment was investigated with respect to behaviour during a 3 to 4 h journey and a 2 h lairage, blood chemistry at slaughter and meat quality characteristics. Pigs were either kept in farm pen groups or were mixed at loading and kept in the groups, so formed, until slaughter. Non-mixed outdoor pigs settled more quickly during transport and lay down to a greater extent at the end of the journey and lairage period compared with conventionally raised pigs. Mixing led to fewer pigs sitting and lying during transport for conventionally raised pigs, where nearly 80% were still standing at the end of the journey. Mixing had no effect on pig posture in the lairage. Outdoor pigs were less aggressive than conventionally raised pigs especially during lairage and had a lower frequency of unacceptable skin damage in the rear and shoulder area. Aggressive interactions were almost exclusively confined to mixed groups and occurred mainly between pigs from different farm pens, i.e. between unfamiliar animals. Mixing at loading led therefore to higher levels of unacceptable skin damage. Cortisol concentrations in slaughter blood were not affected by rearing system or mixing, but mixed, conventionally raised pigs had higher plasma creatine kinase (CK) activities than non-mixed ones (1132 v. 761 U/l, respectively, P < 0.05). Outdoor pigs had similar CK activities, irrespective of mixing (682 and 771 U/l for mixed and non-mixed, respectively). Muscle pH early post mortem was highest in outdoor pigs and muscle temperature lower, but no pig showed pH values below 6.0. Ultimate pH values were both higher (Semimembranosus (S)) and lower (Semispinalis capitis (SC)) than in conventionally raised pigs, and outdoor pigs tended to have a lower frequency of higher than normal pH values. Internal reflectance (MQM) values in Biceps femoris (BF) were highest in outdoor pigs but the incidence of pale, soft and exudative (PSE) meat was low, varying between 0% and 1% for experimental groups. In general, the effects of rearing system and mixing on meat quality measurements taken early post mortem or the day after slaughter were slight, but the trends seen support the CK results, and show that conventionally raised pigs may have found mixing pre-slaughter to be more physically stressful than outdoor pigs did.

A quantitative trait locus (QTL) analysis of female reproductive data from a three-generation experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. Six F1 boars and 23 F1 sows, progeny of six LW boars and six MS sows, produced 573 F2 females and 530 F2 males. Six traits, i.e. teat number (TN), age at puberty (AP), ovulation rate (OR), weight at mating (WTM), number of viable embryos (NVE) and embryo survival (ES) at 30 days of gestation were analysed. Animals were genotyped for a total of 137 markers covering the entire porcine genome. Analyses were carried out based on interval mapping methods, using a line-cross (LC) regression and a half–full sib (HFS) maximum likelihood test. Genome-wide (GW) highly significant (P < 0.001) QTL were detected for WTM on SSC 7 and for AP on SSC 13. They explained, respectively, 14.5% and 8.9% of the trait phenotypic variance. Other GW significant (P < 0.05) QTL were detected for TN on SSC 3, 7, 8, 16 and 17, for OR on SSC 4 and 5, and for ES on SSC 9. Two additional chromosome-wide significant (P < 0.05) QTL were detected for TN, three for WTM, four for AP, three for OR, three for NVE and two for ES. With the exception of the two above-mentioned loci, the QTL explained from 1.2% to 4.6% of trait phenotypic variance. QTL alleles were in most cases not fixed in the grand-parental populations and Meishan alleles were not systematically associated with higher reproductive performance.

Over recent years, selection methodologies have been developed to allow the maximization of genetic gain whilst constraining the rate of inbreeding. The desired rate of inbreeding is achieved by constraining the group coancestry using the numerator relationship matrix computed from pedigree. It is shown that when the method is applied to mixed inheritance models, where a QTL is segregating together with polygenes, the rate of inbreeding achieved in the region around a QTL is greater than the desired level. The constraint on group coancestry at specific positions around the QTL is achieved by using a relationship matrix computed from pedigree and genetic markers. However, the rate of inbreeding realized at the position of constraint is lower than that expected given the assumed relationship between group coancestry and the subsequent rate of inbreeding. The use of markers in the calculation of the relationship matrix allows the selection of candidates with very low or zero relationships because they are homozygous for alternative alleles, which results in a heterozygosity amongst their offspring higher than would be expected given their allele frequencies. A generation of random selection restored the expected relationship between group coancestry and inbreeding.

Statistical models for genetic evaluation often make use of Gaussian distributions. However, some new statistical developments allow the use of an asymmetric distribution for the residuals. Within this context, we analysed three different patterns for the residual term on a data set consisting of 63 208 litter-size records, belonging to 19 255 sows, with a pedigree including 27 911 individuals. The three different residual distributions were: (1) Gaussian distribution, (2) asymmetric Gaussian distribution and (3) asymmetric Gaussian distribution with a hierarchical scheme for the asymmetry parameter. The operational model always included order of parity and herd-year-season as systematic effects, and the permanent environmental and infinitesimal genetic effect of each sow as random effects. The most suitable model using the deviance information criterion (DIC) and posterior predictive checking was model 3. This implies systematic, additive genetic and permanent environmental control of both litter size and the asymmetry parameter of the residual distribution. The asymmetry parameter can be understood as a measure of sensitivity to negative (or positive) environmental influences on phenotypes. The posterior mean (standard deviation) of the additive genetic variance was 0·28 (0·06) for litter size and 0·07 (0·01) for the asymmetry parameter. The posterior mean (standard deviation) of the additive genetic correlation between litter size and the asymmetry parameter was 0·21 (0·07).

Departures of genotype frequencies from Hardy–Weinberg proportions (HWP) for a single autosomal locus due to viability selection in a random mating population have been studied only for the two-allele case. In this article, the analysis of deviations from HWP due to constant viability selection is extended to multiple alleles. The deviations for an autosomal locus with k alleles are measured by means of k fii fixation indices for homozygotes and k(k−1)/2 fij fixation indices for heterozygotes, and expressions are obtained for these indices (FIS statistics) under the multiallele viability model. Furthermore, expressions for fii and fij when the multiallele polymorphism is at stable equilibrium are also derived and it is demonstrated that the pattern of multiallele Hardy–Weinberg deviations at equilibrium is characterized by a global heterozygote excess and a deficiency of each of the homozygotes. This pattern may be useful for detecting whether a given multiallelic polymorphism is at stable equilibrium in the population due to viability selection. An analysis of Hardy–Weinberg deviations from published data for the three-allele polymorphism at the β-globin locus in human populations from West Africa is presented for illustration.

Multiple sex-determining factors have been found in natural populations of the housefly, Musca domestica. Their distribution seems to follow a geographical cline. The ‘standard’ system, with a male-determining factor, M, located on the Y chromosome, prevails at higher latitudes and altitudes. At lower latitudes and altitudes M factors have also been found on any of the five autosomes. Such populations often also harbour a dominant autosomal factor, FD, which induces female development even in the presence of several M factors. Autosomal M factors were first observed some 50 years ago. It has been hypothesized that following their initial appearance, they are spreading northwards, replacing the standard XY system, but this has never been systematically investigated. To scrutinize this hypothesis, we here compare the current distribution of autosomal M factors in continental Europe, on a transect running from Germany to southern Italy, with the distribution reported 25 years ago. Additionally, we analysed the frequencies of the FD factor, which has not been done before for European populations. In contrast to earlier predictions, we do not find a clear change in the distribution of sex-determining factors: as 25 years ago, only the standard XY system is present in the north, while autosomal M factors and the FD factor are prevalent in Italy. We discuss possible causes for this apparently stable polymorphism.

The nature and extent of long-distance seed dispersal are currently poorly understood, largely due to the inherent difficulty in detecting such a phenomenon. Genetic methods provide one of the few general approaches that offer the potential to accurately address this issue. Phenotypic and allozymic approaches were applied to characterize inter-population seed dispersal of the sea rocket (Cakile maritima, Brassicaceae), a glabrous and succulent annual herb. Genetic variation was assessed on 360 individuals sampled from nine populations. Genetic diversity across populations was high, 37% of which was represented by Qst and 16% by Fst. When genetic distances were used to construct the UPGMA dendrogram, populations were clustered into three groups at the 90% similarity level. The pattern of clustering can be explained by examining the direction of sea currents around Tunisian coasts. We have shown in this study that C. maritima seeds can survive up to 4 months immersion in sea water and up to 1 year of floating in sea water; therefore, seed dispersal between populations is possible both in terms of seed survival and current patterns.

Microsatellites or simple sequence repeats (SSRs) are co-dominant molecular markers. When we used fluorescent SSR markers to construct a linkage map for the female heterogametic silkworm (Bombyx mori, ZW), we found that some loci did not segregate in a Mendelian ratio of 1:1 in a backcross population. These loci segregated in a 3:1 ratio of single bands compared with double bands. Further examination of band patterns indicated that three types of SSR bands were present: two homozygotes and one heterozygote. In the beginning, we considered to discard these markers. By scoring male and female F1 individuals, we confirmed that these loci were located on the Z chromosome. Using the sex-linked visible mutation sch (K05) and its wild-type (C108), we constructed an F1 male backcross (BC1M) mapping population. The combination of sch backcross and SSR data enabled us to map the SSR markers to the Z chromosome. By adjusting input parameters based on these data, we were able to use Mapmaker software to construct a linkage map. This strategy takes advantage of co-dominant markers for positional cloning of genes on the Z chromosome. We localized sch to the Z chromosome relative to six SSR markers and one PCR marker, covering a total of 76·1 cM. The sch mutation is an important sex-linked visible mutation widely used in breeding of commercial silkworms (e.g. male silkworm selection rearing). Localization of the sch gene may prove helpful in cloning the gene and developing strains for marker-assisted selection in silkworm breeding.

Wright's (1922) coalescence probabilistic method decomposes the average coancestry or the average inbreeding of the population of interest into contributions of ancestors who are directly responsible for coancestry. These ancestors are less numerous and younger than those given by Caballero & Toro's (2000) method. Then, Wright's method yields a more parsimonious representation of the origin of coancestry or inbreeding. Results of Wright's method, called proximal because ancestors are younger, can be obtained from the latter method using a simple matrix transformation. Detailed algorithms are presented. Both methods can be used for assessing the overall efficiency of a breeding scheme in balancing genetic gain and coancestry rate, yielding very similar results when generations are discrete.

Wood-chip pads represent a low-cost alternative to housing for cattle during the winter. Considering the negative welfare implications associated with housing indoors on concrete, they may also offer welfare benefits to replacement dairy heifers. However, these animals may not be able to withstand winter weather conditions on a grass silage diet. The aim of this experiment was to evaluate behaviour, limb injuries, dirtiness scores, performance and climatic energy demand (CED) of yearling dairy heifers on two levels of nutrition kept outdoors on a wood-chip pad or indoors in cubicles during the winter. Ninety-six 10-month-old heifers were blocked and assigned in groups of eight, to one of the following four treatments in a 2 × 2 factorial design: (a) indoors, silage only; (b) indoors, silage plus concentrate; (c) outdoors, silage only; and (d) outdoors, silage plus concentrate. There were three replicate groups per treatment. All animals were inspected for skin lesions and were weighed and body condition scored (BCS) at the beginning and end of the trial. Instantaneous scan sampling and continuous all-occurrence behaviour sampling were used to collect behaviour data during two 24-h periods. Animals were also dirtiness scored and group feed intakes were recorded during the trial. Significantly more comfort, social and play behaviours were recorded outdoors (P < 0.05) while trips, slips and falls were only recorded indoors (P < 0.001). Groups outdoors had significantly lower limb lesion scores at the end of the experiment (P < 0.05) and fewer groups outdoors were affected by all categories of limb lesions. However, they were consistently dirtier than animals indoors (P < 0.001). Low-nutrition animals had lower feed intakes, smaller BCS changes and lower average daily weight gains than high-nutrition animals (P < 0.01). Heifers outdoors had significantly lower average daily weight gains and BCS changes (P < 0.05) explained by lower feed intakes (P < 0.01). However, outdoor heifers on both the high- and low-nutrition diets and indoor animals on the low-nutrition diet had lower UFL (feed unit for maintenance and lactation (Irish Republic)) intakes (−0.36, −0.35 and −0.22, respectively) than that required to meet the daily live-weight gains they achieved. Heifers indoors on the high-nutrition diet gained 0.98 kg per day but consumed 0.17 UFL more than what would be recommended to achieve a daily weight gain of 1.0 kg. The CED for outdoor heifers was higher than that of indoor heifers (6.18 v. 5.47 MJ/day per m2 body surface area; P < 0.001, s.e.d. 0.044). However, CED did not exceed heat production in any treatment. Although animal performance was reduced outdoors, the wood-chip pad was associated with welfare benefits compared with cubicle housing.

The objective of this study was to test whether the use of tannin-rich shrub legume forage is advantageous for methane mitigation and metabolic protein supply at unchanged energy supply when supplemented in combination with tannin-free legumes to sheep. In a 6 × 6 Latin-square design, foliage of two tannin-rich shrub legume species (Calliandra calothyrsus and Flemingia macrophylla) were used to replace either 1/3 or 2/3, respectively, of a herbaceous high-quality legume (Vigna unguiculata) in a diet composed of the tropical grass Brachiaria brizantha and Vigna in a ratio of 0.55 : 0.45. A Brachiaria-only diet served as the negative control. Each experimental period lasted for 28 days, with week 3 serving for balance measurement and data collection inclusive of a 2-day stay of the sheep in open-circuit respiration chambers for measurement of gaseous exchange. While Vigna supplementation improved protein and energy utilisation, the response to the partial replacement with tannin-rich legumes was less clear. The apparent total tract digestibilities of organic matter, NDF and ADF were reduced when the tannin-rich plants partially replaced Vigna, and the dose–response relationships were mainly linear. The tannin-rich plants caused the expected redistribution of more faecal N in relation to urinary N. While Flemingia addition still led to a net body N retention, even when fed at the higher proportion, adding higher amounts of Calliandra resulted in body protein mobilisation in the growing lambs. With respect to energy, supplementation of Vigna alone improved utilisation, while this effect was absent when a tannin-rich plant was added. The inclusion of the tannin-rich plants reduced methane emission per day and per unit of feed and energy intake by up to 24% relative to the Vigna-only-supplemented diet, but this seems to have been mostly the result of a reduced organic matter and fibre digestion. In conclusion, Calliandra seems less apt as protein supplement for ruminants while Flemingia could partially replace a high-quality legume in tropical livestock systems. However, methane mitigation would be small due to associated reductions in N and energy retention.

A database built from 95 experiments with 303 treatments was used to quantify the ruminal biohydrogenation (BH) of fatty acids (FA), efficiency of microbial protein synthesis (EMPS), duodenal flow and intestinal absorption of total FA and of FA with 12 to 18 C units, in response to variations in dietary FA content, source or technological treatment of fat supplement. Flows of FA were expressed relative to dry matter intake (DMI) to compile data from bovine and ovine species. BH tended to increase curvilinearly with FA intake, whereas dietary FA did not affect EMPS. A linear relationship between FA intake and duodenal flow of total FA was obtained, with a coefficient of 0.75 ± 0.06 g duodenal FA/kg DMI for each g FA intake/kg DMI. Between experiments, positive balances of total FA (intake – duodenum) were related to low EMPS. Relationships between duodenal flows of FA with 12 to 18 C units and their respective intakes were linear, with a coefficient that increased with the number of C units. Duodenal flow of bacterial FA was linearly related to FA intake (coefficient 0.33 ± 0.13), whereas contribution of bacterial lipid to duodenal flow decreased as FA intake increased. For each FA with 12 to 16 C units, prediction of FA absorption from its respective duodenal flow was linear. For total FA and FA with 18 C units, apparent absorption levelled off at high duodenal flows. All these relationships were discussed according to current knowledge on microbial metabolism in the rumen and on the intestinal digestibility of FA in the intestine.

Four male pigs (Duroc × Landrace × Yorkshire; average initial (mean ± SEM) BW = 22.5 ± 1.1 kg), fitted with permanent catheters in the portal vein, ileal vein and carotid artery, were used in a 4 × 4 Latin square experimental design to measure the effect of dietary starch sources on the net portal appearance of glucose and amino acids. Dietary starch sources were resistant starch (RS), maize, sticky rice and brown rice. Diets were provided at 0730, 1530 and 2330 h during a 6-day adjustment period and 1-day collection period. On day 7 of each period, blood samples were collected from the portal vein and carotid artery at 0730 h (prior to feeding) and hourly up to 8 h after meal. Blood samples were used to determine glucose, amino acid, packed cell volume and partial pressure of oxygen (pO2). When calculated per 100 g feed intake, cumulative portal glucose appearance was lower (P < 0.05) for resistant starch than for maize, sticky rice or brown rice up to 8 h after the meal. Cumulative portal glucose appearance was higher (P < 0.05) for sticky rice and brown rice than for other diets until 4 h after the meal, but maize had higher cumulative glucose appearance after 4 h. Net cumulative portal concentrations of most amino acids for resistant starch were also reduced (P < 0.05) than for the other starch sources. Cumulative portal appearance of amino acid represented 48.39%, 63.76%, 61.80% and 59.18% of dietary intake for resistant starch, maize, sticky rice and brown rice, respectively. Collectively, our results indicate that dietary starch sources substantially affect the appearance of amino acids and glucose in the portal circulation.

Microbial transformations in the rumen ecosystem have a major impact on our ability to meet the challenge of reducing the environmental footprint of ruminant livestock agriculture, as well as enhancing product quality. Current understanding of the rumen microbial ecosystem is limited, and affects our ability to manipulate rumen output. The view of ruminal fermentation as the sum of activities of the dominant rumen microbiota is no longer adequate, with a more holistic approach required. This paper reviews rumen functionality in the context of the microbiota of the rumen ecosystem, addressing ruminal fermentation as the product of an ecosystem while highlighting the consequences of this for ruminant agriculture. Microbial diversity in the rumen ecosystem enhances the resistance of the network of metabolic pathways present, as well as increasing the potential number of new pathways available. The resulting stability of rumen function is further promoted by the existence of rumen microbiota within biofilms. These protected, structured communities offer potential advantages, but very little is currently known about how ruminal microorganisms interact on feed-surfaces and how these communities develop. The temporal and spatial development of biofilms is strongly linked to the availability of dietary nutrients, the dynamics of which must also be given consideration, particularly in fresh-forage-based production systems. Nutrient dynamics, however, impact not only on pathway inputs but also the turnover and output of the whole ecosystem. Knowledge of the optimal balance of metabolic processes and the corresponding microbial taxa required to provide a stable, balanced ecosystem will enable a more holistic understanding of the rumen. Future studies should aim to identify key ecosystem processes and components within the rumen, including microbial taxa, metabolites and plant-based traits amenable to breeding-based modification. As well as gaining valuable insights into the biology of the rumen ecosystem, this will deliver realistic and appropriate novel targets for beneficial manipulation of rumen function.

Compensatory growth, a frequent phenomenon observed in ruminants due to seasonal variation in food availability, affects protein metabolism including protein oxidation. These oxidation processes may have an impact on animal health as well as on meat protein degradation during post mortem aging (ie meat maturation). Sixteen male lambs were randomly divided into four groups. One group was fed ad libitum (C) and one group was food-restricted to 60% of the intake of the C group (R). The last two groups were restricted similarly to the R group and refed either ad libitum (RAL) or similarly to the C group (pair-feeding) (RPF). Muscles samples were taken immediately after slaughter. The present study showed that the restriction/refeeding pattern had no effect on protein oxidation in the muscles studied (longissimus dorsi (LD), semitendinosus (ST) and supraspinatus (SP)). However, total antioxidant capacity decreased after food restriction (−51%, −43%, P < 0.01 for ST and LD muscles, respectively) and re-increased only after ad libitum refeeding. This alteration in the total antioxidant status can partially be explained by the similar pattern of change observed in the glutathione concentration of the muscles (−25%, P < 0.05 for ST muscle and NS for the other muscles). However, none of the concentrations of other water-soluble antioxidants studied (carnosine, anserine, glutathione peroxidase and superoxide dismutase) were altered during compensatory growth. This study showed that an inappropriate feeding level following a nutritional stress induced alterations in the total antioxidant status (particularly that of glutathione), which may have consequences on animal health. Other consequences of a decrease of the animal antioxidant status in vivo could be an alteration of the protein oxidation processes during meat maturation.

Four Holstein heifers (264 ± 12 kg initial BW) were used in a 4 × 4 Latin square design with 21-day experimental periods to determine the effect of increasing levels of sodium bicarbonate (BICARB) (0%, 1.25%, 2.5% and 5%, of concentrate dry matter (DM) basis) on chewing and feed intake behavior when fed high-concentrate diets. Concentrate (13.41% CP, 13.35% NDF) and barley straw were fed once a day at 0830 h ad libitum. Feed bunks placed on scales and video recording were used to measure 24-h feed intake and chewing behavior, respectively. The patterns of feeding behavior (feed intake, meal size and length) and chewing behavior (eating, ruminating and total chewing) were studied by dividing the day into 12 intervals of 2-h each, beginning at feeding (interval 1 through 12). Number of meals per day and eating rate decreased linearly with increasing buffer level, but meal length increased linearly. No treatment effects were observed in sum of daily meal lengths or average meal size. The treatment × interval interaction was significant on meal size, length and feed intake. The size and length of those meals occurring during the 4 h post-feeding increased linearly. However, meal size tended to decrease in the evening between 8 and 12 h, whereas feed intake decreased linearly from 6 to 10 h and from 12 to 14 h post-feeding. Buffer concentration did not affect the percentage of time spent ruminating, eating or drinking per day but the buffer level × interval interaction was significant. Time spent eating expressed as min per kg of DM or organic matter (OM) intake increased linearly with buffer levels. Proportion of time spent eating increased linearly during the intervals between 0 and 4 h post-feeding. Time spent ruminating decreased linearly during the 2 h post-feeding, and also in the evening from 12 to 14 h, and at night from 18 to 22 h post-feeding, but the effect was quadratic between 8 and 10 h when intermediate buffer levels showed the greatest ruminating time. Time spent drinking decreased linearly from 6 to 8 h but increased during the 2 h following feeding and from 10 to 12 h post-feeding. Daily eating rate and meal frequency decreased linearly as the buffer level increased, but average meal size and daily chewing times were not affected. However, significant time of the day × buffer level interactions were observed for feed intake, meal size and length and chewing behavior.

Analysis of 16S ribosomal RNA (rRNA)-encoding gene sequences from gut microbial ecosystems reveals bewildering genetic diversity. Some metabolic functions, such as glucose utilisation, are fairly widespread throughout the genetic spectrum. Others, however, are not. Despite so many phylotypes being present, single species or perhaps only two or three species often carry out key functions. Among ruminal bacteria, only three species can break down highly structured cellulose, despite the prevalence and importance of cellulose in ruminant diets, and one of those species, Fibrobacter succinogenes, is distantly related to the most abundant ruminal species. Fatty acid biohydrogenation in the rumen, particularly the final step of biohydrogenation of C18 fatty acids, stearate formation, is achieved only by a small sub-group of bacteria related to Butyrivibrio fibrisolvens. Individuals who lack Oxalobacter formigenes fail to metabolise oxalate and suffer kidney stones composed of calcium oxalate. Perhaps the most celebrated example of the difference a single species can make is the ‘mimosine story’ in ruminants. Mimosine is a toxic amino acid found in the leguminous plant, Leucaena leucocephala. Mimosine can cause thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were toxic to ruminants in some countries but not others led to the discovery of Synergistes jonesii, which metabolises 3-hydroxy-4(1H)-pyridone and protects animals from toxicity. Thus, despite the complexities indicated by molecular microbial ecology and genomics, it should never be forgotten that gut communities contain important metabolic niches inhabited by species with highly specific metabolic capability.