A 4-year interdisciplinary study was performed to compare two organically managed sheep production systems, using 118 ewes and 24 ha each. The systems differed in the ewes’ reproduction rhythm: one lambing per ewe per year (1L/1Y), with the aim of balancing feed self-sufficiency and lamb marketing periods v. three lambings over 2 years (3L/2Y), with the aim of maximising ewes’ productivity. The sustainability was evaluated through ewes’ reproductive performance, lamb growth rate, carcass characteristics and quality, animal health, forage and feed self-sufficiency, soil mineral balance and gross margin. General animal health was assessed by recording ewe and lamb mortality and putative cause of death. Nematode digestive-tract strongyles parasitism was studied using faecal egg counts and necropsies. Carcass quality was assessed by recording carcass weight, conformation and fatness, and colour and firmness of subcutaneous fat. Thirty-three percent of 3L/2Y ewes lambed twice a year against 4% of 1L/1Y. Mean ewe productivity was 161.3% and 151.0% in 3L/2Y and 1L/1Y, respectively, and it was more variable between years in 3L/2Y. Average concentrate feed consumption and the corresponding cost per ewe were higher in 3L/2Y than in 1L/1Y (156 v. 121 kg, and €49.5 v. €39.3, respectively). Finally, average gross margin was lower in 3L/2Y than in 1L/1Y (€59 v. €65 per ewe, respectively). Even in year 2002, when ewe productivity was highest in 3L/2Y (193%), gross margin was not different between systems (€90 v. €86 per ewe in 3L/2Y and 1L/1Y, respectively), because of higher concentrate costs in 3L/2Y. The 3L/2Y animals presented a lower health status, with a higher lamb mortality (P < 0.05) and a higher digestive-tract strongyles and coccidia parasitism level (P < 0.05). Lamb carcass conformation, fatness and fat colour were not different between systems, but carcass weight and subcutaneous dorsal fat firmness were lower in 3L/2Y lambs than in 1L/1Y lambs (P < 0.05 and < 0.001, respectively). Intensification in an organically managed sheep system, through an increased reproduction rhythm, thus did not lead to better economic results and proved riskier, more variable and more difficult to manage, and so less sustainable. The less intensive system (1L/1Y) was both highly efficient from the animal standpoint and highly feed self-sufficient. The technical and economic results of this system were better than those of organic private farms in the same area and matched those of non-organic farms.

In this study, we investigate the extent to which the incidence of Escherichia coli O157:H7 can be predicted in human faeces, from human intake and infection via water contaminated by livestock and carrying this zoonotic pathogen in North-East (NE) and South-West (SW) regions of Scotland. In SW Scotland, there is a risk of coastal recreational waters failing EU standards for faecal indicator organisms, and this is assumed to be the main potential waterborne route of infection. In NE Scotland, the main waterborne route is assumed to be the many private drinking water supplies; these are mainly derived from shallow groundwater and surveys show that there is potential for significant levels of microbial contamination from livestock. The risk to human health from these sources has been assessed using a combination of process models, epidemiological risk-assessment methods and survey data. A key assumption in the calculations is the amount of mixing of pathogenic and non-pathogenic E. coli between animal faecal sources and contaminated water intake by humans. Using the probability distributions of the E. coli O157 content of individual faecal pat material (which would imply no mixing between source and human intake), based on three recent surveys of animal faeces in Scotland, led to predicted annual risks of infection slightly higher than observed human infection incidence. Using the geometric mean to represent partial mixing (which theoretically may over- or underestimate incidence with a concave dose–response curve) gave infection rates similar to those observed for two of the three faecal surveys. Using the arithmetic mean led to over-prediction of risk. This is to be expected if the true dose–response curve is (such as the Beta-Poisson curve used here) concave. Other factors that may lead to over-prediction of incidence are discussed, including under-reporting, loss of infectivity as a result of environmental exposure, immunity and the appropriateness of the Beta-Poisson curve. It is concluded that better epidemiological data for calibration of the dose–response curve, better knowledge of the degree of mixing and understanding of immunity are key requirements for progress in process model-based predictions of infection rate. The paper also explores the potential of improved farm and catchment scale management to deliver cost-effective mitigation of pollution of bathing and drinking water by livestock zoonoses.

This study investigated the relationships amongst personality traits and attitudes of 311 dairy stockpeople and the milk yield they obtained. A questionnaire pack consisting of a big-five measure of personality (which includes the traits of extraversion, agreeableness, conscientiousness, emotional stability and intellect), a four-factor attitude questionnaire and associated demographic and production questions was posted out to Northern Ireland dairy farmers. Pearson correlations were used to assess the relationship between personality and attitudes and partial correlations were calculated between milk yield and these psychometric measures. The personality traits of agreeableness and conscientiousness were most strongly correlated to positive attitudes towards working with dairy cows. None of the stockpeople’s personality traits were significantly correlated with the milk yield they obtained. Three of the attitude scales, however, were significantly correlated with milk yield; milk yield was related to higher levels of empathy and job satisfaction and lower levels of negative beliefs. These findings, along with previous research, suggest stockperson attitudes may be important in relation to dairy cow welfare and production.

The objective of the two studies was to determine the bioavailability of threonine (thr) and tryptophan (trp) in peanut meal, relative to l-thr and l-trp, for starter pigs using the slope-ratio bioassay. Basal diets (BDs) contained surfeit amounts of all amino acids for 10 to 20 kg pigs, except for thr (Experiment 1) or trp (Experiment 2). In the first study, four reference diets were formulated by supplementing the BD with 0, 0.4, 0.8 or 1.2 g of l-thr/kg at the expense of cornstarch; two test diets were formulated by replacing cornstarch in the BD with peanut meal at 32 or 64 g/kg of diet to supply 0.4 or 0.8 g thr/kg, respectively. Four reference diets consisting of the BD supplemented with 0, 0.15, 0.3 or 0.45 g of l-trp/kg at the expense of cornstarch and two test diets in which cornstarch in the BD was replaced with peanut meal at 30 or 60 g/kg of diet to supply 0.14 or 0.28 g trp/kg, respectively were used in the second study. Body weight gain responded in a linear way to supplemental l-thr or thr from peanut meal (P < 0.001). There was a linear response (P < 0.001) to thr supplementation from l-thr or peanut meal in gain-to-feed ratio. The addition of trp to the BD linearly increased (P < 0.05) body weight gain, feed intake and gain-to-feed ratio regardless of the trp source. Common-intercept, multiple linear regression in slope-ratio methodology using weight gain or gain-to-feed ratio as dependent variables and supplemental thr intake as independent variable gave relative bioavailability estimates of 71.9% or 75.7%, respectively. Corresponding values for trp were 92% and 75.7%. The fiducial limits for none of the relative bioavailability estimates included 100%. The data from these studies suggest that the bioavailabilities of thr and trp in peanut meal are less than those of l-thr and l-trp, and that the bioavailabilities of thr and trp in peanut meal are 72% to 76% and 76% to 92%, respectively.

The aim of this work was to evaluate the ability of a line selected for reproductive longevity (LP) to confront productive challenges compared to a line selected during 31 generations for litter size at weaning (V). A total of 133 reproductive rabbit does were used (72 and 61 from LP and V lines, respectively). Within each line, three groups with different levels of productive effort were planned: PP9, inseminated at day 4 after the first partum and with nine kits during the second partum, and inseminated after first weaning (30 days) and with nine (PW9) or five kits (PW5) during the second partum. The reproductive performance, body condition (perirrenal fat thickness (PFT)) and lipolytic response were controlled. LP does showed greater mean live weight (LW; +128 g; P < 0.05), PFT (+0.47 mm; P < 0.05) and estimated body energy (EBE; +0.29 MJ/kg; P < 0.01) than V does at second partum. However, LP does that mated at first post partum did not significantly differ in EBE relative to V does at second partum. During the first week of lactation, dry matter (DM) intake was similar for both lines (94 and 95 g DM/kg LW0.75 day for V and LP does, respectively). There was a significant difference in milk yield between both lines during the first week when litter size was nine (60 v. 54 g of milk/kg LW0.75 day for LP and V does, respectively; P < 0.01), but no difference when litter size was five. Consequently, when litter size was nine, LP does showed a lower recovery of PFT (0.6 mm less; P < 0.05) than V does during the first 10 days of lactation. However, when litter size was five, LP does showed a higher LW (+210 g; P < 0.05) than V does at 10 days of lactation and a similar recovery of PFT. During the last 3 weeks of the lactation, LP does showed a higher feed intake (+6 g DM/kg LW0.75 day; P < 0.05) and milk yield (+27 g/day; P < 0.001) than V does when litter size was nine, resulting in no significant differences in LW at 30 days of lactation. However, when litter size was five, both lines showed similar feed intake and milk yield, maintaining their differences in LW at 30 days of lactation (+206 g for LP does; P < 0.05). These results show that the rabbit line selected for reproductive longevity is more robust with respect to coping with productive challenges, than a line selected for reproductive intensity.

Automatic milking systems have made possible the separation of high- and low-quality milk at the udder quarter level during the milking process. The aim of this study was to investigate the composition and yield of milk from individual udder quarters to determine whether deteriorated milk composition occurs in udders that are assumed to be healthy and whether quarters with high-quality milk are found in udders with high milk somatic cell count (SCC). Milk samples were collected on one occasion from 90 cows at udder quarter level and cow composite level. The milk was analyzed for content of total protein, whey protein, casein, fat, lactose, citric acid and SCC; milk yield was registered. The cows were divided into three groups depending on the SCC of their composite milk. Cows in group 1, cow composite SCC < 100 000 cells/ml, were assumed to have healthy udders. However, instances of increased SCC and decreased milk quality were discovered in one or more udder quarters of approximately 30% of the group. Cows in group 2, cow composite SCC of 100 000 to 300 000 cells/ml, and group 3, cow composite SCC > 300 000 cells/ml, were assumed to have affected udders. However, the majority of these cows had one or more udder quarters in which increased SCC and deteriorated milk quality were not detected. Calculations of bulk-tank milk values, when separation of milk from affected udder quarters was performed, indicate that SCC changes to a much greater degree compared to the other milk components. These results show that milk from affected udder quarters suffers compositional changes, but calculations of simulated separation indicate that the compositional changes in bulk-tank milk are small. The effect of separation of milk from individual udder quarters on bulk-tank milk needs to be further studied.

Lysozyme, an anti-bacterial enzyme, is mostly found in the body fluids, various tissues and secretions of animals and humans, and confers immunity against a wide range of bacterial species. The present study was carried out to elucidate the gene sequence of this enzyme in Indian Sahiwal × Holstein Friesian crossbred cattle and to explore the polymorphism of the gene as well as their association with milk production and somatic cell traits. The total length of lysozyme cDNA was found to be of 447 bp. The similarity with Bos taurus, human, pig, monkey, gorilla, mice, rat, chicken, dog and sheep was estimated as 99.1%, 85%, 81.0%, 85.2%, 84.3%, 77.9%, 77.9%, 41.4%, 40.5% and 24.6%, respectively. Polymorphism study of two fragments, extended exon1 including promoter, exon1 and partial intron1 (268 bp), and extended exon2 including partial intron1 and 2, and exon2 region (287 bp) of milk lysozyme gene was carried out by employing single-stranded conformation polymorphism (SSCP). In the extended exon1 fragment, three alleles namely A, B and C with frequencies of 0.59, 0.28 and 0.12 were observed while in the exon extended fragment, three different alleles – P, Q and R with respective frequencies of 0.61, 0.38 and 0.01 – were determined in Indian Sahiwal × Holstein Friesian cross. A total of eight haplotypes were found in this population where the most predominant one was h1 (0.52). Genotypes of exon1 extended fragment showed significant association with total milk yield, daily milk yield, peak yield and somatic cell score at P < 0.05 while that of exon2 extended fragment had significant correlation with only total lactational milk yield. Haplotype combinations also revealed significant association with total milk production where h1h1 homozygous showed highest yield during first lactation.

Chlormequat is a commonly used plant growth regulator in agriculture. Defined levels of chlormequat residue are allowed in food and an acceptable daily intake is defined for humans. However, there are results in the literature suggesting that a daily intake below the acceptable level for human is detrimental for mammalian reproduction. In the present experiment we investigated the effect of chlormequat at levels up to that acceptable for humans on reproduction in male pigs. Chlormequat (also known as chlorocholine chloride (CCC)) was mixed into the diet and given to the experimental animals at three levels (three treatment groups), i.e. 0 mg CCC/kg BW per day (Control), 0.025 mg CCC/kg BW per day and 0.05 mg CCC/kg BW per day. Eight mother sows per treatment group were used in the experiment. From the day of insemination, the mother sows received the experimental diets. The piglets were weaned at 4 weeks of age and two boar littermates continued on the same treatment as the dam until maturity and delivery of semen for in vitro fertilization (IVF) and in vivo fertilization. Semen volume, sperm concentration and fraction of live sperms were not (P ⩾ 0.46) detrimentally affected by chlormequat intake. The fraction of oocytes developing to more than the one-cell stage at day 5 after IVF was not (P = 0.88) detrimentally affected by chlormequat intake. Chlormequat intake did not detrimentally affect the fraction of gilts being pregnant after one insemination (P = 0.65) or the number of embryos in the pregnant gilts (P = 0.36). Serum chlormequat concentration was 0.9 μg/kg in the 0.025 mg CCC/kg BW per day group and 1.8 μg/kg in the 0.05 mg CCC/kg BW per day group, but was below the detection limit in control animals. In conclusion, the plant growth regulator chlormequat could not be proven to be detrimental to the selected reproduction traits in male pigs. This is in contrast to existing results from the male mouse.

The objective of this study was to estimate heritabilities for and genetic correlations among different pathogen-specific mastitis traits. The traits were unspecific mastitis, which is all mastitis treatments regardless of the causative pathogen as well as mastitis caused by Streptococcus dysgalactiae, Escherichia coli, coagulase-negative staphylococci (CNS), Staphylococcus aureus and Streptococcus uberis. Also groups of pathogens were investigated, Gram-negative v. Gram-positive and contagious v. environmental pathogens. Data from 168 158 Danish Holstein cows calving first time between 1998 and 2006 were used in the analyses. Variances and covariances were estimated using uni- and bivariate threshold models via Gibbs sampling. Posterior means of heritabilities of pathogen-specific mastitis were lower than the heritability of unspecific mastitis, ranging from 0.035 to 0.076 for S. aureus and S. uberis, respectively. The heritabilities of groups of pathogen ranged from 0.053 to 0.087. Genetic correlations among the pathogen-specific mastitis traits ranged from 0.45 to 0.77. These estimates tended to be lowest for bacteria eliciting very different immune responses, which can be considered as the overall pleiotropic effect of genes affecting resistance to a specific pathogen, and highest for bacteria sharing characteristics regarding immune response. The genetic correlations between the groups of pathogens were high, 0.73 and 0.83. Results showed that the pathogen-specific traits used in this study should be considered as different traits. Genetic evaluation for pathogen-specific mastitis resistance may be beneficial despite lower heritabilities than unspecific mastitis because a pathogen-specific mastitis trait is a direct measure of an udder infection, and because the cost of a mastitis case caused by different pathogens has been shown to differ greatly. Sampling bias may be present because there were not pathogen information on all mastitis treatments and because some farms do not record pathogen information. Therefore, improved recording of pathogen information and mastitis treatments in general is critical for a successful genetic evaluation of udder health. Also, economic values have to be specified for each pathogen-specific trait separately.

The aim of this study was to determine the specific characteristics of carcass and meat from an old French chicken breed, the ‘Géline de Touraine’ (GT), characterised by a very slow-growing rate and usually slaughtered at 120 days of age. For this purpose, we compared the GT with an experimental crossbreed (EC) exhibiting the same growth rate, and with a ‘Label rouge’ (LR) genotype usually slaughtered at 84 days of age. A total of 250 males and 250 females per genotype were reared by separating sexes and genotypes. The growth performances were recorded. At 84 days of age, 80 birds per sex and per genotype were slaughtered. The frequency of clawing and pecking injuries on the carcass was noted. We also measured the skin colour and the thickness of wing membrane. The relative percentages of carcass, breast, thigh + drumstick, abdominal fat, testis or ovary to body weight were determined. On breast and thigh muscles the ultimate pH (pHu) and colour were measured. The juice loss after 3 days’ storage at +4°C and after cooking at 85°C, and the shear force value of Warner–Bratzler were only measured on breast muscles. At 120 days of age, we repeated the same measurements but only on EC and GT genotypes in order to compare birds at the same age or at the respective slaughter age for each production. Whatever the slaughter age, the body weight of males was always higher than that of the females but the carcass yield was similar for both sexes. The females had higher breast yield and carcass fatness but lower thigh + drumstick yield than the males. The yellowness of skin and meat was higher for the females than for the males while the contrary was observed for the redness of the meat. The breast meat of the females also had higher cooking loss than that of the males. GT and EC birds exhibited a higher occurrence of carcass defects and a higher pHu in meat than LR birds. The GT chickens were characterised by a lower breast yield, a higher fattiness and an earlier sexual maturity than the other genotypes, which could confer typical sensorial attributes to their meat. Finally, the EC chickens exhibited a skin and a meat more coloured than the other genotypes, particularly for yellowness, a character which could be under genetic control.

Gap junction protein connexin43 (Cx43), encoded by the GJA1 gene, is the most abundant connexin in the cardiovascular system and was reported as a crucial factor maintaining cardiac electrical conduction, as well as having a very important function in facilitating the recycling of potassium ions from hair cells in the cochlea back into the cochlear endolymph during auditory transduction processes. In mammals, bats are the only taxon possessing powered flight, placing exceptional demand on many organismal processes. To meet the demands of flying, the hearts of bats show many specialties. Moreover, ultrasonic echolocation allows bat species to orientate and often detect and locate food in darkness. In this study, we cloned the full-length coding region of GJA1 gene from 12 different species of bats and obtained orthologous sequences from other mammals. We used the maximum likelihood method to analyse the evolution of GJA1 gene in mammals and the lineage of bats. Our results showed this gene is much conserved in mammals, as well as in bats' lineage. Compared with other mammals, we found one private amino acid substitution shared by bats, which is located on the inner loop domain, as well as some species-specific amino acid substitutions. The evolution rate analyses showed the signature of purifying selection on not only different classification level lineages but also the different domains and amino acid residue sites of this gene. Also, we suggested that GJA1 gene could be used as a good molecular marker to do the phylogenetic reconstruction.

In genetic and biological studies, the F2 population is one of the most popular and commonly used experimental populations mainly because it can be readily produced and its genome structure possesses several niceties that allow for productive investigation. These niceties include the equivalence between the proportion of recombinants and recombination rates, the capability of providing a complete set of three genotypes for every locus and an analytically attractive first-order Markovian property. Recently, there has been growing interest in using the progeny populations from F2 (advanced populations) because their genomes can be managed to meet specific purposes or can be used to enhance investigative studies. These advanced populations include recombinant inbred populations, advanced intercrossed populations, intermated recombinant inbred populations and immortalized F2 populations. Due to an increased number of meiosis cycles, the genomes of these advanced populations no longer possess the Markovian property and are relatively more complicated and different from the F2 genomes. Although issues related to quantitative trait locus (QTL) mapping using advanced populations have been well documented, still these advanced populations are often investigated in a manner similar to the way F2 populations are studied using a first-order Markovian assumption. Therefore, more efforts are needed to address the complexities of these advanced populations in more details. In this article, we attempt to tackle these issues by first modifying current methods developed under this Markovian assumption to propose an ad hoc method (the Markovian method) and explore its possible problems. We then consider the specific genome structures present in the advanced populations without invoking this assumption to propose a more adequate method (the non-Markovian method) for QTL mapping. Further, some QTL mapping properties related to the confounding problems that result from ignoring epistasis and to mapping closely linked QTL are derived and investigated across the different populations. Simulations show that the non-Markovian method outperforms the Markovian method, especially in the advanced populations subject to selfing. The results presented here may give some clues to the use of advanced populations for more powerful and precise QTL mapping.

General and genetic statistical methods are commonly used to deal with microsatellite data (highly variable neutral genetic markers). In this paper, the self-organizing map (SOM) that belongs to the unsupervised artificial neural networks (ANNs) was applied to analyse the structure of 58 European and two Chinese pig populations (Sus scrofa) including commercial lines, local breeds and cosmopolitan breeds. Results were compared with other unsupervised classification or ordination methods such as factorial correspondence analysis, hierarchical clustering from an allele sharing distance and the Bayesian genetic model and with principal components analysis and neighbour joining from allelic frequencies and genetic distances between populations. Like other methods, SOMs were able to classify individuals according to their breed origin and to visualize similarities between breeds. They provided additional information on the within- and between-population diversity, allowed differences between similar populations to be highlighted and helped differentiate different groups of populations.