By analysing N2 mice from a cross between the inbred C57BL strain B10.Q and the NMRI-related NFR/N strain, we recently identified a quantitative trait locus (QTL) influencing litter size. This locus is now denoted Fecq4, and it is present on the murine chromosome 9. In the present paper, we describe how the Fecq4 fragment originating form the NFR/N mouse strain will affect B10.Q mice by means of breeding capacity, super-ovulation rate and embryonic development in vitro. Our results show that both the breeding capacity (number of pups produced/breeding cage during a 5 months period) and the mean litter size are significantly increased in B10.Q.NFR/N-Fecq4 congenic mice. Furthermore. B10.Q.NFR/N-Fecq4 congenic mice (both homozygous and heterozygous) did respond much better to super-ovulation than wild-type mice, resulting in a dramatically increased yield of fertilized 1-cell embryos. In addition, embryos containing the Fecq4 fragment were easy to cultivate in vitro, resulting in a higher yield of embryos reaching the blastocyst stage. We propose that B10.Q.NFR/N-Fecq4 congenic mice may be used to improve breeding or super-ovulation rate in different types of genetically modified mice (on C57BL background) that exhibit severe breeding problems. The Fecq4 fragment has been described in detail, and the possible role of polymorphic candidate genes near the linkage peak (58 Mb) has been discussed. Genes of the cytochrome P450 family (1, 11 and 19), such as Cyp19a1, are assumed to be particularly interesting, since they are known to exhibit female-associated reproductive phenotypes, affecting the ovulation rate, if mutated.

Primula sieboldii E. Morren is a perennial clonal herb that is widely distributed in Japan, but in danger of extinction in the wild. In a previous study, we revealed the genetic diversity of the species using chloroplast and nuclear DNA and used this information to define conservation units. However, we lacked information on adaptive genetic diversity, which is important for long-term survival and, thus, for the definition of conservation units. In order to identify adaptive traits that showed adaptive differentiation among populations, we studied the genetic variation in six quantitative traits within and among populations for 3 years in a common garden using 110 genets from five natural populations from three regions of Japan. The number of days to bud initiation was adaptive quantitative trait for which the degree of genetic differentiation among populations (QST) was considerably larger than that in eight microsatellite markers (FST). The relationship between this trait and environmental factors revealed that the number of days to bud initiation was negatively correlated, with the mean temperature during the growing period at each habitat. This suggests that adaptive differentiation in the delay before bud initiation was caused by selective pressure resulting from temperature differences among habitats. Our results suggest that based on adaptive diversity and neutral genetic diversity, the Saitama population represents a new conservation unit.

This study aims to comprehensively examine the mutation rates of one base for another in human gene loci. In contrast to most previous efforts based on divergence data from untranscribed regions, the present study employs the basic theory of the reversible recurrent mutation model using large-scale, high-quality re-sequencing data from public databases of gene loci. Population mutation parameters (4Nν and 4Nμ) are obtained for each pair of base substitutions. The estimated parameters show good strand reversal symmetry, supporting the existence of mutation-drift equilibrium. Analysis of specific gene regions including mRNA, coding sequence (CDS), 5′-untranslated region (5′-UTRs), 3′-UTR and intron shows that there are clear differences in the mutation rates of each base for another depending on the location of the base in question. Results from analyses that take the adjacent bases into account exhibit excellent strand reversal symmetry, confirming that the identity of an adjacent base influences mutation rates. The CpG to TpG (or CpG to CpA) substitution is found at a rate approximately seven-fold higher than the reverse transition in intron regions due to cytosine deamination, but the effect is strongly reduced in mRNA regions and almost entirely lost in 5′-UTRs. However, from the overall increased transitions in sites other than CpGs and the proportion of CpGs in the total sequence, CpG methylation is not the main factor responsible for the increased rate of transitions as compared with transversions. In this report, after adjusting average mutation rates to the sequence compositions, no substitution bias is found between A+T and C+G, indicating base composition equilibrium in human gene loci. Population differences are also identified between groups of people of African and European descent, presumably due to past population histories. By applying the basic theory of population genetics to re-sequenced data, this study contributes new, detailed information regarding mutations in human gene regions.

Segmental duplications are enriched within many eukaryote genomes, and their potential consequence is gene duplication. While previous theoretical studies of gene duplication have mainly focused on the gene silencing process after fixation, the process leading to fixation is even more important for segmental duplications, because the majority of duplications would be lost before reaching a significant frequency in a population. Here, by a series of computer simulations, we show that purifying selection against loss-of-function mutations increases the fixation probability of a new duplicate gene, especially when the gene is haplo-insufficient. Theoretically, the probability of simultaneous preservation of both duplicate genes becomes twice the loss-of-function mutation rate (uc) when the population size (N), the degree of dominance of mutations (h) and the recombination rate between the duplicate genes (c) are all sufficiently large (Nuc>1, h>0·1 and c>uc). The preservation probability declines rapidly with h and becomes 0 when h=0 (haplo-sufficiency). We infer that masking deleterious loss-of-function mutations give duplicate genes an immediate selective advantage and, together with effects of increased gene dosage, would predominantly determine the fates of the duplicate genes in the early phase of their evolution.

Alterations in the activity level or temporal expression of key signalling genes elicit profound patterning effects during development. Consequently, gain-of-function genetic schemes that overexpress or misexpress such loci can identify novel candidates for functions essential for a developmental process. GAL4-Upstream Activating Sequence (UAS)-targeted regulation of gene expression in Drosophila has allowed rapid analyses of coding sequences for potential roles in specific tissues at particular developmental stages. GAL4 has also been combined with randomly mobilized transposons capable of UAS-directed misexpression or overexpression of flanking sequences. This combination has produced a genetic screening system that can uncover novel loci refractory to standard loss of function genetic approaches, such as redundant genes. Available libraries of strains with sequenced insertion sites can allow direct correlation of phenotypes to genetic function. These techniques have also been applied to genetic interaction screening, where a GAL4 driver and UAS-regulated insertion collection are combined with an extant mutant genotype. In this article, we summarize studies that have utilized GAL4-UAS overexpression or misexpression of random loci to screen for candidates involved in specific developmental processes.

Male Drosophila melanogaster transfers many accessory-gland proteins to females during copulation. Sex peptide (SP) is one of these and one of its main effects is to decrease female remating propensity. To date, there has been no investigation of genetic variation in SP-gene expression levels, or if such potential variation directly influences female remating behaviour. We assessed both these possibilities and found significant variation in expression levels of the SP gene across D. melanogaster isolines. A non-linear association between SP expression levels and female remating delay suggestive of disruptive selection on expression levels was also documented. Finally, while some isolines were infected with the endosymbiont Wolbachia, no association between Wolbachia and SP expression level was found.

The degree of starshape of a genealogy is readily detectable using summary statistics and can be taken as a surrogate for the effect of past demography and other non-neutral forces. Summary statistics such as Tajima's D and related measures are commonly used for this. However, it is well known that because of their neglect of the genealogy underlying a sample such neutrality tests are far from ideal. Here, we investigate the properties of two types of summary statistics that are derived by considering the genealogy: (i) genealogical ratios based on the number of mutations on the rootward branches, which can be inferred from sequence data using a simple algorithm and (ii) summary statistics that use properties of a perfectly star-shaped genealogy. The power of these measures to detect a history of exponential growth is compared with that of standard summary statistics and a likelihood method for the single and multi-locus case. Statistics that depend on pairwise measures such as Tajima's D have comparatively low power, being sensitive to the random topology of the underlying genealogy. When analysing multi-locus data, we find that the genealogical measures are most powerful. Provided reliable outgroup information is available they may constitute a useful alternative to full likelihood estimation and standard tests of neutrality.

This paper presents an analysis of the economic implications of alternative methods to surgical castration without anaesthesia. Detailed research results on the economic implications of four different alternatives are reported: castration with local anaesthesia, castration with general anaesthesia, immunocastration and raising entire males. The first three alternatives have been assessed for their impact on pig production costs in the most important pig-producing Member States of the EU. The findings on castration with anaesthesia show that cost differences among farms increase if the anaesthesia cannot be administered by farmers and when the veterinarian has to be called to perform it. The cost of veterinarian service largely affects the total average costs, making this solution economically less feasible in small-scale pig farms. In all other farms, the impact on production costs of local anaesthesia is however limited and does not exceed 1 €ct per kg. General anaesthesia administered by inhalation or injection of Ketamin in combination with a sedative (Azaperone, Midazolan) is more expensive. These costs depend heavily on farm size, as the inhalation equipment has to be depreciated on the largest number of pigs possible. The overall costs of immunocastration – including the cost of the work load for the farmer – has to be evaluated against the potential benefits derived from higher daily weight gain and feed efficiency in comparison with surgical castrates. The economic feasibility of this practice will finally depend on the price of the vaccine and on consumer acceptance of immunocastration. The improvement in feed efficiency may compensate almost entirely for the cost of vaccination. The main advantages linked to raising entire males are due to the higher efficiency of feed conversion, to the better growth rate and to the higher leanness of carcass. A higher risk of boar taint on the slaughter line has to be accounted for. Raising entire males should not generate more than 2.5% of boar taint among slaughter pigs, in order to maintain the considerable economic benefits of better feed efficiency of entire males with respect to castrates.

The objective of the study was to determine standardized ileal digestibilities (SID) of crude protein (CP) and amino acids (AA) in six ingredients commonly used in weanling pigs diets. The ingredients consisted of extruded soybeans (SBe), high-protein soybean meal (SBMhp), soy protein concentrate (SPC), hydrolyzed wheat gluten (WGh), conventional fish meal 1 (FM1) and extracted fish meal 2 (FM2e). Each assay feed ingredient was added to a purified cornstarch-based basal diet supplemented with casein and crystalline AA, and SID of CP and AA of assay ingredients were estimated using the difference method. A total of 12 3-week-old barrows were surgically fitted with T-cannulas at the distal ileum. The piglets were allocated to four simultaneous 3 × 3 Latin-square designs with three animals and three periods each, resulting in six observations per assay diet. After 3 to 5 days recovery from surgery, each assay diet was fed at a level of 30 g/kg body weight. Each experimental period consisted of 5 days for adaptation to the assay diets and 2 days for ileal digesta collection. The SID of CP, Lys, Met, Thr and Trp were 73%, 78%, 76%, 66% and 71% in SBe; 80%, 84%, 87%, 75% and 81% in SBMhp; 86%, 89%, 89%, 78% and 83% in SPC; 87%, 60%, 88%, 76% and 79% in WGh; 87%, 92%, 94%, 86% and 86% in FM1; and 79%, 86%, 89%, 80% and 74% in FM2e, respectively. The greatest SID of indispensable AA were observed for FM1 and SPC (SID ⩾ 85% for most indispensable AA), followed by WGh, FM2e and SBMhp (SID ⩾ 80% for most indispensable AA) and the smallest SID were obtained for SBe (SID < 80% for most indispensable AA). The SID of CP and indispensable AA in both types of fish meal, SBMhp and WGh were similar to SPC (P = 0.063 to 0.855), except for Arg (P = 0.010) and Lys (P = 0.001) in WGh, and Phe (P = 0.044) and Trp (P = 0.037) in FM2e. The SID of CP and indispensable AA were smaller in SBe compared with SPC (P < 0.001 to P = 0.017), except for Lys (P = 0.136). The SID of CP and indispensable AA were consistently smaller in FM2e compared with FM1 with significant differences for CP (P = 0.035), Phe (P = 0.028) and Trp (P = 0.008). Digestibility values measured in the present study can be used to formulate diets for piglets based on standardized ileal digestible contents of CP and AA.

Rumen fill may be a strong intake constraint for dairy cows fed on pasture, even though pasture is highly digestible in the grasslands of temperate climates. This constraint may also depend on the cows’ maturity. Moreover, indoor feeding of fresh herbage may not always be a good model for the study of intake regulation at grazing. To test these hypotheses, four mature (6.3 ± 0.72 year old) and four young (3.8 ± 0.20 year old) dairy cows were offered fresh perennial ryegrass indoors or at grazing. The impact of rumen fill on intake was evaluated by addition of rumen inert bulk (RIB; coconut fiber, 15 l) compared to a control. The experimental design was a double 4 × 4 Latin square with four 14-day periods and a 2 × 2 factorial arrangement of two feeding methods (indoor feeding v. grazing), combined with the addition, or not, of RIB (RIB v. control), repeated for four mature and four young cows. Digestibility of offered herbage was 0.81. The average ytterbium measured dry matter intake (Yb DMI) was 19.0 and 15.5 kg/day for mature and young cows respectively (P = 0.019). The effect of RIB on predicted Yb DMI interacted with feeding method and cow age (P = 0.043). The presence of RIB decreased Yb DMI by 4.4 kg/day in mature cows at grazing and by 3.4 kg/day in young cows indoors, whereas it did not affect the Yb DMI of mature cows indoors or grazing young cows. Both grazing and young age constituted a clear constraint on the feeding behavior of the cows. Grazing cows had fewer ingestion and rumination sequences, which were longer and less evenly distributed throughout the day and night. Young cows had lower intake rates that were less adaptable to the feeding method and the presence of RIB. Mature cows clearly decreased their daily intake rate at grazing compared to indoor feeding, and with RIB compared to control, whereas the intake rate of young cows did not vary. These results indicate that rumen fill can represent a constraint on intake in grazing cows, even when highly digestible perennial ryegrass is offered. The study also shows that the impact of RIB on intake is highly dependent upon other constraints applied to the chewing behavior, which in this experiment were methods of offering herbage and cow age.

The Finnish mating records of Standardbred trotters (SB; n = 33 679) and Finnhorses (FH; n = 32 731) were analysed to study the effect of the level of inbreeding on foaling rates and to estimate the heritability of foaling rate. A linear mixed model was assumed, with the outcome of the foaling (foal or no foal) as the trait of the study. A restricted maximum likelihood-based method was used to calculate the estimates of the variance components. Predictions of breeding values and estimates of fixed effects were also calculated. The average level of inbreeding was 9.9% in the SB and 3.6% in the FH. The average foaling rates were better in the SB (72.6%) than in the FH (66.3%), but within each breed intense inbreeding had a statistically significant negative effect on foaling rate (P < 0.05). Also, the mating type, the age and breeding type of the mare, and the age of the stallion had statistically significant effects on foaling rate (P < 0.001). The heritability of foaling rate was between 3.4% and 3.7% in SBs and between 5.5% and 9.8% in FHs, when the outcome of the foaling was considered to be a trait of the expected foal. With the same model, the estimates of maternal genetic effect were 4.7% for SBs and 3.2% for FHs, and the estimates of the permanent environmental effects of the stallion were between 1.3% and 1.7%. Avoiding matings with very high inbreeding coefficients would improve foaling rates. It would also be possible to devise a breeding program for better equine fertility, but because the heritability is low, improvement of environmental factors deserves special attention.

The first part of this study was a cross-sectional analysis of the impact of 29 management factors on udder health in organic dairy farms in Switzerland. All 77 farms joined the extension program ‘pro-Q’. As a measure of udder health the theoretical bulk milk somatic cell count (TBMSCC) calculated by the monthly cow composite somatic cell count over a time period of 1 year was chosen. The basic udder health of the farms was determined by TBMSCC during the year prior to the start of the project (mean for all farms = 176 460 cells/ml). In the multivariable analysis, the five factors ‘swiss brown breed’, ‘alpine summer pasturing’, ‘calf feeding with milk from mastitis diseased cows’, ‘hard bedding’ and ‘no post-milking’ remained as significant risk factors on udder health. In the second part of the study, the development of management factors and the udder health situation affected by an extension program after 1 year was investigated. A partial improvement of the management factors on the farms but no overall improvement on udder health and no association between management changes and udder health changes were found. Improvement of udder health was more likely in farms with higher basic TBMSCC than in those farms with less udder health problems at the beginning of the project.

Aggression when pigs are mixed into new social groups has negative impacts on welfare and production. Aggressive behaviour is moderately heritable and could be reduced by genetic selection. The possible wider impacts of selection for reduced aggressiveness on handling traits and activity in the home pen were investigated using 1663 male and female pedigree pigs (898 purebred Yorkshire and 765 Yorkshire × Landrace). Aggressive behaviour was observed over 24 h after pigs were mixed at 10 weeks of age into groups balanced for unfamiliarity and weight. Aggression was highly heritable (duration of involvement in reciprocal fighting h2 = 0.47 ± 0.03, and duration of delivering one-sided aggression h2 = 0.34 ± 0.03). Three weeks after mixing, home pen inactivity (indicated by the frequency of lying) was observed over 24 h. Inactivity was weakly heritable (h2 = 0.05 ± 0.01) but showed no significant genetic association with aggression. Pigs’ behaviour during handling by humans was assessed on entry to, whilst inside and on exit from a weigh crate at both mixing and end of test at 22 weeks. Pigs were generally easy to handle, moving easily into and out of the crate. Scores indicating ‘very difficult to move’ were rare. Handling scores at weighing were weakly heritable (h2 = 0.03 to 0.17), and moderately correlated across the two weighings (rg = 0.28 to 0.76). Aggressive behaviour at mixing was genetically associated with handling at the end of test weighing: pigs that fought and delivered one-sided aggression had handling scores indicating more active behaviour at weighing (e.g. moving quickly into the crate v. fighting rg = 0.41 ± 0.05 and v. bullying rg = 0.60 ± 0.04). Also, there was a genetic association between receiving one-side aggression at mixing and producing high-pitched vocalisations in the weigh crate (rg = 0.78 ± 0.08). Correlated behavioural responses occurring across different challenging situations (e.g. social mixing and human handling) have been described by the concept of animal temperament (also known as coping styles, personality or behavioural syndromes), but this has rarely been demonstrated at the genetic level in farm animals. These findings may have practical implications for the development of breeding programmes aimed at altering animal temperament. Breeding to reduce aggression could result in some reduction in activity at weighing. This would have consequences for animal production, because pigs which are inactive at weighing take longer to move into and out of the weigh crate, and perhaps also for animal welfare.

The objective of this study was to evaluate changes in ruminal microorganisms and fermentation parameters due to dietary supplementation of soybean and linseed oil alone or in combination. Four dietary treatments were tested in a Latin square designed experiment using four primiparous rumen-cannulated dairy cows. Treatments were control (C, 60 : 40 forage to concentrate) or C with 4% soybean oil (S), 4% linseed oil (L) or 2% soybean oil plus 2% linseed oil (SL) in a 4 × 4 Latin square with four periods of 21 days. Forage and concentrate mixtures were fed at 0800 and 2000 h daily. Ruminal fluid was collected every 2 h over a 12-h period on day 19 of each experimental period and pH was measured immediately. Samples were prepared for analyses of concentrations of volatile fatty acids (VFA) by GLC and ammonia. Counts of total and individual bacterial groups (cellulolytic, proteolytic, amylolytic bacteria and total viable bacteria) were performed using the roll-tube technique, and protozoa counts were measured via microscopy in ruminal fluid collected at 0, 4 and 8 h after the morning feeding. Content of ruminal digesta was obtained via the rumen cannula before the morning feeding and used immediately for DNA extraction and quantity of specific bacterial species was obtained using real- time PCR. Ruminal pH did not differ but total VFA (110 v. 105 mmol/l) were lower (P < 0.05) with oil supplementation compared with C. Concentration of ruminal NH3-N (4.4 v. 5.6 mmol/l) was greater (P < 0.05) due to oil compared with C. Compared with C, oil supplementation resulted in lower (P < 0.05) cellulolytic bacteria (3.25 × 108v. 4.66 × 108 colony-forming units (CFU)/ml) and protozoa (9.04 × 104v. 12.92 × 104 cell/ml) colony counts. Proteolytic bacteria (7.01 × 108v. 6.08 × 108 CFU/ml) counts, however, were greater in response to oil compared with C (P < 0.05). Among oil treatments, the amount of Butyrivibrio fibrisolvens, Fibrobacter succinogenes and Ruminococcus flavefaciens in ruminal fluid was substantially lower (P < 0.05) when L was included. Compared to C, the amount of Ruminococcus albus decreased by an average of 40% regardless of oil level or type. Overall, the results indicate that some ruminal microorganisms, except proteolytic bacteria, are highly susceptible to dietary unsaturated fatty acids supplementation, particularly when linolenic acid rich oils were fed. Dietary oil effects on ruminal fermentation parameters seemed associated with the profile of ruminal microorganisms.

It has been suggested that United Kingdom recommendations for feeding the neonatal calf (∼500 g milk replacer (MR)/day; ∼200–230 g CP/kg milk powder) are inadequate to sustain optimal growth rates in early life. The current study was undertaken with 153 high genetic merit, male and female Holstein-Friesian calves (PIN2000 = £48) born between September and March, with heifers reared and bred to calve at 24 months of age. Calves were allocated to one of four pre-weaning dietary treatments arranged in a 2 MR feeding level (5 v. 10 l/day) × 2 MR protein content (210 v. 270 g CP/kg dry matter (DM)) factorial design. MR was reconstituted at a rate of 120 g/l of water, throughout, and was offered via computerised automated milk feeders. Calves were introduced to pre-weaning diets at 5 days of age and weaned at day 56. During the first 56 days of life, calves offered 10 l MR/day had significantly higher liveweight gains (P < 0.001) than calves fed 5 l MR/day. No significant differences in liveweight gain were found between calves fed 210 g CP/kg DM MR and those fed 270 g CP/kg DM MR from birth to day 56. Differences in live weight and body size due to feeding level disappeared by day 90. Neither MR feeding level nor MR CP content affected age at first service or age at successful service, and with no milk production effects, the results indicate no post-weaning benefits of increased nutrition during the milk-feeding period in dairy heifers.

A quantitative trait locus (QTL) for increased loin muscularity (TM-QTL) has previously been identified in purebred Texel sheep. Crossbred lambs born out of Mule ewes mated to heterozygous Texel sires for the TM-QTL were evaluated for a range of carcass traits. Lambs were genotyped and classified as carriers (n = 62) of a single copy of the TM-QTL and non-carriers (n = 49). In this study, the effects of the TM-QTL on carcass attributes were investigated using subjective classification scores for conformation and fatness, and measurements from a video image analysis (VIA) system. In addition, refined prediction equations to estimate weights of primal joints (leg, chump, loin, breast and shoulder) were obtained by calibrating the VIA system against computer tomography (CT) measurements in the loin region. The new refined prediction models increased the accuracy of prediction of all primal cuts on an average of 16% compared to previously derived standard VIA prediction equations. The coefficient of determination (R2) of the VIA system to predict in vivo CT measurements ranged from 0.39 to 0.72 for measurements of Musculus longissimus lumborum (MLL) area, width and depth, lumbar spine length, loin muscle volume and loin muscularity index. Using VIA estimates of CT-measured loin muscle traits, a significant increase in depth (+2.7%) of the MLL was found to be associated with the TM-QTL. Conformation and fatness scores and the shape of the carcass measured as individual lengths, widths and areas by VIA were not significantly influenced by the TM-QTL. Primal meat yields estimated using both standard and refined VIA prediction equations were not significantly affected by the TM-QTL. However, carcass ‘compactness’ was found to have significantly increased in carrier lambs. The weight of the dissected MLL estimated using VIA information was greater (+2.6%) for carriers compared to non-carriers. To conclude, neither the current industry carcass evaluation system for conformation and fatness nor the standard VIA system is able to identify the effect of the TM-QTL in the loin region in the moment. However, the calibration of the VIA system against CT measurements resulted in improved VIA prediction equations for primal meat yields and also showed moderate potential to estimate loin muscle traits measured by CT and to detect, partially, the effect of the TM-QTL on these traits.