The objective of this study was to estimate (co)variance components using random regression on B-spline functions to weight records obtained from birth to adulthood. A total of 82 064 weight records of 8145 females obtained from the data bank of the Nellore Breeding Program (PMGRN/Nellore Brazil) which started in 1987, were used. The models included direct additive and maternal genetic effects and animal and maternal permanent environmental effects as random. Contemporary group and dam age at calving (linear and quadratic effect) were included as fixed effects, and orthogonal Legendre polynomials of age (cubic regression) were considered as random covariate. The random effects were modeled using B-spline functions considering linear, quadratic and cubic polynomials for each individual segment. Residual variances were grouped in five age classes. Direct additive genetic and animal permanent environmental effects were modeled using up to seven knots (six segments). A single segment with two knots at the end points of the curve was used for the estimation of maternal genetic and maternal permanent environmental effects. A total of 15 models were studied, with the number of parameters ranging from 17 to 81. The models that used B-splines were compared with multi-trait analyses with nine weight traits and to a random regression model that used orthogonal Legendre polynomials. A model fitting quadratic B-splines, with four knots or three segments for direct additive genetic effect and animal permanent environmental effect and two knots for maternal additive genetic effect and maternal permanent environmental effect, was the most appropriate and parsimonious model to describe the covariance structure of the data. Selection for higher weight, such as at young ages, should be performed taking into account an increase in mature cow weight. Particularly, this is important in most of Nellore beef cattle production systems, where the cow herd is maintained on range conditions. There is limited modification of the growth curve of Nellore cattle with respect to the aim of selecting them for rapid growth at young ages while maintaining constant adult weight.

Two experiments (EXPs) were conducted to evaluate models of immune system stimulation (ISS) that can be used in nutrient metabolism studies in growing pigs. In EXP I, the pig's immune response to three non-pathogenic immunogens was evaluated, whereas in EXP II the pig's more general response to one of the immunogens was contrasted with observations on non-ISS pigs. In EXP I, nine growing barrows were fitted with a jugular catheter, and after recovery assigned to one of three treatments. Three immunogens were tested during a 10-day ISS period: (i) repeated injection of increasing amounts of Escherichiacoli lipopolysaccharide (LPS); (ii) repeated subcutaneous injection of turpentine (TURP); and (iii) feeding grains naturally contaminated with mycotoxins (MYCO). In EXP II, 36 growing barrows were injected repeatedly with either saline (n = 12) or increasing amounts of LPS (n = 24) for 7 days (initial dose 60 μg/kg body weight). Treating pigs with TURP and LPS reduced feed intake (P < 0.02), whereas feed intake was not reduced in pigs on MYCO. Average daily gain (ADG; kg/day) of pigs on LPS (0.50) was higher than that of pigs on TURP (0.19), but lower than that of pigs on MYCO (0.61; P < 0.01). Body temperature was elevated in pigs on LPS and TURP, by 0.8°C and 0.7°C, respectively, relative to pre-ISS challenge values (39.3°C; P < 0.02), but remained unchanged in pigs on MYCO. Plasma concentrations of interleukin-1β were increased in pigs treated with LPS and TURP (56% and 55%, respectively, relative to 22.3 pg/ml for pre-ISS; P < 0.01), but not in MYCO-treated pigs. Plasma cortisol concentrations remained unchanged for pigs on MYCO and TURP, but were reduced in LPS-treated pigs (30% relative to 29.8 ng/ml for pre-ISS; P < 0.05). Red blood cell glutathione concentrations were lower in TURP-treated pigs (13% relative to 1.38 μM for pre-ISS; P < 0.05), but were unaffected in pigs on LPS and MYCO. In EXP I, TURP caused severe responses including skin ulceration and substantial reductions in feed intake and ADG, whereas MYCO did not induce effective ISS. In EXP II, ISS increased relative organ weights, eye temperature, white blood cell count and plasma acute-phase proteins (P < 0.05), confirming that repeated injection with increasing amounts of LPS induced chronic and relatively mild ISS. Repeated injection with increasing amounts of LPS is a suitable model for studying nutrient metabolism and evaluating the efficacy of nutritional intervention during chronic ISS in growing pigs.

The effect of propylene glycol drenching on ovarian and hormonal dynamics was studied in heifers. Five cycling heifers were used twice (as control and treatment) with crossover design. After the confirmation of ovulation (day 0), the heifers in the treatment group received propylene glycol on days 6, 7 and 8 as an oral drench (250 ml of 90% propylene glycol). On day 10, prostaglandin F2α (PGF2α), 15 mg per head of dinoprost, was administered intramuscularly to induce luteal regression followed by the follicular phase and then propylene glycol was again administered twice daily (500 ml/day) on days 10, 11 and 12. Palpation per rectum and ovarian ultrasonography were performed every other day from days 0 to 10, and daily after PGF2α administration until the subsequent ovulation (second ovulation) for analysis of follicular and luteal dynamics. Blood samples were also collected every other day from days 0 to 10, and then at 6 h intervals after PGF2α administration until the second ovulation. For the samples taken at 6-h intervals after PGF2α administration, the concentrations of glucose showed clear daily fluctuations in both groups. Changes in the plasma concentration of glucose in the treatment group were significantly (P < 0.05) higher than those of the control groups during the period between 0 and 72 h after PGF2α administration. No significant difference was detected in the growth of dominant follicles, maximum diameter of the ovulatory follicles and the changes in oestradiol and progesterone during the follicular phase between treatment and control groups. This study showed the clear daily fluctuations and stimulatory changes in the blood glucose concentrations at 24-h intervals during the short-term treatment of propylene glycol drenching in heifers. However, no significant changes in ovarian and hormonal dynamics were found under such metabolic conditions.

Studies suggested that in human adults, linoleic acid (LA) inhibits the biosynthesis of n-3 long-chain polyunsaturated fatty acids (LC-PUFA), but their effects in growing subjects are largely unknown. We used growing pigs as a model to investigate whether high LA intake affects the conversion of n-3 LC-PUFA by determining fatty acid composition and mRNA levels of Δ5- and Δ6 desaturase and elongase 2 and -5 in liver and brain. In a 2 × 2 factorial arrangement, 32 gilts from eight litters were assigned to one of the four dietary treatments, varying in LA and α-linolenic acid (ALA) intakes. Low ALA and LA intakes were 0.15 and 1.31, and high ALA and LA intakes were 1.48 and 2.65 g/kg BW0.75 per day, respectively. LA intake increased arachidonic acid (ARA) in liver. ALA intake increased eicosapentaenoic acid (EPA) concentrations, but decreased docosahexaenoic acid (DHA) (all P < 0.01) in liver. Competition between the n-3 and n-6 LC-PUFA biosynthetic pathways was evidenced by reductions of ARA (>40%) at high ALA intakes. Concentration of EPA (>35%) and DHA (>20%) was decreased by high LA intake (all P < 0.001). Liver mRNA levels of Δ5- and Δ6 desaturase were increased by LA, and that of elongase 2 by both ALA and LA intakes. In contrast, brain DHA was virtually unaffected by dietary LA and ALA. Generally, dietary LA inhibited the biosynthesis of n-3 LC-PUFA in liver. ALA strongly affects the conversion of both hepatic n-3 and n-6 LC-PUFA. DHA levels in brain were irresponsive to these diets. Apart from Δ6 desaturase, elongase 2 may be a rate-limiting enzyme in the formation of DHA.

The objective of this study was to characterize the condensed tannins (CTs) in wrapped silage bales of sainfoin (Onobrychis viciifolia) and examine their potential action on in vivo and in situ digestive characteristics in sheep. Silage was made from sainfoin, cut at two phenological stages. The first phenological stage, at which silage was made, was from the first vegetation cycle at the end of flowering and the second stage silage was made from regrowth, 5 weeks after the first cut, but before flowering. The silages made from the two phenological stages were fed to 12 rumen-fistulated sheep in a crossover design. Of the 12 sheep, six received polyethylene glycol (PEG) to bind with and remove the effects of CT, whereas the other six were dosed with water. Organic matter digestibility, total-tract N digestibility and N (N) balance were measured over 6 days. Kinetic studies were performed on total N, ammonia N (NH3-N) and volatile fatty acids (VFAs) in rumen fluid before and 1.5, 3 and 6 h after feeding. The kinetics of degradation of dry matter and N from Dacron bags suspended in the rumen were also determined. Biological activity of CT (protein-binding capacity) and CT concentration were greater for the silage made from sainfoin at the early flowering stage. Total-tract N digestibility was increased by the addition of PEG (P < 0.001) to the sainfoin silage before flowering (P < 0.001). CTs decreased N excretion in urine (P < 0.05) and increased faecal N excretion (P < 0.001), but had no effect on body N retention, which is beneficial for the animal. Ruminal N degradability was smaller in the presence of active CT (P < 0.001) at both phenological stages; however, soluble N (P = 0.2060) and NH3-N (P = 0.5225) concentrations in rumen fluid remained unchanged. The results of this experiment indicate that CT in the sainfoin retain their ability to affect the nutritive value of preserved forage legumes.

The fluctuation experiment is the preferred method for estimating microbial mutation rates. A difficult task facing the data analyst is to infer the mean number of mutations from the number of mutant cells that only indirectly reflects the number of mutations. Partial plating, commonly practised in the laboratory, renders this task even more challenging by allowing only a portion of the mutant cells to be counted. In this paper, we propose a Bayesian approach to correcting for partial plating in the analysis of fluctuation experiments.

The fast multipoint maximum likelihood mapping algorithm for crosses between inbred lines, introduced by Jansen et al. (2001),is extended for mapping in a full-sib family of an outbreeding species. The method accommodates different segregation types of markers and differences in recombination between parents. The two separate parental multipoint maximum likelihood maps are joined into an integrated map by averaging lengths over anchored segments and by interpolating or extrapolating for markers segregating in one parent only. The method is illustrated with simulated data. The method will enable a more accurate estimation of maps in outbreeding species than current methods.

The aim of this study was to compare the n-alkanes and the ytterbium (Yb)/faecal index techniques as two methods for estimating the herbage intake of dairy cows fed indoors on different herbage : supplement ratios and feeding levels. The supplement was a mixture of maize silage and soyabean meal (ratio of 87 : 13 on a dry matter (DM) basis). In all, four treatments were studied. The herbage : supplement ratio in the diet was 25 : 75, 50 : 50, 75 : 25 and 50 : 50 for treatments 1, 2, 3 and 4, respectively. Animals were offered for treatments 1, 2 and 3, 100% of ad libitum intake measured before the experiment and 70% of ad libitum intake for treatment 4. Cows were fed herbage in the morning and supplement in the evening. A total of six lactating Holstein dairy cows were used in a 4 × 4 Latin square with four 14-day periods. Herbage and supplement intakes, faecal output (FO), in vivo organic matter (OM) digestibility and faecal recovery of markers were measured on the last 5 days of each period. Intake was estimated with the two methods and from two faecal sampling techniques, that is, total faecal collection v. grab sampling during milking. Mean herbage intake as fed, or estimated from n-alkanes or from the Yb/faecal index was 7.7, 8.1 and 10.2 kg DM, respectively. The mean prediction error, expressed as a fraction of actual herbage intake, was 0.10 and 0.50 for the n-alkanes and Yb/faecal index methods, respectively. The n-alkanes method clearly showed much better accuracy than the Yb/faecal index method for estimating intake, irrespective of the faecal sampling method, herbage : silage proportion or feeding level. For the n-alkanes method, herbage intake was slightly overestimated (7%) when herbage proportion in the diet was high, due to a ratio of faecal C33 : C32 recovery >1. The high bias for the Yb/faecal index was due to the cumulative effect of overestimation of FO (mean recovery of Yb = 0.92) and underestimation of the diet indigestible fraction (−8%). Between-treatment variations of FO were on average well estimated by Yb. Between-treatment variations of OM digestibility estimated using the faecal index technique were lower than those observed in vivo. It is concluded that intake of grazing dairy cows receiving high levels of maize silage supplement should be estimated using the n-alkanes method.

Understanding the relative influence of genetic drift and selection is fundamental in evolutionary biology. The theory of neutrality predicts that the genetic differentiation of a quantitative trait (QST) equals the genetic differentiation at neutral molecular markers (FST) if the quantitative trait has not been under selection. Thus, the relative magnitude of observed QST and expected QST under neutral expectations suggests the importance of selection and genetic drift for any observed phenotypic divergence. Because QST is based on additive genetic variance, estimating QST based on phenotypic measurements is problematic due to unknown environmental effects. To account for this, we used a model where the environmental component was allowed to vary when estimating QST. The model was used on data from 14 house sparrow (Passer domesticus) populations in Norway. In accordance with the significant phenotypic inter-population differences our analyses suggested that directional selection may have favoured different optimal phenotypes for some morphological traits across populations. In particular, different body mass and male ornamental phenotypes seemed to have been favoured. The conclusions are, however, dependent on assumptions regarding the proportion of the observed inter-population variation that is due to additive genetic differences, showing the importance of collecting such information in natural populations. By estimating QST, allowing the additive genetic proportion of phenotypic inter-population variation to vary, and by making use of recent statistical methods to compare observed QST with neutral expectations, we can use data that are relatively easy to collect to identify adaptive variation in natural populations.

Allelic expression of the rice yield-related gene, leucine-rich receptor-like kinase 6 (LRK6), in the hybrid of 93-11 (Oryza sativa L. subsp. Indica var. 93-11) and Nipponbare (O. sativa L. subsp. Japonica var. Nipponbare) is determined by allelic promoter cis-elements. Using deletion analysis of the LRK6 promoter, we identified two distinct regions that might contribute to LRK6 expression. Sequence alignment revealed differences in these LRK6 promoter regions in 93-11 and Nipponbare. One of the segments, named differential sequence of LRK6 promoter 2 (DSLP2), contains potential transcription factor binding sites. Using a yeast one-hybrid assay, we isolated an ethylene-responsive factor (ERF) protein that binds to DSLP2. Sequence analysis and a GCC-box assay showed that the ERF gene, O. sativa ERF 3 (OsERF3), which belongs to ERF subfamily class II, has a conserved ERF domain and an ERF-associated amphiphilic repression repressor motif. We used an in vivo mutation assay to identify a new motif (5′-TAA(A)GT-3′) located in DSLP2, which interacts with OsERF3. These results suggest that OsERF3, an AP2 (APETALA 2 Gene)/ERF transcription factor, binds the LRK6 promoter at this new motif, which might cause differential expression of LRK6 in the 93-11/Nipponbare hybrid.

Several studies have reported data on comparisons between two methods: the total collection of feces and the internal markers method. The aim of this study was to assess the apparent digestibility of two concentrates and to compare the apparent digestion coefficients using the total collection of feces and acid-insoluble ash (AIA) as the internal marker method. In 2009, six adult geldings aged between 3 and 11 years, with an average weight per trial of 543, 540 and 542 kg, respectively, were used to determine the apparent digestibility by means of three in vivo digestibility trials on hay, hay plus wheat bran (60 : 40) and hay plus extruded flax (80 : 20). Feces were collected over a 6-day period with a previous 14-day adaptation period. The three digestibility trials were carried out to determine the digestion coefficients of the three diets and, indirectly, of the two concentrates. The digestion coefficients of the diets were determined for the dry matter, organic matter, crude protein and gross energy, whereas the apparent digestion coefficients of the same parameters were calculated for wheat bran and extruded flax, by calculating the difference from the previous results. The data were analyzed using the Student t-test for paired samples. The digestion coefficients obtained were similar when the total collection of feces and the AIA method were used. Higher data variability, confirmed by a greater standard deviation, was observed using the AIA method to estimate the apparent digestion coefficients. It can be concluded that the use of AIA as an internal marker in digestibility trials on average leads to values similar to those obtained with the total collection of feces and can therefore be considered a less-expensive method to determine apparent digestion coefficients. Nevertheless, the total collection of feces should still be considered the best choice to determine the digestibility of some specific feedstuffs.

Preservation of rare genetic stocks requires assessment of within-population genetic diversity and between-population differentiation to make inferences on their degree of uniqueness. A total of 194 Tuscan cattle (44 Calvana, 35 Chianina, 25 Garfagnina, 31 Maremmana, 31 Mucca Pisana and 28 Pontremolese) individuals were genotyped for 34 microsatellite markers. Moreover, 56 samples belonging to Argentinean Creole and Asturiana de la Montaña cattle breeds were used as an outgroup. Genetic diversity was quantified in terms of molecular coancestry and allelic richness. STRUCTURE analyses showed that the Tuscan breeds have well-differentiated genetic backgrounds, except for the Calvana and Chianina breeds, which share the same genetic ancestry. The between-breed Nei's minimum distance (Dm) matrices showed that the pair Calvana–Chianina was less differentiated (0.049 ± 0.006). The endangered Tuscan breeds (Calvana, Garfagnina, Mucca Pisana and Pontremolese) made null or negative contributions to diversity, except for the Mucca Pisana contribution to allelic richness (CT = 1.8%). The Calvana breed made null or negative within-breed contributions (W = 0.0%; CW = −0.4%). The Garfagnina and Pontremolese breeds made positive contributions to between-breed diversity but negative and high within-breed contributions, thus suggesting population bottleneck with allelic losses and increase of homozygosity in the population. Exclusion of the four endangered Tuscan cattle breeds did not result in losses in genetic diversity (T = −0.7%; CT = −1.2%), whereas exclusion of the non-endangered breeds (Chianina and Maremmana) did (T = 2.1%; CT = 3.9%); the simple exclusion of the Calvana breed from the former group led to losses in genetic diversity (T = 0.47%; CT = 2.34%), indicating a diverse significance for this breed. We showed how quantifying both within-population diversity and between-population differentiation in terms of allelic frequencies and allelic richness provides different and complementary information on the genetic backgrounds assessed and may help to implement priorities and strategies for conservation in livestock.

The objective of this study was to investigate the effect of different body condition score (BCS) at 30 days before calving (−30 days) induced by a differential nutritional management from −100 days until −30 days on productive parameters, the interval to first ovulation and blood parameters in primiparous and multiparous Holstein cows under grazing conditions until 60 days post partum. The experimental arrangement was a randomized complete block design, where cows were blocked according to BW and expected calving date and then randomly assigned to different nutritional treatments from –100 to –30 days relative to calving to induce different BCS. As the assignment of cows to treatments was random, cows had to lose, maintain or gain BCS; thus, different planes of nutrition were offered with approximately 7, 14 or 20 kg dry matter per day. The BCS score was assessed every 15 days and animals were reassigned in order to achieve the desired BCS at –30 days. Only animals that responded to nutritional treatment were considered and this was defined as follows: primiparous and multiparous high cows (PH and MH) had to gain 0.5 points of BCS, primiparous low (PL) had to lose 0.5 points of BCS and multiparous low (ML) had to maintain BCS at least in two subsequent observations from −100 to −30 days. From −30 days to calving, primiparous and multiparous cows (P and M cows) were managed separately and cows were offered a diet once a day. From calving to 60 days post partum, cows of different groups grazed in separate plots a second year pasture. Cows were also supplemented individually with whole-plant maize silage and commercial concentrate. Cows had similar BCS at −100 days and differed after the nutritional treatment; however, all groups presented similar BCS at 21 days post partum. The daily milk production and milk yield at 60 days post partum was higher in M than P cows. The percentage of milk fat was higher in PH cows compared with PL cows. Concentrations of non-esterified fatty acids (NEFA) were affected by the BCS at −30 days within parity, and in PH cows the concentration of NEFA was higher than in PL cows. The concentrations of total protein were higher in M cows. A lower probability of cycling was found in PL than in PH cows (P < 0.05) and in ML than in MH cows (P < 0.05). Treatment affected various endocrine/metabolic profiles according to parity, suggesting that the metabolic reserves signal the productive/reproductive axis so as to induce a differential nutrient partitioning in adult v. first-calving cows.

Milk yield per cow has continuously increased in many countries over the last few decades. In addition to potential economic advantages, this is often considered an important strategy to decrease greenhouse gas (GHG) emissions per kg of milk produced. However, it should be considered that milk and beef production systems are closely interlinked, as fattening of surplus calves from dairy farming and culled dairy cows play an important role in beef production in many countries. The main objective of this study was to quantify the effect of increasing milk yield per cow on GHG emissions and on other side effects. Two scenarios were modelled: constant milk production at the farm level and decreasing beef production (as co-product; Scenario 1); and both milk and beef production kept constant by compensating the decline in beef production with beef from suckler cow production (Scenario 2). Model calculations considered two types of production unit (PU): dairy cow PU and suckler cow PU. A dairy cow PU comprises not only milk output from the dairy cow, but also beef output from culled cows and the fattening system for surplus calves. The modelled dairy cow PU differed in milk yield per cow per year (6000, 8000 and 10 000 kg) and breed. Scenario 1 resulted in lower GHG emissions with increasing milk yield per cow. However, when milk and beef outputs were kept constant (Scenario 2), GHG emissions remained approximately constant with increasing milk yield from 6000 to 8000 kg/cow per year, whereas further increases in milk yield (10 000 kg milk/cow per year) resulted in slightly higher (8%) total GHG emissions. Within Scenario 2, two different allocation methods to handle co-products (surplus calves and beef from culled cows) from dairy cow production were evaluated. Results showed that using the ‘economic allocation method’, GHG emissions per kg milk decreased with increasing milk yield per cow per year, from 1.06 kg CO2 equivalents (CO2eq) to 0.89 kg CO2eq for the 6000 and 10 000 kg yielding dairy cow, respectively. However, emissions per kg of beef increased from 10.75 kg CO2eq to 16.24 kg CO2eq due to the inclusion of suckler cows. This study shows that the environmental impact (GHG emissions) of increasing milk yield per cow in dairy farming differs, depending upon the considered system boundaries, handling and value of co-products and the assumed ratio of milk to beef demand to be satisfied.

In this study, computed tomography (CT) technology was used to measure body composition on live pigs for breeding purposes. Norwegian Landrace (L; n = 3835) and Duroc (D; n = 3139) boars, selection candidates to be elite boars in a breeding programme, were CT-scanned between August 2008 and August 2010 as part of an ongoing testing programme at Norsvin's boar test station. Genetic parameters in the growth rate of muscle (MG), carcass fat (FG), bone (BG) and non-carcass tissue (NCG), from birth to ∼100 kg live weight, were calculated from CT data. Genetic correlations between growth of different body tissues scanned using CT, lean meat percentage (LMP) calculated from CT and more traditional production traits such as the average daily gain (ADG) from birth to 25 kg (ADG1), the ADG from 25 kg to 100 kg (ADG2) and the feed conversion ratio (FCR) from 25 kg to 100 kg were also estimated from data on the same boars. Genetic parameters were estimated based on multi-trait animal models using the average information–restricted maximum likelihood (AI-REML) methodology. The heritability estimates (s.e. = 0.04 to 0.05) for the various traits for Landrace and Duroc were as follows: MG (0.19 and 0.43), FG (0.53 and 0.59), BG (0.37 and 0.58), NCG (0.38 and 0.50), LMP (0.50 and 0.57), ADG1 (0.25 and 0.48), ADG2 (0.41 and 0.42) and FCR (0.29 and 0.42). Genetic correlations for MG with LMP were 0.55 and 0.68, and genetic correlations between MG and ADG2 were −0.06 and 0.07 for Landrace and Duroc, respectively. LMP and ADG2 were clearly unfavourably genetically correlated (L: −0.75 and D: −0.54). These results showed the difficulty in jointly improving LMP and ADG2. ADG2 was unfavourably correlated with FG (L: 0.84 and D: 0.72), thus indicating to a large extent that selection for increased growth implies selection for fatness under an ad libitum feeding regime. Selection for MG is not expected to increase ADG2, but will yield faster growth of the desired tissues and a better carcass quality. Hence, we consider MG to be a better biological trait in selection for improved productivity and carcass quality. CT is a powerful instrument in conjunction with breeding, as it combines the high accuracy of CT data with measurements taken from the selection candidates. CT also allows the selection of new traits such as real body composition, and in particular, the actual MG on living animals.