In order to study the effect of grazing pastures with a different botanical composition on rumen and intramuscular fatty acid metabolism, 21 male lambs were assigned to three botanically different pastures: botanically diverse (BD) (consisting for 65% of a variety of grass species); Leguminosa rich (L) (consisting for 61% of Leguminosae) and intensive English ryegrass (IR) (with 69% Lolium perenne). Pastures were sampled weekly for 12 weeks for analysis of their fatty acid content and composition and on nine occasions to determine the botanical composition. Ruminal and abomasal contents were sampled at slaughter and muscle and subcutaneous fat 24 h after slaughter. All samples were prepared and analysed for fatty acid composition. The L pasture showed a higher fatty acid content (29.8 mg/g dry matter (DM) v. 18.5 and 25.5 mg/g DM, for BD and IR pastures, respectively), but the sum of the proportions of the major polyunsaturated fatty acids, C18:2 n-6 and C18:3 n-3, were similar for the three pastures (69.9, 69.4 and 71.1% of fatty acids methyl esters (FAME) for BD, L and IR pastures, respectively). The BD pasture was richer in C18:2 n-6 (18.2% of FAME), while IR pasture had a higher C18:3 n-3 content (57.2% of FAME). Rumen data showed that animals grazing the BD pasture presented higher proportions of biohydrogenation intermediates, mainly C18:1 t11, C18:2 t11c15 and CLA c9t11, suggesting an inhibition of biohydrogenation. These changes were associated with shifts in the rumen microbial population as indicated by differences in the rumen pattern of volatile fatty acids, microbial odd- and branched-chain fatty acids. In L pasture animals, the content of C18:2 n-6 and C18:3 n-3 in the abomasum and subcutaneous fat was higher. Finally, higher proportions of C20:4 n-6, C20:5 n-3 and C22:5 n-3 and higher indices for elongation and desaturation activity in the intramuscular fat of BD grazing animals suggest some stimulation of elongation and desaturation of long-chain fatty acids, although this also might have been provoked partially by reduced fat deposition (due to a lower growth rate of the animals).

In many cases health and welfare problems are observed in organic egg production systems, as are high environmental risks related to nutrient leaching. These disadvantages might be reduced if the layers are allowed to utilise their ability to forage to a higher degree thereby reducing the import of nutrients into the system and stimulating the hens to perform a natural behaviour. However, very little is known about the ability of modern high-producing layers to take advantage of foraging to cover their nutritional needs, and the aim of the present work was to clarify this subject. Six flocks, each of 26 hens and one cock, were moved regularly in a rotation between different forage crops for a period of 130 days. Half of the flocks were fed typical layer feed for organic layers and half were fed whole wheat. The forage crops consisted of grass/clover, pea/vetch/oats, lupin and quinoa. At the beginning of the experiment, wheat-fed hens had a lower intake of supplementary feed (wheat) and a lower laying rate, egg weight and body weight. However, after a period of 6 to 7 weeks, the intake of wheat increased to approximately 100 g per hen per day and the laying rate increased to the same level as for the hens fed layer feed. For both groups of hens egg weight and body weight increased during the remaining part of the experiment. Crop analysis revealed different food preferences for hens fed layer feed and wheat-fed hens. Wheat-fed hens ate less of the cultivated seeds, whereas the amounts of plant material, oyster shells, insoluble grit stone and soil were larger in the crops from wheat-fed hens. Floor eggs were significantly more frequent in the hens fed layer feed, whereas wheat-fed hens only rarely laid floor eggs. Irrespective of treatment, hens were found to have excellent health and welfare. We conclude that nutrient-restricted, high-producing organic layers are capable of finding and utilising considerable amounts of different feed items from a cultivated foraging area without negative effects on their health and welfare.

The objectives of this study were to compare the effects of post-ruminal and intravenous infusions of wheat starch or glucose (CHO) or a mixture of amino acids (AA) on milk protein yield, nitrogen utilisation, plasma metabolites and mammary extraction rate of dairy cows in early lactation. Eight cow, ruminally fistulated, was assigned to two 4 × 4 Latin squares during 14-day periods, where the last 7 days were for infusions. Infusions were: (1) starch in the abomasum (SP), (2) glucose in the blood (GB), (3) AA in the abomasum (AP), and (4) AA in the blood (AB). The experiment started 54 ± 4 days (mean ± s.e.) post partum (milk yield 33.4 ± 1.7 kg). Daily amounts of nutrients infused were 378, 365, 341, and 333 g for SP, GB, AP and AB, respectively. The cows were fed a basal diet consisting of a concentrate mixture and grass silage (55:45 on dry-matter (DM) basis), and DM intake was 17.2 kg/day. Milk production was affected by site of infusion within substrate, whereas infusion substrates within infusion site (CHO or AA) were of minor importance. Compared with SP infusion, GB infusion increased ( P < 0.05) milk protein yield and concentration by 55 g and 1 g/kg. The AB infusion tended to ( P < 0.10) increase milk yield and ECM and increased ( P < 0.05) protein yield and concentration by 1.8 and 2.2 kg, 83 g and 1.1 g/kg compared with AP infusion, respectively. Nitrogen balance data indicated higher losses of metabolic faecal nitrogen (MFN) by abomasal than by intravenous infusions, and an increased ( P < 0.05) catabolism for AP and AB infusions compared with SP and GB infusions. GB infusion did not increase ( P>0.10) plasma glucose or insulin concentrations above that of SP infusion. Compared with the SP infusion, the GB infusion had minor effect on plasma AA. AP infusion increased ( P < 0.05) plasma non-essential AA (NEAA) concentration compared with AB infusion, whereas infusion site of AA had no effect ( P>0.05) on essential AA (EAA) or branched-chain AA (BCAA). Although a higher milk protein synthesis was observed for AB infusion, the mammary extraction rate was not higher ( P>0.05) than for AP infusion. Across infusion site, AP and AB infusions increased plasma concentration of EAA and BCAA, but compared with GB infusion, the mammary extraction rates tended ( P < 0.10) to be lower. It is concluded that abomasal nutrient infusion increases loss of MFN and that the gastrointestinal metabolism influences the nutrients available for milk synthesis. Our conclusion is that when glucose was infused, AA limited a further milk protein synthesis, but when AA was infused, glucose or energy substrate might have been the limiting factor. Our results verify that glucogenic substrates are limiting when cows are in negative energy balance.

Three change-over design experiments investigated the origin of hydrogen sulphide in the rumen head-space gas of dairy cows, comparing the effects of single iso-S additions of methionine, cysteine and sodium sulphate, as well as the effects of single meals of fresh ryegrass or white clover. The concentration of hydrogen sulphide in rumen gas declined close to zero within 4 h after withdrawal of the previous feed. Sulphur sources were then given to cows and concentrations of hydrogen sulphide recorded in rumen head-space gas at 30-min intervals. Cysteine addition (8 g) led to a rapid (within 30 min) and a large (490 and 957 p.p.m. respectively in two experiments) increase in hydrogen sulphide concentration. Concentrations were significantly less following methionine addition. Increasing levels of cysteine addition led to significant increases in hydrogen sulphide concentrations ( P < 0.001 for the linear effect), although peak hydrogen sulphide was delayed and concentrations remained higher for longer with the highest (12 g) addition of cysteine ( P < 0.01 for the ‘cysteine level’ × ‘time’ interaction). The increase in concentration of hydrogen sulphide from sodium sulphate was smaller (230 p.p.m.) and slower (2 h) than for cysteine. Despite the much higher intake of cystine for white clover in comparison with perennial ryegrass ( P < 0.001), there was almost no increase in hydrogen sulphide concentration in rumen head-space gas from cows fed white clover. It seems likely that this is associated with the use of sulphur to produce thiocyanate to detoxify the hydrogen cyanide from cyanogenic white clover.

The effect of a dietary supplementation with mannan-oligosaccharide (MOS, Bio-Mos, Alltech Inc.) and inulin (Frutafit® IQ) on growth, health, and caecal traits was studied on 348 rabbits (Hyplus®), weaned at 25 days of age. Three hundred and thirty rabbits (110 per group) were used for the health status and growth performance trial, while 18 rabbits (six per group) were used for caecal metabolism evaluation at the age of 42 days of age. Three diets were formulated: C (control), M (0.3% MOS) and I diet (4% inulin). Digestibility of the diets was measured in 10 rabbits per group between 36 and 40 days of age. The control diet was fed to rabbits of the C group from weaning to 74 days of age (slaughter). Diets M and I were fed to rabbits of the respective group from weaning to 46 days of age, then were fed with control diet till slaughter. From 25 to 46 days of age, the weight gain was slightly higher in control rabbits ( P = 0.11), while no differences were recorded for the whole period. No differences among groups in the mortality, which was high due to an enteropathy-infected environment, were significant. The lowest morbidity ( P = 0.05) as well as the health risk index were recorded in rabbits fed the diet with inulin ( P = 0.03). After change of diet, the health risk index increased in the rabbits previously fed the diet with additives, thereby no significant differences in the health status were recorded for the whole period. Total caecal volatile fatty acids concentration was higher ( P < 0.01) and the pH ( P < 0.01) and ammonia concentration ( P = 0.01) lower in rabbits fed the inulin diet than in other rabbits. In these animals, acetate molar proportion was higher ( P = 0.01) and that of propionate as well as the propionate/butyrate ratio significantly lower than in other rabbits. Butyrate molar proportion was higher in rabbits fed the diet with MOS ( P < 0.01). In rabbits fed the inulin diet a higher activity of inulinase was recorded ( P < 0.001) than in other rabbits. A significantly lower digestibility of cellulose was observed in rabbits fed the diet with MOS. The results of our study suggest the importance of using inulin-type fructans in the nutrition of young rabbits. The higher health risk index of rabbits after change of diets indicates that prebiotics should be given for a longer time during the fattening period.

Mechanistic animal growth models can incorporate a description of the genotype as represented by underlying biological traits that aim to specify the animal's genetic potential for performance, independent from the environmental factors captured by the models. It can be argued that these traits may therefore be more closely associated to genetic potential, or components of genetic merit that are more robust across environments, than the environmentally dependent phenotypic traits currently used for genetic evaluation. The prediction of merit for underlying biological traits can be valuable for breeding and development of selection strategies across environments.

Model inversion has been identified as a valid method for obtaining estimates of phenotypic and genetic components of the biological traits representing the genotype in the mechanistic model. The present study shows how these estimates were obtained for two existing pig breeds based on genetic and phenotypic components of existing performance trait records. Some of the resulting parameter estimates associated with each breed differ substantially, implying that the genetic differences between the breeds are represented in the underlying biological traits. The estimated heritabilities for the genetic potentials for growth, carcass composition and feed efficiency as represented by biological traits exceed the heritability estimates of related phenotypic traits that are currently used in evaluation processes for both breeds. The estimated heritabilities for maintenance energy requirements are however relatively small, suggesting that traits associated with basic survival processes have low heritability, provided that maintenance processes are appropriately represented by the model.

The results of this study suggest that mechanistic animal growth models can be useful to animal breeding through the introduction of new biological traits that are less influenced by environmental factors than phenotypic traits currently used. Potential value comes from the estimation of underlying biological trait components and the explicit description of their expression across a range of environments as predicted by the model equations.

The carry-over effect of a pre-starter diet (0 to 3 days of age) deficient in lysine on subsequent growth and body composition (3 to 10 days) was examined in two experiments on male broiler chicks raised in cages. In experiment 1, lysine deficiency was applied from 3 to 10 days after providing a balanced pre-starter control feed (D+, 1.40% lysine) or a lysine deficient feed (D−) during the first 3 days. Three levels of deficiency (A = 0.63%, B = 0.72%, C = 0.82%) were tested. Growth and feed intake were higher in D+ than in D− chicks ( P < 0.001). However, the feed conversion ratio from 3 to 10 days of age was higher in D+ chicks ( P < 0.001); pre-starter and starter feeds interacted ( P < 0.04) with the feed conversion of treatment D+/A = 2.07 being better than treatment D+/A = 2.61 ( P < 0.05). This suggests that chicks deficient from hatching exhibit a relatively lower sensitivity to lysine deficiency than chicks started on a control diet. In experiment 2, performance, slaughter parameters and body composition were analysed at 3 and 10 days of age, in chicks having received a lysine deficient feed (D0, 0.72% lysine), a control feed (D+, 1.40% lysine) or having been pair fed with control feed adjusted to D0 intake (PF) from 0 to 3 days of age, and then fed D0 ad libitum from 3 to 10 days of age. At 3 days, PF chicks had a higher body weight ( P < 0.05) than D0, and thus a better feed conversion. Body composition in relative values was little or not affected by dietary treatments, but the breast muscle weight at 3 days was higher in D+ and PF chicks compared with D0 ( P < 0.05) and this effect was even accentuated at 10 days of age. The present work confirms that early nutrition can have subsequent consequences on the adjustment of fast growing broiler chicks to their nutritional conditions. It also suggests that breast muscle development is a more reactive parameter than whole body composition in this kind of experiments.

The objectives of this study were to see if the body condition score curve during lactation could be described using a model amenable to biological interpretation, a non-linear function assuming exponential rates of change in body condition with time, and to quantify the effect of breed and parity on curves of body condition during lactation. Three breeds were represented: Danish Holstein (n = 112), Danish Red (n = 97) and Jerseys (n = 8). Cows entered the experiment at the start of first lactation and were studied during consecutive lactations (average number of lactations 2, minimum 1, maximum 3). They remained on the same dietary treatment throughout. Body condition was scored to the nearest half unit on the Danish scale (see Kristensen (1986); derived from the Lowman et al. (1976) system) from 1 to 5 on days: 2, 14, 28, 42, 56, 84, 112, 168, 224 after calving. Additionally, condition score was recorded on the day of drying off the cow, 35, 21, and 7 days before expected calving and finally on the day of calving. All condition scores were made by the trained personal on the research farm, where the same person made 92% of the scores. The temporal patterns in condition score were modelled as consisting of two underlying processes, one related to days from calving, referred to as lactation only, the other to days from (subsequent) conception, referred to as pregnancy. Both processes were assumed to be exponential functions of time. Each process was modelled separately using exponential functions, i.e. one model for lactation only and one for pregnancy, and then a combined model for both lactation only and pregnancy was fitted. The data set contained 467 lactation periods and 378 pregnancy periods. The temporal patterns in condition score of cows kept under stable and sufficient nutritional conditions were successfully described using a two component non-linear function. First lactation cows had shallower curves, they had greater condition scores at the nadir of the curve. Danish Holstein and Jersey were thinner at the end of the mobilisation period having lost more body condition than the Danish Red breed. Although the dairy breeds ended up being thinner there were no significant differences in the rate at which they lost body condition.

The experiment tested the hypothesis that short-term feeding of barley just before lambing would be as effective as maize in stimulating early production of colostrum. Both grains are high in starch, and should provide a substrate for lactose which, in turn, promotes lactogenesis. Thirty-five Corriedale ewes bearing single foetuses and 25 bearing twin-foetuses from a synchronised mating were fed on pasture during most of gestation. Fourteen days before the expected time of lambing the single- and twin-bearing ewes were allocated to three treatments and fed (1) a basal diet of lucerne hay to meet their nutrient requirements, (2) the basal diet plus a supplement of whole barley; or (3) the basal diet plus a supplement of cracked maize. The twin-bearing control ewes accumulated more colostrum than the single-bearing control ewes at birth (292 v. 190 g). However, supplementation with barley or maize increased the colostrum at birth to 360 and 541 g in singles and 648 and 623 g in twins. We conclude that barley is a good alternative to maize to stimulate production of colostrum especially in twin-bearing ewes whose lambs are the most likely to benefit from the supplement.

Food waste from fish and fruit shops was used as an alternative to the grain in grower-finisher pig diets. Two diets were formulated on an iso-nutrient basis (14 MJ digestible energy per kg, 160 g crude protein per kg on a dry-matter basis) to contain 0 g of food waste per kg in the control diet and 50 g of fish-shop waste per kg and 120 g of fruit-shop waste per kg in the experimental diet. In the study, 28 pigs per diet (seven pigs per pen) were fed ad libitum from 20 kg to 100 kg, then, they were slaughtered and the carcass characteristics determined. The inclusion of food waste in the diet had no significant effect (P>0.05) on average daily feed intake (2.12 v. 2.20 kg/day), average daily gain (0.74 v. 0.78 kg/day), or gain/feed (0.35 v. 0.35 kg per kg). In the case of the experimental diet, backfat thickness was significantly lower (18.0 v. 21.3 mm, P < 0.01). The results of the taste test indicated that the meat from food waste-fed pigs had acceptable organoleptic quality although a very light aroma to fish was observed in the bacon (P < 0.01).

It was concluded that food waste from the fish and fruit shops could be included in grower-finisher pig diets without any detrimental effect on growth performance and only minor effects on carcass characteristics and meat quality.

Deng et al. have recently proposed that estimates of an upper limit to the rate of spontaneous mutations and their average heterozygous effect can be obtained from the mean and variance of a given fitness trait in naturally segregating populations, provided that allele frequencies are maintained at the balance between mutation and selection. Using simulations they show that this estimation method generally has little bias and is very robust to violations of the mutation–selection balance assumption. Here I show that the particular parameters and models used in these simulations generally reduce the amount of bias that can occur with this estimation method. In particular, the assumption of a large mutation rate in the simulations always implies a low bias of estimates. In addition, the specific model of overdominance used to check the violation of the mutation–selection balance assumption is such that there is not a dramatic decline in mean fitness from overdominant mutations, again implying a low bias of estimates. The assumption of lower mutation rates and/or other models of balancing selection may imply considerably larger biases of the estimates, making the reliability of the proposed method highly questionable.

Agrostis species are mainly used in athletic fields and golf courses. Their integrity is maintained by fungicides, which makes the development of disease-resistance varieties a high priority. However, there is a lack of knowledge about resistance (R) genes and their use for genetic improvement in Agrostis species. The objective of this study was to identify and clone constitutively expressed cDNAs encoding R gene-like (RGL) sequences from three Agrostis species (colonial bentgrass (A. capillaris L.), creeping bentgrass (A. stolonifera L.) and velvet bentgrass (A. canina L.)) by PCR-based motif-directed RNA fingerprinting towards relatively conserved nucleotide binding site (NBS) domains. Sixty-one constitutively expressed cDNA sequences were identified and characterized. Sequence analysis of ESTs and probable translation products revealed that RGLs are highly conserved among these three Agrostis species. Fifteen of them were shown to share conserved motifs found in other plant disease resistance genes such as MLA13, Xa1, YR6, YR23 and RPP5. The molecular evolutionary forces, analysed using the Ka/Ks ratio, reflected purifying selection both on NBS and leucine-rich repeat (LRR) intervening regions of discovered RGL sequences in these species. This study presents, for the first time, isolation and characterization of constitutively expressed RGL sequences from Agrostis species revealing the presence of TNL (TIR-NBS-LRR) type R genes in monocot plants. The characterized RGLs will further enhance knowledge on the molecular evolution of the R gene family in grasses.

Indirect estimates of the genomic rate of deleterious mutations (λ), their average homozygous effect (s) and their degree of dominance (h) can be obtained from genetic parameters of natural populations, assuming that the frequencies of the loci controlling a given fitness trait are at mutation–selection equilibrium. In 1996, H.-W. Deng and M. Lynch developed a general methodology for obtaining these estimates from inbreeding/outbreeding experiments. The prediction of the sign and magnitude of the biases incurred by these estimators is essential for a correct interpretation of the empirical results. However, the assessment of these biases has been tested so far under a rather limited model of the distribution of dominance effects. In this paper, the application of this method to outbred populations is evaluated, focusing on the level of variation in h values (σh2) and the magnitude of the negative correlation (rs,h) between s and h. It is shown that the method produces upwardly biased estimates of λ and downwardly biased estimates of the average s in the reference situation where rs,h=0, particularly for large values of σh2, and biases of different sign depending on the magnitude of the correlation. A modification of the method, substituting the estimates of the average h for alternative ones, allows estimates to be obtained with little or no bias for the case of rs,h=0, but is otherwise biased. Information on rs,h and σh2, gathered from mutation-accumulation experiments, suggests that σh2 may be rather large and rs,h is usually negative but not higher than about −0·2, although the data are scarce and noisy, and should be used with caution.

The loop design of Kerr and Churchill is a clever application of incomplete blocks of size 2 to two-channel microarray experiments. In this paper, we extend the loop design to include more replicates, biological and technical replication, multi-factor experiments, and blocking. Loop and extended loop designs are shown to be more efficient than the reference design for any given number of arrays. We also show that adding new treatments to a loop design requires the same number of additional arrays as adding treatments to a reference design, with a greater gain in power. Given the flexibility of extended loop designs and their power, we propose that these should be the designs of choice for most experiments using two-channel microarrays.

This study is aimed at improving the analysis of data used in identifying marker-associated effects on quantitative traits, specifically to account for possible departures from a Gaussian distribution of the trait data and to allow for asymmetry of marker effects attributable to phenotypic divergence between parental lines. A Bayesian procedure for analysing marker effects at the whole-genome level is presented. The procedure adopts a skewed t-distribution as a prior distribution of marker effects. The model with the skewed t-process includes Gaussian prior distributions, skewed Gaussian prior distributions and symmetric t-distributions as special cases. A Markov Chain Monte Carlo algorithm for obtaining marginal posterior distributions of the unknowns is also presented. The method was applied to a dataset on three traits (live weight, carcass length and backfat depth) measured in an F2 cross between Iberian and Landrace pigs. The distribution of marker effects was clearly asymmetric for carcass length and backfat depth, whereas it was symmetric for live weight. The t-distribution seems more appropriate for describing the distribution of marker effects on backfat depth.

Covariance components for test day milk yield using 263 390 first lactation records of 32 448 Holstein cows were estimated using random regression animal models by restricted maximum likelihood. Three functions were used to adjust the lactation curve: the five-parameter logarithmic Ali and Schaeffer function (AS), the three-parameter exponential Wilmink function in its standard form (W) and in a modified form (W*), by reducing the range of covariate, and the combination of Legendre polynomial and W (LEG+W). Heterogeneous residual variance (RV) for different classes (4 and 29) of days in milk was considered in adjusting the functions. Estimates of RV were quite similar, rating from 4.15 to 5.29 kg2. Heritability estimates for AS (0.29 to 0.42), LEG+W (0.28 to 0.42) and W* (0.33 to 0.40) were similar, but heritability estimates used W (0.25 to 0.65) were highest than those estimated by the other functions, particularly at the end of lactation. Genetic correlations between milk yield on consecutive test days were close to unity, but decreased as the interval between test days increased. The AS function with homogeneous RV model had the best fit among those evaluated.