Despite the fact that the ruminant diet is rich in polyunsaturated fatty acids (PUFA), ruminant products – meat, milk and dairy – contain mainly saturated fatty acids (SFA) because of bacterial lipolysis and subsequent biohydrogenation of ingested PUFA in the rumen. The link between SFA consumption by man and coronary heart disease is well established. In contrast, ruminant products also contain fatty acids that are known to be beneficial to human health, namely conjugated linoleic acids (CLAs). The aims of research in this field have been to understand the microbial ecology of lipolysis and biohydrogenation and to find ways of manipulating ruminal microbes to increase the flow of PUFA and CLA from the rumen into meat and milk. This review describes our present understanding of the microbial ecology of ruminal lipid metabolism, including some apparently anomalous and paradoxical observations, and the status of how the metabolism may be manipulated and the possible consequential effects on other aspects of ruminal digestion. Intuitively, it may appear that inhibiting the ruminal lipase would cause more dietary PUFA to reach the mammary gland. However, lipolysis releases the non-esterified fatty acids that form the substrates for biohydrogenation, but which can, if they accumulate, inhibit the whole process. Thus, increasing lipase activity could be beneficial if the increased release of non-esterified PUFA inhibited the metabolism of CLA. Rumen ciliate protozoa do not carry out biohydrogenation, yet protozoal lipids are much more highly enriched in CLA than bacterial lipids. How could this happen if protozoa do not metabolise PUFA? The answer seems to lie in the ingestion of plant organelles, particularly chloroplasts, and the partial metabolism of the fatty acids by contaminating bacteria. Bacteria related to Butyrivibrio fibrisolvens are by far the most active and numerous biohydrogenating bacteria isolated from the rumen. But do we misunderstand the role of different bacterial species in biohydrogenation because there are uncultivated species that we need to understand and include in the analysis? Manipulation methods include dietary vegetable and fish oils and plant-derived chemicals. Their usefulness, efficacy and possible effects on fatty acid metabolism and on ruminal microorganisms and other areas of their metabolism are described, and areas of opportunity identified.

Decreasing enteric methane (CH4) emissions from ruminants without altering animal production is desirable both as a strategy to reduce global greenhouse gas (GHG) emissions and as a means of improving feed conversion efficiency. The aim of this paper is to provide an update on a selection of proved and potential strategies to mitigate enteric CH4 production by ruminants. Various biotechnologies are currently being explored with mixed results. Approaches to control methanogens through vaccination or the use of bacteriocins highlight the difficulty to modulate the rumen microbial ecosystem durably. The use of probiotics, i.e. acetogens and live yeasts, remains a potentially interesting approach, but results have been either unsatisfactory, not conclusive, or have yet to be confirmed in vivo. Elimination of the rumen protozoa to mitigate methanogenesis is promising, but this option should be carefully evaluated in terms of livestock performances. In addition, on-farm defaunation techniques are not available up to now. Several feed additives such as ionophores, organic acids and plant extracts have also been assayed. The potential use of plant extracts to reduce CH4 is receiving a renewed interest as they are seen as a natural alternative to chemical additives and are well perceived by consumers. The response to tannin- and saponin-containing plant extracts is highly variable and more research is needed to assess the effectiveness and eventual presence of undesirable residues in animal products. Nutritional strategies to mitigate CH4 emissions from ruminants are, without doubt, the most developed and ready to be applied in the field. Approaches presented in this paper involve interventions on the nature and amount of energy-based concentrates and forages, which constitute the main component of diets as well as the use of lipid supplements. The possible selection of animals based on low CH4 production and more likely on their high efficiency of digestive processes is also addressed. Whatever the approach proposed, however, before practical solutions are applied in the field, the sustainability of CH4 suppressing strategies is an important issue that has to be considered. The evaluation of different strategies, in terms of total GHG emissions for a given production system, is discussed.

The potential of the composition of the forerib measured by X-ray computed tomography (CT) as a predictor of carcass composition was evaluated using data recorded on 30 Aberdeen Angus and 43 Limousin crossbred heifers and steers. The left sides of the carcasses were split into 20 cuts, which were CT scanned and fully dissected into fat, muscle and bone. Carcass and forerib tissue weights were assessed by dissection and CT. Carcass composition was assessed very accurately by CT scanning of the primal cuts (adj-R2 = 0.97 for the three tissues). CT scanning predicted weights of fat, muscle and bone of the forerib with adj-R2 of 0.95, 0.91 and 0.75, respectively. Single regression models with the weights of fat, muscle or bone in the forerib measured by CT as the only predictors to estimate fat, muscle or bone of the left carcass obtained by CT showed adjusted coefficients of determination (adj-R2) of 0.79, 0.60 and 0.52, respectively. By additionally fitting breed and sex, accuracy increased to 0.85, 0.73 and 0.67. Using carcass and forerib weights in addition to the previous predictors improved significantly the prediction accuracy of carcass fat and muscle weights to adj-R2 values of 0.92 and 0.96, respectively, while the highest value for carcass bone weight was 0.77. In general, equations derived using CT data had lower adj-R2 values for bone, but better accuracies for fat and muscle compared to those obtained using dissection. CT scanning could be considered as an alternative very accurate and fast method to assess beef carcass composition that could be very useful for breeding programmes and research studies involving a large number of animals, including the calibration of other indirect methods (e.g. in vivo and carcass video image analysis).

Mink skin size in Finland, as well as in other countries, has increased considerably during last decade. However, there are signs that selection for large body size has a negative impact on litter size (LS) and also for survival of kits. Therefore, it is important to study the genetic relationships among fertility traits and animal size (AS). The variance components for age at first mating (AFM) and first three parity LS and AS were estimated using multi-trait restricted maximum likelihood animal model. Data included 82 945 animals born during 1990 to 2004, originating from nine farms. Heritability estimates for the fertility traits were from 0.10 to 0.15. For AS, heritability was estimated to be 0.18. Genetic correlation between AS and all fertility traits was estimated to be negative (varying from −0.004 to −0.38). It is important to recognize this antagonistic relationship and include the reproductive traits into breeding goals to maintain good reproductive performance when selecting for increased body size and hence larger pelts in fur animals. Genetic correlations between the traits should be accounted in breeding value evaluations by using a multi-trait model. Including AFM into breeding value estimation would also improve the accuracy of breeding value estimation for fertility, because females missing the first LS still have record on AFM.

Beet pulp contains high amounts of pectins that can reduce the risk of rumen disorders compared to using feedstuffs high in starch. The objective was to study the effects of inclusion of ensiled pressed beet pulp in total mixed rations (TMR) for high-yielding dairy cows. Two TMR containing no or about 20% (on dry matter (DM) basis) beet pulp silage were used. The beet pulp silage mainly replaced maize silage and corn cob silage. The TMR were intentionally equal in the concentrations of energy and utilisable crude protein (CP) at the duodenum. TMR were fed to 39 and 40 dairy cows, respectively, for 118 days. The average daily milk yield was about 43 kg/day. No significant differences in milk yield and milk fat or milk protein content were detected. DM intake of cows was significantly reduced by the inclusion of beet pulp silage (23.0 v. 24.5 kg/day). However, a digestibility study, separately conducted with sheep, showed a significantly higher organic matter digestibility and metabolisable energy concentration for the TMR that contained beet pulp silage. In vitro gas production kinetics indicated that the intensity of fermentation was lower in the TMR that contained beet pulp silage. In vitro production of short-chain fatty acids, studied using a Rusitec, did not differ between the TMR. However, the inclusion of beet pulp silage in the ration caused a significant reduction in the efficiency of microbial CP synthesis in vitro. The amino acid profile of microbial protein remained unchanged. It was concluded that beet pulp silage has specific effects on ruminal fermentation that may depress feed intake of cows but improve digestibility. An inclusion of beet pulp silage of up to 20% of DM in rations for high-yielding dairy cows is possible without significant effects on milk yield and milk protein or milk fat.

The objectives of this study were to evaluate the influence of diet composition on ruminal parameters, more particularly redox potential (Eh). Four Holstein dry dairy cows, fitted with ruminal cannulas, were allocated in a 4 × 4 Latin square design. They were given four experimental hay-based diets D0, D25, D42 and D56 consisting of 0%, 25%, 42% and 56% of ground wheat and barley concentrate mixture, respectively. They were fed at a daily feeding rate of 8.0 kg DM per cow during a 24-day experimental period (a 21-day diet adaptation, three consecutive days of measurement and sampling). The physicochemical parameters, such as pH and Eh, were measured and Clark’s exponent (rH) was calculated from 1 h before feeding to 8 h after feeding at 1-h interval. Samples of ruminal fluid were taken at 0, 1, 2, 4, 6 and 8 h after feeding for the determination of volatile fatty acid (VFA) and ammonia N (NH3-N) concentrations. Ruminal bacterial populations were also studied by means of capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) technique to focus on the structure of the ruminal microbiota and the diversity index was calculated. Mean ruminal Eh and rH were not modified by the concentrate-to-forage ratio and averaged – 210 mV and 6.30, respectively, across diets. The pH decreased slightly by 0.10 pH unit between treatments D0 and D56 with an average of 6.58. Nevertheless, the time during which physicochemical parameters remained at nadir value after feeding varied with diets: 2 and 7 h for D0 and 6 and 5 h for D56, respectively for pH and Eh. Moreover, fermentative parameters were altered by treatments: total VFA and NH3-N were greater in D56 (72.2 mM and 17.5 mg/100 ml) compared with D0 (65.2 mM and 14.2 mg/100 ml). However, neither the structure of bacterial populations of the rumen nor the diversity index (Shannon) was altered by treatments.

A better understanding of the factors regulating feed efficiency and their potential as predictors of feed efficiency in cattle is needed. Therefore, the potential of three classes of traits, namely, feeding behavior characteristics: daily time at feeder (TF; min/day), time per meal (TM; min), meal size (MS; g DM), eating rate (ER; g DM/min), number of daily meals (NM) and daily visits to the feeder (VF); infrared (IR) thermography traits (°C): eye (EY), cheek (CK), snout (SN), ribs (RB) and hind area (HA); and glucocorticoid levels: fecal cortisol metabolites (FCM; ng/g) and plasma cortisol (PC; ng/ml) as predictors of efficiency were evaluated in 91 steers (436 ± 37 kg) over 2 years (Y1 = 46; Y2 = 45). Additionally, the individual traits of each of these three classes were combined to define three single traits. Individual daily feed intake of a corn silage and high-moisture corn-based diet was measured using an automated feeding system. Body weight and thermographs were taken every 28 days over a period of 140 days. Four productive performance traits were calculated: daily dry matter intake (DMI), average daily gain (ADG), feed to gain ratio (F : G) and residual feed intake (RFI). Steers were also classified into three RFI categories (low-, medium- and high-RFI). Among the feeding behavior characteristics, MS and ER were correlated with all efficiency traits (range: 0.26 to 0.75). Low-RFI (more efficient steers) had smaller MS, lower ER and fewer VF in comparison to high-RFI steers. Less efficient steers (high-RFI) performed more VF during the nocturnal period than more efficient steers. More efficient steers had lower CK and SN temperatures than less efficient steers (28.1°C v. 29.2°C and 30.0°C v. 31.2°C), indicating greater energetic efficiency for low-RFI steers. In terms of glucocorticoids, PC was not correlated with efficiency traits. In contrast, more efficient steers had higher FCM in comparison to less efficient steers (51.1 v. 31.2 ng/g), indicating that a higher cortisol baseline is related to better feed efficiency. The overall evaluation of the three classes of traits revealed that feeding behavior, IR thermography and glucocorticoids accounted for 18%, 59% and 7% of the total variation associated with RFI, respectively. These classes of traits have usefulness in the indirect assessment of feed efficiency in cattle. Among them, IR thermography was the most promising alternative to screen cattle for this feed efficiency. These findings might have application in selection programs and in the better understanding of the biological basis associated with productive performance.

Knowing the large difference in daily feed intake (DFI) between Large White (LW) and Piétrain (PI) growing pigs, a backcross (BC) population has been set up to map QTL that could be used in marker assisted selection strategies. LW × PI boars were mated with sows from two LW lines to produce 16 sire families. A total of 717 BC progeny were fed ad libitum from 30 to 108 kg BW using single-place electronic feeders. A genome scan was conducted using genotypes for the halothane gene and 118 microsatellite markers spread on the 18 porcine autosomes. Interval mapping analyses were carried out, assuming different QTL alleles between sire families to account for within breed variability using the QTLMap software. The effects of the halothane genotype and of the dam line on the QTL effect estimates were tested. One QTL for DFI (P < 0.05 at the chromosome-wide (CW) level) and one QTL for feed conversion ratio (P < 0.01 at the CW level) were mapped to chromosomes SSC6 – probably due to the halothane alleles – and SSC7, respectively. Three putative QTL for feed intake traits were detected (P < 0.06 at the CW level) on SSC2, SSC7 and SSC9. QTL on feeding traits had effects in the range of 0.20 phenotypic s.d. The relatively low number of QTL detected for these traits suggests a large QTL allele variability within breeds and/or low effects of individual loci. Significant QTL were detected for traits related to carcass composition on chromosomes SSC6, SSC15 and SSC17, and to meat quality on chromosome SSC6 (P < 0.01 at the genome-wide level). QTL effects for body composition on SSC13 and SSC17 differed according to the LW dam line, which confirmed that QTL alleles were segregating in the LW breed. An epistatic effect involving the halothane locus and a QTL for loin weight on SSC7 was identified, the estimated substitution effects for the QTL differing by 200 g between Nn and NN individuals. The interactions between QTL alleles and genetic background or particular genes suggest further work to validate QTL segregations in the populations where marker assisted selection for the QTL would be applied.

The growth performance, carcass characteristics and meat quality measurements were evaluated on broiler chicks fed different dietary levels of whole inedible dates (WID). WID used in this study were consisted of date fruits (∼850 g/kg) and date pits (∼150 g/kg). Three hundred unsexed Lohman broiler chicks were randomly and equally distributed into six groups. Each was formed of 50 chicks (five replicates, 10 chicks per replicate), and was assigned to a dietary treatment. Six dietary treatments of WID (0, 30, 60, 90, 120 and 150 g/kg feed) were included in the formation of isocaloric (metabolizable energy of ∼3060 kcal/kg feed) and isonitrogenous (CP of ∼192 g/kg feed) broiler rations. The treated rations were fed to the group chicks between 15 and 42 days of age (the experimental period). A straight-run design was considered. At 42 days of age, five males from each treatment were randomly chosen and slaughtered to determine carcass characteristics, internal organs and meat quality measurements. Digestibility of nutrients was measured at the end of the experimental period using five caged-individual males per treatment. The inclusion of broiler rations on WID for up to 150 g/kg feed, over the experimental period, did not significantly influence body weight gain (1452 to 1521 g/chick), feed intake (3268 to 3621 g/chick), feed conversion ratio (2.26 to 2.36 kg/kg) and dressed carcass (63.4% to 67.3%). In addition, levels of WID for up to 150 g/kg feed did not significantly influence the digestibility of nutrients and meat quality measurements. Such results suggest the possible inclusion of broiler rations on WID for up to 150 g/kg feed, during the period of 15 to 42 days of age without adverse effects on growth performance and meat quality.

To unravel the underlying mechanisms that explain the positive effects of prefermented cereals on in vivo gastrointestinal (GI) architecture and function, an in vitro experiment using a human small intestinal epithelial cell model (Caco-2) was performed. A range of dilutions (0% to 10%) of the supernatants of three liquid experimental diets, as well as Na-lactate were used in an in vitro experiment to assess their effect on cellular growth, metabolism, differentiation and mucosal integrity using Caco-2. The experimental diets contained, in addition to a protein rich basal diet (60%), (1) a liquid control diet (C) containing 40% of a mixture of barley and wheat (ratio 3 : 1) or (2) a liquid diet (F) containing 40% prefermented barley and wheat or (3) C with the addition of the fermentation end-products (organic acids and ethanol) in concentrations similar to those in the fermented diet (FP). For F, the mixture of barley and wheat was fermented at 35°C for 48 h. Parallel to the in vitro experiment, 18 groups of eight weanling pigs were assigned to one of the experimental diets during a 14-day in vivo experiment. Each group was fed restrictively. The results of the in vitro experiment showed that the lowest dose of both F- and FP-supernatants had no clear effects on the cell proliferation, but incubation with 5% and 10% of the F- and FP-supernatants decreased the cell numbers at day 19. DNA, RNA, protein and glycoprotein synthesis in differentiated Caco-2 cells were stimulated by incubation with the lower concentrations (0.5% to 2.5%) of F- and FP-supernatants whereas the higher concentrations (5% and 10%) had no effect. Both the F- and FP-supernatants decreased the specific sucrase–isomaltase activity in a dose-dependent manner, but the effects on the specific aminopeptidase activities were less clear. Mucosal integrity initially decreased after incubation with the highest F- and FP-supernatants and started to recover between 24 and 48 h. The results of the in vivo experiment showed no dietary effects (P > 0.1) on GI morphology and brush-border enzyme activities at day 5 or at day 14. Time related changes in GI characteristics followed a normal pattern. In conclusion, the supernatants of diets containing either prefermented cereals or their fermentation end-products clearly modulate cellular growth, metabolism, differentiation and mucosal integrity in an in vitro model, although these effects were not observed in the in vivo characteristics measured in weanling pigs.

Elevated dietary nitrate (NO3−) is associated with production losses in ruminant livestock, resulting in substantial economic losses incurred by producers. Severe drought, fertilization practices and poorly maintained pastures increase the risk of elevated NO3− intake among cattle and sheep. Nitrate is metabolized to nitrite (NO2−) in the rumen and further reduced to ammonia. Ruminants consuming high dietary NO3− vary in ability to efficiently reduce excess NO2− to ammonia. This leads to methemoglobin formation and ultimately NO3− toxicity signs. Variation in individual tolerance to elevated dietary NO3− can be partially attributed to rate and duration of exposure, rate of elimination, metabolism, species and dose. Our objectives were to confirm and quantify variation in individual tolerance to subacute levels of dietary NO3−, and determine if individuals could be identified as highly or lowly tolerant to elevated dietary NO3− based on production traits, plasma analytes and(or) signs of subacute NO3− toxicity. Purebred Suffolk ewes were administered supplement mixed with tap water (control; n = 8) or potassium nitrate (NO3− treated; 300 mg NO3−/kg BW daily; n = 47) for 8 days. Coefficients of variation (CV) indicated that supplement intake was more variable in NO3− treated ewes (CV = 59.3%) than in control ewes (CV = 13.6%). Among NO3− treated ewes, six ewes highly tolerant and six ewes lowly tolerant to elevated dietary NO3− were identified based on individual performance, NO3− treated supplement intake, and signs of toxicity. Supplement intake was lower (P < 0.0001) in NO3− treated ewes than in control ewes, indicating elevated dietary NO3− influences feed intake. Supplement intake differed (P < 0.0001) between control, highly tolerant and lowly tolerant ewes. Supplement intake of highly and lowly tolerant ewes was 82% and 23%, respectively, of the control ewes’ intake. Weight change and plasma concentrations of NO2−, cortisol, glucose and retinol were not different (P ⩾ 0.38) among control, highly tolerant and lowly tolerant ewes. Plasma urea nitrogen (PUN) levels were not different (P = 0.25) between control and lowly tolerant ewes, but were lower (P = 0.02) in highly tolerant ewes than in control ewes. Furthermore, PUN and NO3− treated supplement intake were highly correlated (0.71; P < 0.0001) in lowly tolerant ewes. These results confirm and quantify variation in response to subacute levels of dietary NO3− and indicate that individuals can be identified as highly or lowly tolerant to elevated dietary NO3− based on their performance and NO3− toxicity signs.

Mammalian hair follicles are complex multicellular structures in the skin, which produce hair fibre under the influence of locally produced and systemic signalling systems. Investigation to determine mechanisms of regulation, follicular responses and the importance of nutritional supply have utilised a number of in vivo and in vitro approaches. Included in these are studies on isolated intact anagen secondary follicles singly or in groups with incubation in culture medium. These utilise techniques developed for investigation of follicles from human skin. Results from selected studies reviewed here demonstrate differences in capacity for hair growth and protein synthesis between secondary follicles from Angora and cashmere-bearing goats. Mohair follicles were shown to exhibit faster hair shaft elongation both in vivo and in vitro, to have greater DNA content per follicle and to deposit significantly more protein per follicle and per unit of DNA. Incubation of anagen mohair and cashmere follicles in the presence of melatonin or prolactin showed positive responses in hair shaft growth and protein synthesis to both signalling molecules. This result indicated directly acting effects on the follicle in addition to any indirect effects arising at a whole animal level in response to, for example, variation in photoperiod. Similarly, epidermal growth factor was shown to alter elongation and protein synthesis in mohair follicles and to produce, at higher concentration, club hair structures similar to effects observed in other species. The vitamin biotin was shown to be important in maintaining viability of isolated sheep secondary hair follicles where supplementation increased the proportion continuing to grow. Effects on growth and apparent protein synthesis suggested comparatively lesser effects on follicles, which remained viable. Histology on follicles indicated effects of biotin deficiency in reducing proliferation of basal keratinocytes. The final study, included in this review, demonstrated that supply of the essential sulphur-containing amino acid l-methionine was necessary to maintain the viability and growth of mohair follicles. l-cysteine was not required in the presence of l-methionine, although there was evidence of an optimisation when both amino acids were present in adequate concentrations. Consideration is given to the importance of transport mechanisms and capacity to utilise absorbed nutrients when considering optimising nutritional supply to individual follicles. These may then provide targets for attainment in applied nutrition of animals in vivo.

This research developed two real-time PCR assays, employing high-resolution melt and allele-specific analysis to accurately genotype the F94L mutation in cattle. This mutation (g.433C > A) in the growth differentiation factor 8 or myostatin gene has recently been shown to be functionally associated with increased muscle mass and carcass yield in cattle. The F94L mutation is not, like other myostatin mutations, associated with reduced fertility and dystocia. It is therefore a candidate for introgression into other breeds to improve retail beef yield and the development of a simple and accurate test to genotype this specific mutation is warranted. Variations in the efficiency of enzyme cleavage compromised the accuracy of genotyping by published methods, potentially resulting in an overestimation of the frequency of the mutant allele. The frequency of the F94L mutation was determined by real-time PCR in 1140 animals from 15 breeds of cattle in Australia. The mutation was present in Simmental (0.8%), Piedmontese (2%), Droughtmaster (4%) and Limousin (94.2%) but not found in Salers, Angus, Poll Hereford, Hereford, Gelbvieh, Charolais, Jersey, Brahman, Holstein, Shorthorn or Maine Anjou. The low prevalence of F94L in all beef breeds except Limousin indicates the significant potential for this mutation to improve retail yield in Australian beef cattle.

Ruminant production is under increased public scrutiny in terms of the importance of cattle and other ruminants as major producers of the greenhouse gas methane. Methanogenesis is performed by methanogenic archaea, a specialised group of microbes present in several anaerobic environments including the rumen. In the rumen, methanogens utilise predominantly H2 and CO2 as substrates to produce methane, filling an important functional niche in the ecosystem. However, in addition to methanogens, other microbes also have an influence on methane production either because they are involved in hydrogen (H2) metabolism or because they affect the numbers of methanogens or other members of the microbiota. This study explores the relationship between some of these microbes and methanogenesis and highlights some functional groups that could play a role in decreasing methane emissions. Dihydrogen (‘H2’ from this point on) is the key element that drives methane production in the rumen. Among H2 producers, protozoa have a prominent position, which is strengthened by their close physical association with methanogens, which favours H2 transfer from one to the other. A strong positive interaction was found between protozoal numbers and methane emissions, and because this group is possibly not essential for rumen function, protozoa might be a target for methane mitigation. An important function that is associated with production of H2 is the degradation of fibrous plant material. However, not all members of the rumen fibrolytic community produce H2. Increasing the proportion of non-H2 producing fibrolytic microorganisms might decrease methane production without affecting forage degradability. Alternative pathways that use electron acceptors other than CO2 to oxidise H2 also exist in the rumen. Bacteria with this type of metabolism normally occupy a distinct ecological niche and are not dominant members of the microbiota; however, their numbers can increase if the right potential electron acceptor is present in the diet. Nitrate is an alternative electron sinks that can promote the growth of particular bacteria able to compete with methanogens. Because of the toxicity of the intermediate product, nitrite, the use of nitrate has not been fully explored, but in adapted animals, nitrite does not accumulate and nitrate supplementation may be an alternative under some dietary conditions that deserves to be further studied. In conclusion, methanogens in the rumen co-exist with other microbes, which have contrasting activities. A better understanding of these populations and the pathways that compete with methanogenesis may provide novel targets for emissions abatement in ruminant production.

In gene expression analysis, a key step to obtain informative data from reverse transcription quantitative PCR (RT qPCR) assay is normalization, that is usually achieved by ratio to correct the abundance of the gene of interest against that of an endogenous reference gene. The finding of such reference genes, ideally expressed in a stable way in multiple tissue samples and in different experimental conditions, is a non-trivial problem. In this work, a set of genes potentially useful as reference for gene expression studies in water buffalo has been identified and evaluated. In the first step, a publicly available Bos taurus expressed sequence tags database has been downloaded from the TIGR Gene Index and mined by some simple frequency algorithms to find out which tentative consensuses are present in a remarkable number of different cDNA libraries and, consequently, are more suitable to be included in a starter set of candidate reference genes. To validate the potential of such candidates for their use as normalizers in buffalo gene expression analysis, an RT qPCR analysis has been carried out, in which the expression stability of these genes has been evaluated on a panel of buffalo tissues and organs. Our results indicate that ribosomal proteins L4 and L5 and Gek protein encoding genes can be useful as normalizers to compare gene expression levels across tissues and organs in buffalo.

Osteochondrosis (OC) is a major factor causing joint problems that affect animal welfare and pork production profitability. Strong bones are also important in the slaughtering process, especially as broken bones can lead to rejections of parts of the carcass. In this study, 326 Finnish Yorkshire and 464 Finnish Landrace test station pigs were examined post mortem for bone strength and osteochondral lesions. The objective was to estimate genetic parameters for OC and bone strength and their genetic and phenotypic correlations with carcass meat percentage. Two formulas were used for lean meat percentage, the first one (Hennessy meat-%) comprising two fat thickness measurements and one muscle depth measurement, and the second one (test station meat-%) also including the weight of lean meat in ham. Finnish Yorkshire had stronger bones than Finnish Landrace on average, but also more OC in the proximal end of the humerus (36%) and the distal end of the femur (51%) than Finnish Landrace (29% and 31% OC in the humerus and femur, respectively). By using the data on both breeds, the OC heritability estimated was 0.05 in the humerus and 0.26 in the femur. The estimated heritability of bone strength was also moderate (0.26). Test station meat-% showed higher heritability (0.40) than meat-% based on the Hennessy formula (0.29). Genetic correlations between meat percentage and the other studied traits were weak and associated with high standard errors. The results show that a mild form of OC is common in both Finnish pig breeds; bone strength and OC in the distal end of the femur are moderately heritable and can be improved through selection; and selection for high meat percentage does not seem to affect bone strength or OC.

In the mountainous areas of Europe with a humid climate, dairy cattle production is a major agricultural activity, and the milk is often processed into cheese according to protected designation of origin (PDO) specifications. We analyzed the extent to which PDO specifications and/or a mountain environment influence the spatial distribution of estimated breeding values (EBVs) of cows and the herd–year effects (HYEs) for milk yield (kg/lactation) and protein and fat contents (g/kg), as well as lactation ranks and calving months. The study focused on the northern French Alps. A total of 37 023 lactations, recorded in 2006, in 1153 herds were analyzed. The cows belonged to the Montbéliarde (21 516 lactations), Abondance (10 346 lactations) and Tarentaise (5161 lactations) breeds. The two factors of variation considered were the status of the commune where the farm was located in relation to PDO (three categories: area with no PDO, area with a PDO with no milk yield limit, area with a PDO with a milk yield limit) and ‘mountain’ environment (four categories based on the European regulation: plain, piedmont, mountain and high mountain). In the Abondance breed, the average lactation rank increased with an increase in production constraints due to the PDO or to a mountain environment. In the Abondance and Tarentaise breeds, grouping of calving in winter was most marked in the ‘PDO with a milk yield limit’ and ‘high-mountain’ categories. In the Tarentaise breed, no significant effect on any trait and any variable was found in the ‘PDO’ or ‘mountain’ categories. In the other two breeds, the average EBV for milk yield decreased with an increase in the constraints due to PDO, with differences of 226 and 93 kg between extreme values in the Abondance and Montbéliarde breeds, respectively. The average HYE for milk yield was higher in the Abondance breed in the ‘PDO with no milk yield limit’ category than in the other categories (+740 and +1110 kg, respectively); HYE was not affected by the ‘PDO’ factor in the Montbéliarde breed or by the ‘mountain’ factor in either breed. Concerning the protein and fat contents, the effect of the ‘PDO’ and ‘mountain’ factors depended on the trait, the variable and the breed. The proportion of individual decisions (the farmer makes the decision) v. collective decisions (breed management) concerning herd dynamics in the face of existing constraints is discussed.

Genetic improvement of livestock is a particularly effective technology, producing permanent and cumulative changes in performance. This paper highlights some of the options for including mitigation in livestock breeding schemes, focusing on ruminant species, and details three routes through which genetic improvement can help to reduce emissions per kg product via: (i) improving productivity and efficiency, (ii) reducing wastage in the farming system and (iii) directly selecting on emissions, if or when these are measurable. Selecting on traits that improve the efficiency of the system (e.g. residual feed intake, longevity) will have a favourable effect on the overall emissions from the system. Specific examples of how genetic selection will have a favourable effect on emissions for UK dairy systems are described. The development of breeding schemes that incorporate environmental concerns is both desirable and possible. An example of how economic valuation of public good outcomes can be incorporated into UK dairy selection indices is given. This paper focuses on genetic selection tools using, on the whole, currently available traits and tools. However, new direct and indirect measurement techniques for emissions will improve the potential to reduce emissions by genetic selection. The complexities of global forces on defining selection objectives are also highlighted.

The objective of this study was to quantify the genetic association of body energy assessed throughout lactation with a cow’s fertility. Nine direct and indirect body energy traits were defined at different stages of lactation. Four were daily records of energy balance, energy content, cumulative effective energy (CEE) and body condition score (BCS) calculated between lactation days 4 and 311. The other five traits included duration of negative energy balance (DNEB), rate of recovery during DNEB (RNEB), sum of negative energy balance (SNEB), nadir of energy content (NEC) and number of days from calving to NEC. Of these traits, energy balance, DNEB, RNEB and SNEB were primarily based on individual cow feed intake and milk yield, and considered direct measures of body energy. The other traits were calculated from body lipid and protein changes, predicted from BCS and live weight profiles, and were considered indirect measures of body energy. Fertility was defined by number of days between calving and commencement of luteal activity (DLA), first observed oestrus (DH) and conception (DC), and number of services per conception. A total of 957 cows in their first four lactations were considered in the study. Genetic models fitted cubic splines to define longitudinal traits (energy balance, energy content, CEE and BCS) and calculate heritability and genetic correlation with fertility. Daily heritability estimate ranges were 0.10 to 0.34, 0.35 to 0.61, 0.32 to 0.53 and 0.24 to 0.56 for energy balance, energy content, CEE and BCS, respectively, and, in most cases, tended to increase towards the middle of lactation and remain relatively stable thereafter. Of the other body energy traits, heritability of NEC (0.44) was the most notable. Statistically significant (P < 0.05) genetic correlations of DH with daily energy balance, energy content, CEE and BCS ranged from −0.16 to −0.28, −0.35 to −0.48, −0.16 to −0.26 and −0.37 to −0.44, respectively. For DC, respective estimates were −0.28 to −0.64, −0.37 to −0.60, −0.30 to −0.48 and −0.29 to −0.53. For DLA, they ranged from −0.47 to −0.56 with energy content and from −0.50 to −0.74 with BCS. Of special interest was the genetic correlation of NEC with DH (−0.54) and DC (−0.48). Results suggest that indirect measures of body energy have the strongest genetic association with cow fertility. NEC and early lactation (circa day 50) BCS and energy content are the most useful traits for selection in terms of the correlated improvement in a cow’s capacity to resume her reproductive activity post partum.

Mitochondrial (mt) DNA D-loop heterogeneity, haplotype distribution and possible sub-population structures within the relevant populations are important for DNA-based traceability. To gain insight into this distribution, we compared 1515 Bos taurus mtDNA D-loop sequences available from GenBank to 219 sequences that we sequenced de novo. A pronounced ambiguous trace typical of C-track length heteroplasmy was encountered in 5% of the samples, which were excluded from the analysis. Previously undescribed mutations and haplotypes were observed in 6% and 63% of the sequences, respectively. B. taurus haplotypes divided into the taurus, indicus and grunniens types and 302 variable sites formed the 858 taurus haplotypes detected. Fifty-five sites displayed a complex level of variation. As each level represents an independent mutation event, a total of 399 mutations were traced, which could potentially explain independent formation of less than half (47%) of the haplotypes encountered: most haplotypes were derived from different combinations of these mutations. We suggest that a mutational hotspot may explain these results and discuss the usefulness of mtDNA for identity and maternity assurance.