•Body energy reserves are the main source of energy in ruminants facing negative energy balance.•In situations of negative energy balances, the flexibility of ewes’ body reserves is of major ...importance in the current context of breeding for resilience.•PhenoBR is a model to quantify the body condition score flexibility at individual level.•PhenoBR contributes to better adapting feeding systems to the individual characteristics of animal.•PhenoBR helps geneticists to develop animal breeding programmes for more resilient animals by including body reserve dynamics.
In situations of negative energy balance (NEB) due to feed scarcity or high physiological demands, body energy reserves (BRs), mainly stored in adipose tissues, become the main sources of energy for ruminants. The capacity to mobilise and restore such BRs in response to different challenges is of major concern in the current context of breeding for resilience. Body condition score (BCS) is a common, practical indicator of BR variations throughout successive productive cycles, and quantitative tools for characterising such dynamics at the individual level are still lacking. The main objective of this work was to characterise body condition dynamics in terms of BR mobilisation and accretion capacities of meat sheep during their productive lifespan through a modelling approach, using BCS measurements. The animal model used in this work was the reproductive meat ewe (n = 1 478) reared in extensive rangeland. Regular measurements of BCS for each productive cycle were used as the indicator of BR variations. A hybrid mathematical model and a web interface, called PhenoBR, were developed to characterise ewes’ BCS variations through four synthetic and biologically meaningful parameters for each productive cycle i: BR accretion rate (kbi), BR mobilisation rate (kpi), plus the time of onset and the duration of the BR mobilisation, tbi and ΔTi, respectively. The model PhenoBR converged for all the ewes included in the analysis. Estimation of the parameters indicated the inter-individual variability for BR accretion and mobilisation rates, and the length of the mobilisation period. The present study is a proof of concept that the combination of data-driven and concept-driven models is required for the estimation of biologically meaningful parameters that describe body reserve dynamics through consecutive productive cycles. Individual characterisation of animals by these parameters makes it possible to rank them for their efficiency in the use of body reserves when facing NEB challenges. Such parameters could contribute to better management and decision-making by farmers and advisors, e.g. by adapting feeding systems to the individual characteristics of BR dynamics, or by geneticists as criteria to develop future animal breeding programmes including BR dynamics for more robust and resilient animals.
L’agro-écologie utilise les processus naturels et les ressources locales plutôt que des intrants chimiques pour assurer la production tout en limitant l’impact environnemental de l’agriculture. A ...cette fin, des innovations en génétique sont nécessaires pour disposer d’animaux productifs et adaptés à des contextes locaux variés. Pour toute filière d’élevage, réorienter les programmes de sélection actuels semble plus utile que développer des programmes spécifiques qui peineront à être efficaces en termes de coûts et de progrès génétiques attendus. Améliorer la robustesse des animaux vise à promouvoir leurs capacités d’adaptation en intégrant de nombreux critères de sélection, en particulier de reproduction, santé, et d’adaptation à des ressources alimentaires peu digestibles et au changement climatique. Cela amène à considérer les interactions génotype-environnement dans la prédiction des valeurs génétiques et à évaluer les performances des animaux dans des systèmes à bas intrants pour sélectionner ceux qui sont adaptés à des conditions limitantes. La standardisation tant des animaux que des conditions d’élevage paraît antinomique avec les principes de l’agro-écologie prônant une adaptation des animaux aux ressources et contraintes locales dans des systèmes peu artificialisés et très liés à leur environnement physique. Il n’y a donc pas UN animal type agro-écologique, mais DES animaux aux profils variés permettant de répondre aux attentes de l’agro-écologie. Face à la diversité des milieux et des systèmes d’élevage, il faut conserver une diversité génétique importante intra-race, mais aussi préserver la diversité génétique entre races. Cela nécessite une caractérisation phénotypique et génétique des races locales. Enfin, il s’agit de favoriser l'appropriation par les éleveurs et les techniciens d’élevage des outils et des ressources génétiques disponibles pour répondre à leurs besoins.
Breeding for resilience requires a better understanding of intra-flock variability and the related mechanisms responsible for robustness traits. Among such traits, the animals’ ability to cope with ...feed fluctuations by mobilizing or restoring body reserves (BR) is a key mechanism in ruminants. The objective of this work was to characterize individual variability in BR dynamics in productive Romane ewes reared in extensive conditions. The BR dynamics profiles were characterized by combining individual longitudinal measurements of BW and body condition scores (BCS) over several production cycles. Historical data, including up to 2628 records per trait distributed in 1146 ewes, underwent cluster analysis. Two to four trajectories were observed for BW depending on the cycle, while three trajectories were found for BCS, whatever the cycle. Most trajectories suggested that BR dynamics were similar but the level of BR may differ between ewes. Nevertheless, some trajectories suggested that both BR dynamics and levels were different for a proportion of ewes. Clustering on BW and BCS profiles adjusted for individual level trends, resulted in differences only in the level of BW or BCS, rather than differences in trajectories. Thus, the overall shape of trajectories was not changed considering or not the individual level trend across cycles. In addition to individual variability, the ewe’s age at first lambing and litter size contributed to the distribution of the ewes between the trajectories. Regarding the entire productive life, three trajectories were observed for BW and BCS changes over three productive cycles. Increase in BW at each cycle suggested that ewes kept growing up until 3 to 4 years old in our conditions. Similar alternation of BCS gains and losses across cycles suggested BR dynamics might be repeatable. Many individual trajectories remained the same throughout a ewe’s life, whatever the age at first lambing, parity or litter size. Our results demonstrate the relevance of using BW and BCS changes for characterizing the diversity of BR mobilization–accretion profiles in sheep in a long timespan perspective.
The main limitation for determining feed efficiency of freely grazing ruminants is measurement of daily individual feed intake. This paper describes an investigation that assessed a method for ...estimating intake of forage based on changes in BW of ewes. A total of 24 dry and non-pregnant Romane ewes (12 hoggets, HOG; mean±SD 51.8±2.8 kg BW; body condition score (BCS) 2.6±0.2; and 12 adults, ADU; 60.4±8.5 kg BW; BCS 2.7±0.8) were selected for the study and moved from their rangeland system to a confined pen with controlled conditions and equipped with individual automatic feeders. The experiment lasted for 28 days (21 days adaptation and 7 days feed intake measurement). Ewes were fed hay and trained to use the electronic feeders (one feeding station per ewe) in which actual daily intake (H intake24) was measured. The pens were designed to maximize movement of trained ewes through an automated Walk-over-Weighing device, by using water and mineral salts as attractants. Total individual intake of hay measured in the automatic feeder at each meal (H intake) was compared with indirect estimates of feed intake determined using differences in the BW of the ewes (∆BW) before and 1 h following morning and afternoon feeding at fixed times. The BW, BCS, H intake, H intake24, as well as plasma non-esterified fatty acids (NEFA), glucose and insulin profiles were determined. The BW was higher in ADU v. HOG but BCS was not affected by parity. The H intake24 was affected by day of experiment as a consequence of reduced availability and intake of water on one day. Plasma glucose, NEFA and insulin were not affected by parity or day of experiment. The H Intake was and ∆BW tended to be higher in the morning in HOG, whereas H intake was and ∆BW tended to be higher in ADU at the afternoon meal. Irrespective of parity or feeding time, there was very strong correlation (r 2=0.93) between H intake and ∆BW. This relationship confirms that our indirect method of estimating individual forage intake was reliable within the strictly controlled conditions of the present experiment. The method appears suitable for use in short-term intensive group feeding situations, and has potential to be further developed for longer-term forage intake studies, with a view to developing a method for freely grazing ruminants.
Gentle handling seems to elicit positive states in sheep. The study investigated whether spatial distance alters sheep responses to brushing and whether spatial distance is influenced by reactivity. ...Twenty Romane ewes were assessed in three sessions: in Sessions 1 and 3, one grid separated the test animal from pen mates, with no distance between them, and in Session 2 two grids separated the test animal from pen mates by a distance of about 1.7 m. Ewes had been genetically selected for low (R-) or high (R+) behavioural reactivity to social isolation. Body postures, head orientation, ear postures, closed and half-closed eyes, tail wagging and feeding behaviour, in addition to heart rate (HR) and HR variability, as the root mean square of successive differences (RMSSD), standard deviation of all normal-to-normal (NN) intervals (SDNN), RMSSD/SDNN ratio and ratio between low-frequency (LF) and high-frequency (HF) powers (LF/HF) were assessed. Data were analysed using generalized linear models and linear mixed models. Session, genetic line and phase (pre-, brushing and post-brushing) were considered fixed effects. Increased distance in Session 2 might not have influenced ewes' responses. Fewer changes in ear postures were noted in Session 3 than 1 (P<0.01), suggesting that ewes were more relaxed in Session 3. The RMSSD/SDNN ratio was higher mainly during brushing in Sessions 1 and 3 (P<0.05), indicating that ewes were more relaxed during brushing, and at no distance between pen mates. However, spatial distance influenced R- and R+ ewes' responses; R+ ewes performed more asymmetric ear postures in Session 2 than 1 and 3 (P<0.01), and in Session 3 than 1 (P<0.01), indicating that spatial distance had a negative effect on R+ ewes. Low reactive ewes spent less time on horizontal ear postures in Session 2 than 1 and 3 (P<0.01), and R+ ewes spent more time on horizontal postures in Session 1 than 3 (P<0.01). Curiously, R- ewes spent more time eating and ruminating in Session 3 than 1 (P<0.01), and in Session 2 than 1 and 3 (P<0.01), whereas R+ ewes ate and ruminated more in Session 1 than 3 (P<0.05). Higher HR was found among R- ewes in Session 2 than 1 and 3, and in Session 3 than 1 (P<0.01). High reactive ewes showed higher HR in Session 1 than 3 (P<0.01). The findings suggest that the social context might influence sheep responses to gentle handling, and the effects depend on their reactivity traits.
In sheep, social reactivity and reactivity to humans are relevant behavioral responses that are used to investigate the behavioral adaptation of farm animals to various rearing conditions. Such ...traits were previously reported as heritable and associated with several QTLs. However, few behavior-related genotype by environment (G × E) interactions have been reported to date. The experiment was performed on 2,989 male and female lambs issued from 30 sires. Every sire had progeny reared under both intensive and extensive conditions. After weaning, all lambs were individually exposed to two standardized behavioral tests. A broad range of behaviors including vocalizations, locomotion, localization, vigilance, and flight distance were assessed. Two complementary statistic approaches, with and without assumptions on the biological significance of behaviors, were performed to investigate social reactivity and reactivity to humans. G × E interactions were investigated based on the genetic correlations estimated for each factor or trait between farming conditions; those significantly different from 1 indicating a G × E. Environmental effects showed that social reactivity and reactivity to humans were higher in intensively reared lambs. The heritability of factors or traits used to measure social reactivity and reactivity to humans was similar in both rearing conditions. Estimated heritabilities were high for vocalizations in response to social isolation, moderate for locomotion and vigilance in response to social isolation, and low for both flight distance to an approaching human and proximity to a motionless human. No significant G × E interaction was found for vocalizations. G × E interactions were found for locomotion, vigilance and flight distance. Genetic correlations between both environments were low to moderate for vigilance, locomotion and flight distance. Vocalization in response to social isolation with or without human presence was identified as a robust trait and could be used to improve sheep sociability, independently of the environment. A G × E interaction was observed for behavioral reactivity to humans. Although moderate, the genetic correlation for this trait between intensive and extensive conditions could be used to select sires in the same environment by taking into account the G × E and to produce in different environments progenies that are less reactive to humans.
When studying nosocomial infections, resource-efficient sampling designs such as nested case-control, case-cohort, and point prevalence studies are preferred. However, standard analyses of these ...study designs can introduce selection bias, especially when interested in absolute rates and risks. Moreover, nosocomial infection studies are often subject to competing risks. We aim to demonstrate in this tutorial how to address these challenges for all three study designs using simple weighting techniques.
We discuss the study designs and explain how inverse probability weights (IPW) are applied to obtain unbiased hazard ratios (HR), odds ratios and cumulative incidences. We illustrate these methods in a multi-state framework using a dataset from a nosocomial infections study (n = 2286) in Moscow, Russia.
Including IPW in the analysis corrects the unweighted naïve analyses and enables the estimation of absolute risks. Resulting estimates are close to the full cohort estimates using substantially smaller numbers of patients.
IPW is a powerful tool to account for the unequal selection of controls in case-cohort, nested case-control and point prevalence studies. Findings can be generalized to the full population and absolute risks can be estimated. When applied to a multi-state model, competing risks are also taken into account.
Agroecology uses natural processes and local resources rather than chemical inputs to ensure production while limiting the environmental footprint of livestock and crop production systems. Selecting ...to achieve a maximization of target production criteria has long proved detrimental to fitness traits. However, since the 1990s, developments in animal breeding have also focussed on animal robustness by balancing production and functional traits within overall breeding goals. We discuss here how an agroecological perspective should further shift breeding goals towards functional traits rather than production traits. Breeding for robustness aims to promote individual adaptive capacities by considering diverse selection criteria which include reproduction, animal health and welfare, and adaptation to rough feed resources, a warm climate or fluctuating environmental conditions. It requires the consideration of genotype×environment interactions in the prediction of breeding values. Animal performance must be evaluated in low-input systems in order to select those animals that are adapted to limiting conditions, including feed and water availability, climate variations and diseases. Finally, we argue that there is no single agroecological animal type, but animals with a variety of profiles that can meet the expectations of agroecology. The standardization of both animals and breeding conditions indeed appears contradictory to the agroecological paradigm that calls for an adaptation of animals to local opportunities and constraints in weakly artificialized systems tied to their physical environment.
Agroecology uses ecological processes and local resources rather than chemical inputs to develop productive and resilient livestock and crop production systems. In this context, breeding innovations ...are necessary to obtain animals that are both productive and adapted to a broad range of local contexts and diversity of systems. Breeding strategies to promote agroecological systems are similar for different animal species. However, current practices differ regarding the breeding of ruminants, pigs and poultry. Ruminant breeding is still an open system where farmers continue to choose their own breeds and strategies. Conversely, pig and poultry breeding is more or less the exclusive domain of international breeding companies which supply farmers with hybrid animals. Innovations in breeding strategies must therefore be adapted to the different species. In developed countries, reorienting current breeding programmes seems to be more effective than developing programmes dedicated to agroecological systems that will struggle to be really effective because of the small size of the populations currently concerned by such systems. Particular attention needs to be paid to determining the respective usefulness of cross-breeding v. straight breeding strategies of well-adapted local breeds. While cross-breeding may offer some immediate benefits in terms of improving certain traits that enable the animals to adapt well to local environmental conditions, it may be difficult to sustain these benefits in the longer term and could also induce an important loss of genetic diversity if the initial pure-bred populations are no longer produced. As well as supporting the value of within-breed diversity, we must preserve between-breed diversity in order to maintain numerous options for adaptation to a variety of production environments and contexts. This may involve specific public policies to maintain and characterize local breeds (in terms of both phenotypes and genotypes), which could be used more effectively if they benefited from the scientific and technical resources currently available for more common breeds. Last but not least, public policies need to enable improved information concerning the genetic resources and breeding tools available for the agroecological management of livestock production systems, and facilitate its assimilation by farmers and farm technicians.
Abstract Two genotypes of Japanese quail have been divergently selected since the 1980s for long (LTI) or short (STI) duration of tonic immobility Mills, A.D., Faure, J.M., 1991. Divergent selection ...for duration of tonic immobility and social reinstatement behavior in Japanese quail ( Coturnix coturnix japonica ) chicks. J. Comp. Psychol. 105(1), 25–38., an unlearnt catatonic state characteristic of a behavioral fear response (Jones, R.B., 1986. The tonic immobility reaction of the domestic fowl: a review. World’s Poult. Sci. J. 42(1), 82–97.; Mills, A.D., Faure, J.M., 1991. Divergent selection for duration of tonic immobility and social reinstatement behavior in Japanese quail ( Coturnix coturnix japonica ) chicks. J. Comp. Psychol. 105(1), 25–38.). The results of several behavioral tests conducted in LTI and STI quail have led to the conclusion that LTI quail are more fearful than STI quail Faure, J.M., Mills, A.D., 1998. Improving the adaptability of animals by selection. In: Grandin, T. (Eds.), Genetics and the behavior of domestic animals. Academic Press, San Diego, pp. 235–264.). However, few studies to date have focused on the Hypothalamic-Pituitary-Adrenal (HPA) axis response to stressful situations in LTI and STI quail, although the HPA axis is involved in fear responses Siegel, H.S., 1971. Adrenals, Stress and the Environment. World’s Poult. Sci. J. 27, 327–349.. The corticosterone (CORT) response to various putatively stressful situations was therefore assessed in LTI and STI genotypes of quail in order to investigate their HPA axis reactivity to stress. Repeated induction of TI or 1 min manual restraint induced significant and comparable increases in CORT levels in both genotypes as a TI response. On the other hand, higher CORT responses were found in STI than in LTI quail when the manual restraint period lasted for 2 min or after restraint in a crush cage. Maximum CORT responses and genotype differences were maintained throughout the latter test even when it lasted for 120 min. Investigation of the CORT response to a single TI episode showed that CORT levels at the end of TI were negatively correlated with TI duration. Other experimental contexts consisting of isolation in a familiar or novel environment or the presentation of a novel object induced slight but significant and comparable increases in CORT response in both genotypes, whereas change of cagemates did not. In conclusion, the present findings indicate that differences in HPA axis response are observed between LTI and STI genotypes when quail are submitted to intense stressors, resulting in a high and prolonged CORT response. By contrast, plasma corticosterone concentrations do not differ between STI and LTI quail in response to stressful situations of lower intensity, which evoke responses limited in amplitude and duration. Genetic selection for divergent duration of TI has thus affected the HPA axis response to stress, and LTI and STI quail constitute an interesting model to investigate genetic variability of HPA axis activity in birds. More specifically, these genotypes of quail could be used to investigate the occurrence of functional differences at different levels of the HPA axis in order to explain the present findings.
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