29 Jan 2024
Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National CryobankAlicia Jacques, Delphine Duclos, Coralie Danchin-Burge, Marie-Jose Mercat, Michele Tixier-Boichard, Gwendal Restoux https://doi.org/10.1101/2023.07.19.549644
Exploring Genetic Diversity Management: Unveiling the Potential of Germplasm Collections in the French National CryobankRecommended by Yuliaxis Ramayo-Caldas based on reviews by Roy Costilla and 1 anonymous reviewer
The study by Jacques et al. (2024) addresses a critical concern in the context of genetic diversity erosion in domesticated animal populations. The research uses data from the cryopreserved resources from the French National Cryobank to manage genetic diversity in livestock species. The authors employ a comprehensive methodology to propose novel biodiversity metrics to characterize the status of genetic diversity of cryopreserved collections including cattle, sheep, goat, horse, donkey, and pig livestock species. The findings reveal significant variations of genetic diversity at species and breed levels. Breeds with a large commercial distribution had more donors in the collection than local breeds. The authors propose a practical framework for assessing germplasm collections, providing a valuable tool for planning and managing collections at both national and international levels. The study also highlights the usefulness of the Gini-Simpson and effective donor numbers indices to plan a more efficient sampling, whereas the index of diversity impact can be employed in the selection of the most suitable donors for immediate use, based on pedigree but also using genetic markers.
In resume, this study makes a significant contribution to the field by offering a framework for the assessment of germplasm collections. Its innovative metrics provide insights that could guide strategic decision-making in planning, managing, and utilizing cryopreserved resources. This research is relevant and can benefit conservationists, and population genetics working towards the preservation and sustainable use of genetic resources in livestock species.
Jacques, A., Duclos, D., Danchin-Burge, C., Mercat, M. J., Tixier-Boichard M., Restoux, G. (2024). Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank. bioRxiv 2023.07.19.549644. ver. 3 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2023.07.19.549644
|Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank
|Alicia Jacques, Delphine Duclos, Coralie Danchin-Burge, Marie-Jose Mercat, Michele Tixier-Boichard, Gwendal Restoux
|<p>Through a combination of selective pressure and genetic drift, there has been a notable erosion of genetic diversity in domesticated animal populations. In response, many countries, including France, have developed gene banks in order to conser...
14 Dec 2022
Feed efficiency of lactating Holstein cows was not as repeatable across diets as within diet over subsequent lactation stagesAmelie Fischer, Philippe Gasnier, philippe faverdin https://doi.org/10.1101/2021.02.10.430560
A focus on feed efficiency reproducibility and repeatability of dairy cows fed different diets over the lactation stage.Recommended by Alberto Atzori based on reviews by Ioannis Kaimakamis, Angela Schwarm and 2 anonymous reviewers
The topic of feed efficiency is under discussion in the scientific community and several studies pointed out that lactation stage has to be accounted for when estimates of feed efficiency are carried out, especially for genetic ranking of animals and their performances, as highlighted by Li et al. (2017). Other researchers applied a latin square design to test dietary effects across lactation (Ipharraguerre et al. 2002) but this approach cannot be followed out of experimental conditions and particularly does not allow, nowadays, to valorize precision livestock farm data to get phenotypic information from individual animals at farm level.
The current manuscript by Fischer, et al. (2022a) describes an experimental trial in which cows were first fed a high starch diet-low fibre then switched over to a low starch diet-high fibre and individually monitored over time. Data were analyzed with the objective to investigate effects within diets and across diets. Since all cows went through the same sequence at the same time it was not possible to completely separate the confounding effect of lactation stage and diet as stated by the authors. However, this manuscript adds methodological discussions and opens research questions especially to the matter of repeatability and reproducibility of feed efficiency of individual animals over the lactation stage. These variables are fundamental to evaluate nutritional traits and phenotypic performances of dairy cows at farm level, as highlighted by a paper of the same first author (Fischer, et al. 2022b) dealing to reproducibility and repeatability with a similar approach. My opinion is that this manuscript gives the opportunity to enlarge the scientific discussions on the calculation of repeatability and reproducibility of feed efficiency of individual animals over time. In particular, as in this study, specific mathematical approaches need to be carried out with the final goal to analyze and valorize precision livestock farm data for cow phenotyping and to propose new methods of feed efficiency evaluations. It also needs complete databases carried out under experimental conditions. In fact it has to be considered that this manuscript makes available to the scientific community all the data and the R code developed for data analysis giving the opportunity to replicate the calculations and propose new advancements in the feed efficiency evaluations of dairy cows.
Fischer A, Gasnier P, Faverdin P (2022a) Feed efficiency of lactating Holstein cows was not as repeatable across diets as within diet over subsequent lactation stages. bioRxiv, 2021.02.10.430560, ver. 3 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2021.02.10.430560
Fischer A, Dai X, Kalscheur KF (2022b) Feed efficiency of lactating Holstein cows is repeatable within diet but less reproducible when changing dietary starch and forage concentrations. animal, 16, 100599. https://doi.org/10.1016/J.ANIMAL.2022.100599
Ipharraguerre IR, Ipharraguerre RR, Clark JH (2002) Performance of Lactating Dairy Cows Fed Varying Amounts of Soyhulls as a Replacement for Corn Grain. Journal of Dairy Science, 85, 2905–2912. https://doi.org/10.3168/JDS.S0022-0302(02)74378-6
Li B, Berglund B, Fikse WF, Lassen J, Lidauer MH, Mäntysaari P, Løvendahl P (2017) Neglect of lactation stage leads to naive assessment of residual feed intake in dairy cattle. Journal of Dairy Science, 100, 9076–9084. https://doi.org/10.3168/JDS.2017-12775
|Feed efficiency of lactating Holstein cows was not as repeatable across diets as within diet over subsequent lactation stages
|Amelie Fischer, Philippe Gasnier, philippe faverdin
|<p> Background: Improving feed efficiency has become a common target for dairy farmers to<br>meet the requirement of producing more milk with fewer resources. To improve feed<br>efficiency, a prerequisite is to ensure that the cows identified...
|Cattle production, Ruminant nutrition
|Anonymous, Ioannis Kaimakamis, Giuseppe Conte, Angela Schwarm
09 Apr 2022
The impact of housing conditions on porcine mesenchymal stromal/stem cell populations differ between adipose tissue and skeletal muscleAudrey Quéméner, Frédéric Dessauge, Marie-Hélène Perruchot, Nathalie Le Floc’h, Isabelle Louveau https://doi.org/10.1101/2021.06.08.447546
Housing conditions affect cell populations in adipose and muscle tissues of pigsRecommended by Hervé Acloque based on reviews by 2 anonymous reviewers
The adaptability of livestock to changing environments is based in particular on their genetic characteristics but also on the farming conditions to which they are subjected. However, this last point is poorly documented and little is known about its contribution to environmental challenges. The study by Quéméner and colleagues  addresses this question by assessing the effect of two hygiene conditions (good vs poor) on the distribution of cell populations present in adipose and muscle tissues of pigs divergently selected for feed efficiency .
The working hypothesis is that degraded housing conditions would be at the origin of an hyper stimulation of the immune system that can influence the homeostasis of adipose tissue and skeletal muscle and consequently modulate the cellular content of these tissues. Cellular compositions are thus interesting intermediate phenotypes for quantifying complex traits. The study uses pigs divergently selected for residual feed intake (RFI+ and RFI-) to assess whether there is a genetic effect associated with the observed phenotypes.
The study characterized different stromal cell populations based on the expression of surface markers: CD45 to separate hematopoietic lineages and markers associated with the stem properties of mesenchymal cells: CD56, CD34, CD38 and CD140a. The authors observed that certain subpopulations are differentially enriched according to the hygiene condition (good vs poor) in adipose and skeletal tissue (CD45-CD56-) sometimes with an associated (genetic) lineage effect. This pioneering study validates a number of tools for characterizing cell subpopulations present in porcine adipose and muscle tissue. It confirms that housing conditions can have an effect on intermediate phenotypes such as intra-tissue cell populations. This pioneering work will pave the way to better understand the effects of livestock systems on tissue biology and animal phenotypes and to characterize the nature and function of progenitor cells present in muscle and adipose tissue.
 Quéméner A, Dessauge F, Perruchot MH, Le Floc’h N, Louveau I. 2022. The impact of housing conditions on porcine mesenchymal stromal/stem cell populations differ between adipose tissue and skeletal muscle. bioRxiv 2021.06.08.447546, ver. 3 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2021.06.08.447546
 Gilbert H, Bidanel J-P, Gruand J, Caritez J-C, Billon Y, Guillouet P, Lagant H, Noblet J, Sellier P. 2007. Genetic parameters for residual feed intake in growing pigs, with emphasis on genetic relationships with carcass and meat quality traits. Journal of Animal Science 85:3182–3188. https://doi.org/10.2527/jas.2006-590.
|The impact of housing conditions on porcine mesenchymal stromal/stem cell populations differ between adipose tissue and skeletal muscle
|Audrey Quéméner, Frédéric Dessauge, Marie-Hélène Perruchot, Nathalie Le Floc’h, Isabelle Louveau
|<p><strong>Background.</strong> In pigs, the ratio between lean mass and fat mass in the carcass determines production efficiency and is strongly influenced by the number and size of cells in tissues. During growth, the increase in the number of c...
|Monogastrics, Physiology, Veterinary science
02 Sep 2021
A modelling framework for the prediction of the herd-level probability of infection from longitudinal dataAurélien Madouasse, Mathilde Mercat, Annika van Roon, David Graham, Maria Guelbenzu, Inge Santman Berends, Gerdien van Schaik, Mirjam Nielen, Jenny Frössling, Estelle Ågren, Roger Humphry, Jude Eze, George Gunn, Madeleine Henry, Jörn Gethmann, Simon J. More, Nils Toft, Christine Fourichon https://doi.org/10.1101/2020.07.10.197426
Modelling freedom from disease - how do we compare between countries?Recommended by Rowland Raymond Kao based on reviews by Arata Hidano and 1 anonymous reviewer
In this paper, Madouasse et al. (2021) present a generalisable Bayesian method for calculating the probability that a herd is free from disease, based on its prior disease status, and using data (herd status over time over a sufficient number of herds to inform the model) and reasonable prior estimates of the sensitivity and specificity of tests being used to determine animal infection status. Where available, the modelling approach can also include relevant additional risk factors.
By bringing all these factors together, it allows for most countries to use the same analytical approach on their data, with differences across datasets expressed in terms of the uncertainty around the central estimates.
Having a single methodology that generates both a central estimate of disease freedom, and uncertainty thus provides the opportunity (given typically available data) to compare the probability of freedom across different systems. This is relevant in terms of the context of trade (since international trade of livestock in many cases depends on disease freedom). It is also important when evaluating, for example, transnational burdens of disease - and with different regulations in place in different countries, this is invaluable and can be used, for example, to assess risks of zoonotic infection including for zoonotic infection emergence. In the BVD example provided, the point is made that, since regular testing would probably pick up infection rapidly, the addition of risk factors is most valuable where testing is infrequent. This emphasizes the advantages of direct incorporation of risk factors into a single modelling framework.
From a technical point of view, the analysis compares two different packages for the Markov Chain Monte Carlo (MCMC) implementation necesary to run the model. They show that, while there are some slight systematic differences, the estimates provided by the two methods are similar to each other; as one method is approximate but substantially more stable and generally much more computationally efficient, this is an important outcome. Both implementations are freely available and with relevant additional software made similarly available by the authors. This is extremely welcome and should encourage its general adoption across different countries.
No single model can of course account for everything. In particular, the reliance on past data means that there is an implicit assumption common to all purely statistical methods that the underlying risks have not changed. Thus projections to altered circumstances (changing underlying risk factors or systematic changes in testing or test performance) cannot so easily be incorporated, since these factors are complicated by the dynamics of infection that lie outside the modelling approach. Of course the well known quote from George Box that "all models are wrong" applies here - the generality of approach, statistical robustness and open source philosophy adopted make this model very useful indeed.
Madouasse A, Mercat M, van Roon A, Graham D, Guelbenzu M, Santman Berends I, van Schaik G, Nielen M, Frössling J, Ågren E, Humphry RW, Eze J, Gunn GJ, Henry MK, Gethmann J, More SJ, Toft N, Fourichon C (2021) A modelling framework for the prediction of the herd-level probability of infection from longitudinal data. bioRxiv, 2020.07.10.197426, ver. 6 peer-reviewed and recommended by PCI Animal Science. https://doi.org/10.1101/2020.07.10.197426
|A modelling framework for the prediction of the herd-level probability of infection from longitudinal data
|Aurélien Madouasse, Mathilde Mercat, Annika van Roon, David Graham, Maria Guelbenzu, Inge Santman Berends, Gerdien van Schaik, Mirjam Nielen, Jenny Frössling, Estelle Ågren, Roger Humphry, Jude Eze, George Gunn, Madeleine Henry, Jörn Gethmann, Sim...
|<p>The collective control programmes (CPs) that exist for many infectious diseases of farm animals rely on the application of diagnostic testing at regular time intervals for the identification of infected animals or herds. The diversity of these ...
|TEST, Veterinary epidemiology
|Rowland Raymond Kao
24 Mar 2023
The use of pigs vocalisation structure to assess the quality of human-pig relationshipAvelyne S Villain, Carole Guérin, Céline Tallet https://doi.org/10.1101/2022.03.15.484457
Qualitative aspects of grunts vary with pigs' mental statesRecommended by Isabelle Veissier based on reviews by Matteo Chincarini and 1 anonymous reviewer
Villain et al., (2023) investigated the structure of vocalisations in piglets in relation to human-animal-relationship. They first established a positive relationship by habituating piglets to be positively handled at weaning or later on after weaning. They then compared the reactions of piglets previously positively handled at weaning to that of non-handled piglets during tests in presence of a human (interacting or not), and also before and after the conditioning period when all piglets received positive contacts. They showed that the duration and frequency of grunts emitted in the presence of the human depends on previous contacts. More specifically, grunts are shorter and higher pitched in pigs that have been positively handled, in line with a positive human-animal relationship which is also observed through proximity of the piglets with the human. The authors concluded that the structure of pig vocalisation can reflect the quality of their relationship with humans.
The authors also showed that not only the response to humans is modified by positive contacts but also the general mood of piglets, with piglets positively handled at weaning emitting shorter grunts than non-handled piglets, whatever the context.
Another interesting finding is the temporality of behaviour of pigs habituated to positive contacts: during the first tests, they stay close to the human, probably being reassured by the proximity of the human. Then, when tests are repeated, they explore more the test room, using the human as an exploratory basis as already reported in the literature.
The hypotheses of the study are clear. The methods are reported in details so that the work is reproducible. The interpretation of results is sound. The manuscript is clearly written.
This paper brings new and original knowledge in the field of animals’ emotional responses and human-animal relationship: on the structure of grunts in relation to positive affects (positive emotion, positive mood) and on the temporality of the responses to human presence.
I recommend this manuscript for its originality and quality.
Villain, A.S., Guérin, C., Tallet, C., 2023. The use of pigs vocalisation structure to assess the quality of human-pig relationship. bioRxiv 2022.03.15.484457, ver. 5 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2022.03.15.484457
|The use of pigs vocalisation structure to assess the quality of human-pig relationship
|Avelyne S Villain, Carole Guérin, Céline Tallet
|<p>Studying human-animal interactions in domestic species and how they affect the establishment of a positive Human-Animal Relationship (HAR) may help us improve animal welfare and better understand the evolution of interspecific interactions asso...
|Animal behaviour , Animal cognition, Animal welfare
06 Sep 2019
Lactation curve model with explicit representation of perturbations as a phenotyping tool for dairy livestock precision farming.Ben Abdelkrim Ahmed, Puillet Laurence, Gomes Pierre, Martin Olivier https://doi.org/10.1101/661249
Developing smart fitting algorithms to identify random perturbations in time-series dataRecommended by Luis Tedeschi based on reviews by Alberto Atzori, Jennifer Spencer and 1 anonymous reviewer
The ability to adequately characterize the lactation curve of livestock is important not only to ensure proper nutrition of the lactating animal but, among many other benefits, it can assist in diagnosing the incidence of diseases, predicting the quantity of milk production, and comparing animals within the herd for managerial strategies such as culling. Eventually, such smart fitting algorithms can lead to improved genetic selection of more productive animals after genetic-unrelated noises are removed from the data, systematically.
 Johansson, I. (1961). Genetic Aspects of Dairy Cattle Breeding. University of Illinois Press, Urbana, IL.
 Nelder, J. A. (1966). Inverse polynomials, a useful group of multi-factor response functions. Biometrics. 22 (1):128-141. doi: 10.2307/2528220
|Lactation curve model with explicit representation of perturbations as a phenotyping tool for dairy livestock precision farming.
|Ben Abdelkrim Ahmed, Puillet Laurence, Gomes Pierre, Martin Olivier
|<p>Background Understanding the effects of environment on livestock provides valuable information on how farm animals express their production potential, and on their welfare. Ruminants are often confronted with perturbations that affect their per...
|Lactation biology , Mathematical modelling, Precision livestock farming
23 Aug 2023
Ensuring ethical animal welfare research: Are more ethics review committees the solution?Birte L. Nielsen, Huw D.R. Golledge, Jen-Yun Chou, Irene Camerlink, Péter Pongrácz, Maria Camila Ceballos, Alexandra L. Whittaker and I. Anna S. Olsson https://www.doi.org/10.31219/osf.io/s6459
Can a consensus be reached on the ethical review of animal experimentation for livestock species?Recommended by Hervé Acloque based on reviews by Christian Nawroth, Patrick Gonin and Leon borgdorf
"Ensuring ethical animal welfare research: Are more ethics review committees the solution?" by Birte Nielsen and colleagues  provides food for thought on the ethical assessment of experiments involving farm animals. While regulations can provide a precise framework, they differ from country to country and do not consider several cases, mainly when the experimentation involves non- or minimally invasive manipulations. It is also the case when research projects use farmed animals that do not fall within the scope of the regulations on animal experimentation but have undergone practices that can be authorised on farms but may raise ethical questions (tail docking, live castration, tooth filing, beak trimming, dehorning). On the other hand, the heterogeneity of the criteria taken into account by the ethics committees, when they exist (and this can differ greatly from one country to another), do not necessarily correspond to the criteria of the journals, the reviewers and the bodies brought in to evaluate the research project, or to the regulations specific to each country.
All these paradoxes lead the authors to propose solutions, the most straightforward and spontaneous of which is to ask ourselves questions about this issue upstream of the experimental design required to answer a given scientific question. While increasing the number of ethical review committees may be an insufficient option, the authors insist on the importance of improving committee members' training, taking into consideration jurisdictions' differences between countries and spending more time on ethics evaluation during manuscripts' reviewing. In addition, the upstream assessment of research projects by ethics committees, specific to an institution (research institute, universities, companies), a scientific publisher or even a dedicated international ethical review board may also be a good option.
The ethical evaluation of research projects is a question at the heart of our research activities, for which we do not have all the answers. As with scientific reviewing, we must take on the role of evaluator or be evaluated ourselves, using criteria and feelings that are not always consensual. The heterogeneity of evaluation systems within the scientific community, the lack of training for scientists in the fundamentals of ethical evaluation, and the different perceptions of the animal condition between countries and cultures can lead to a reciprocal lack of understanding between evaluator and evaluated, and sometimes a feeling of injustice, as some research may be easy to conduct in one country but difficult in another. Indeed, it is exciting to read the exchanges between the authors and the three reviewers who assessed this opinion paper to appreciate the diversity of points of view and see specific points of divergence.
In addition to animal experimentation, the judgment handed down on 30 June 2023 by the French court penalising a pig farmer for the abusive use of an authorised breeding practice (tail docking) is a perfect illustration of the fact that the ethical assessment of practices and handling of farm animals now extends far beyond the scientific world and is becoming an increasingly important factor in the relationship between society and animal breeding. Failure to consider this evolution, whether in experimentation or animal husbandry, may have legal consequences and increase the lack of understanding between our practices and how society perceives them. The questions raised and the solutions proposed in the article by Nielsen et al. are central to our concerns, not only for the scientific community but also to meet the expectations of all stakeholders.
Finally, although the authors do not directly address the question of genome editing and research using edited farm animals, this is and will be at the heart of future issues concerning the ethical evaluation of research projects. As with practices and manipulations, the intentionality of the modifications induced leads us to question and evaluate, in farmed species, their consequences on animal welfare and their relevance to society and the development of more sustainable and socially accepted animal husbandry.
 Nielsen, B. L., Golledge, H. D. R., Chou, J., Camerlink, I., Pongrácz, P., Ceballos, M., Whittaker, A. L., Olsson, I. S. (2023) Ensuring ethical animal welfare research: Are more ethics review committees the solution? OSF Preprints. Ver. 3 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.31219/osf.io/s6459
|Ensuring ethical animal welfare research: Are more ethics review committees the solution?
|Birte L. Nielsen, Huw D.R. Golledge, Jen-Yun Chou, Irene Camerlink, Péter Pongrácz, Maria Camila Ceballos, Alexandra L. Whittaker and I. Anna S. Olsson
|<p>As the article is a short Opinion Paper, it has no abstract, but it aims to highlight the inherent challenges to ethics review of animal (welfare) science research, especially the differences between different countries and jurisdictions which ...
|Animal behaviour , Animal welfare, Open science, Veterinary science
05 Jul 2022
Impact of pre-breeding feeding practices on rabbit mammary gland development at mid-pregnancy.Cathy Hue-Beauvais, Karine Bebin, Raphael Robert, Delphine Gardan-Salmon, Mickael Maupin, Nicolas Brun, Etienne Aujean, Florence Jaffrezic, Steve Simon, Madia Charlier, Fabienne Le Provost https://doi.org/10.1101/2022.01.17.476562
Managing the feeding of rabbits to improve metabolic efficiencyRecommended by Giuseppe Conte based on reviews by Marion Boutinaud, Davi Savietto and 1 anonymous reviewer
A correct execution of feeding plan for growing rabbit decreases the possibility of post-weaning digestive disorders, thus enhancing the feed efficiency in the animals. However, a limitation of feed daily quantity is required between 10 weeks of age and the first artificial insemination. This limitation causes energy deficiency with a consequent reduction in fertility. Beauvais et al. (2022) studied the impact of feed restriction strategies in female rabbits. Four feed restriction strategies were applied in two distinct periods (post-weaning and puberty) and evaluated by different physiological parameters (growth rate, metabolic profiles, reproductive parameters and mammary gland development). In the first part of the paper, the authors evaluated the association between weight slopes and feeding strategies in the late post-weaning and peripartum period in the four groups. As revealed by the authors, a significant difference was observed during the late post-weaning period, which remained significant between the pubertal and fattening phases. Probably these differences are related to the restriction feeding pattern. The results indicated that restrictive feeding changes in the first step of post-weaning period is associated with a significant difference in body weight. This difference occurs from the third week of diet, highlighting the high sensitivity of growing rabbit to nutrition during the post-weaning period.
In the second part of the paper, the authors evaluated the expression of genes involved in the lipid metabolism. During the mid-pregnancy, was revealed a significant higher expression of lipogenic genes, which may be considered as useful markers for the mammary epithelial development in less restrictive strategies during early life period.
The results proposed by Beauvais et al. (2022) enlighten the important role played by the feeding conditions of young female rabbits in the early life rearing. In particular, this activity provides specific recommendations for optimizing lactation and thus preventing neonatal mortality of the offspring. Moreover, the authors provide indications about the effect of feeding strategies on the mammary development and gene expression with absolute consequences on the development of offspring. Mammary lipid metabolism affects the milk profile and therefore the growth performance of the young animals.
Hue-Beauvais C, Bebin K, Robert R, Gardan-Salmon D, Maupin M, Brun N, Aujean E, Jaffrezic F, Simon S, Charlier M, Le Provost F (2022). Impact of pre-breeding feeding practices on rabbit mammary gland development at mid-pregnancy. biorXiv, 2022.01.17.476562, ver. 3 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2022.01.17.476562
|Impact of pre-breeding feeding practices on rabbit mammary gland development at mid-pregnancy.
|Cathy Hue-Beauvais, Karine Bebin, Raphael Robert, Delphine Gardan-Salmon, Mickael Maupin, Nicolas Brun, Etienne Aujean, Florence Jaffrezic, Steve Simon, Madia Charlier, Fabienne Le Provost
|<p>Optimizing rabbit does preparation during early life to improve reproductive potential is a major challenge for breeders. Does selected for reproduction have specific nutritional needs, which may not be supplied with the common practice of feed...
|Animal nutrition modelling
15 Dec 2020
Accuracy of predicting chemical body composition of growing pigs using dual-energy X-ray absorptiometryClaudia Kasper, Patrick Schlegel, Isabel Ruiz-Ascacibar, Peter Stoll, Giuseppe Bee https://doi.org/10.1101/2020.09.15.286153
Accurate predictions of chemical composition of pigs for a wide range of body weights: no longer a myth!Recommended by Florence Gondret based on reviews by Mathieu Monziols and 1 anonymous reviewer
Assessing body or carcass composition in growing pigs is essential to refine nutritional models, select for specific traits and evaluate pork products. The gold standard methods are dissection and chemical measurements, which are time-consuming and invasive ways to obtain the data. Different teams have tested dual-energy x-ray absorptiometry (DEXA), especially for determining total and regional body composition of fat, soft lean tissues and bone minerals [1-3]. The DEXA measurements are quick, non-invasive, precise, and operator independent. However, the instruments from different manufacturers are unique in implementation so that it is difficult to obtain and share generalized equations. In addition, the validity and accuracy of the measures when applied to pigs having very different composition have been scarcely addressed.
The present manuscript shows that carcass analysis by DEXA can be used to predict empty body chemical composition, and it provides accuracy values for the content in single nutrients (protein, lipids, Ca, P). The body weight range used to generate differences in body composition is very large (20 to 100 kg), which is important when studying pigs along growth. Moreover, regression equations within weight classes (20, 60 and 100 kg) show no important biases, with the exception for body fat especially at the earliest growth stages. Limitations of the technique are the needs of anesthesia when applied to living pigs, and of standardizing the positions of body, carcass and cuts when applied to living or dissected pigs. Another originality of the manuscript is the comparison of the obtained calibrations with previously published prediction models, showing that the differences do not preclude the possibility to use a single model when built from a meta-analysis of the different data. Taken together, this work offers good perspectives to refine nutritional models by inputs from rapidly analyzed body chemical composition and to monitor body and carcass composition in several pigs for genetics applications.
 Mitchell AD., Scholz AM., Pursel VG., and Evock-Clover CM. (1998). Composition analysis of pork carcasses by dual-energy x-ray absorptiometry. Journal of Animal Science. 76(8), 2104-14. https://doi.org/10.2527/1998.7682104x
 Marcoux M., Bernier JF., and Pomar C. (2003). Estimation of Canadian and European lean yields and composition of pig carcasses by dual-energy X-ray absorptiometry. Meat Science. 63(3), 359-65. https://doi.org/10.1016/S0309-1740(02)00094-3
 Kipper M., Marcoux M., Andretta I., and Pomar C. (2018). Repeatability and reproducibility of measurements obtained by dual-energy X-ray absorptiometry on pig carcasses. Journal of Animal Science, 96(5), 2027-2037. https://doi.org/10.1093/jas/skx046 "
|Accuracy of predicting chemical body composition of growing pigs using dual-energy X-ray absorptiometry
|Claudia Kasper, Patrick Schlegel, Isabel Ruiz-Ascacibar, Peter Stoll, Giuseppe Bee
|<p>Studies in animal science assessing nutrient and energy efficiency or determining nutrient requirements necessitate gathering exact measurements of body composition or body nutrient contents. Wet chemical analysis methods or standardized dissec...
|Agricultural sustainability, Animal nutrition modelling, Monogastrics, Physiology, Pig nutrition
31 Jan 2020
OneARK: Strengthening the links between animal production science and animal ecologyDelphine Destoumieux-Garzón, Pascal Bonnet, Céline Teplitsky, François Criscuolo, Pierre-Yves Henry, David Mazurais, Patrick Prunet, Gilles Salvat, Philippe Usseglio-Polatera, Etienne Verrier and Nicolas Friggens https://doi.org/10.5281/zenodo.3632731
When scientific communities intertwineRecommended by Pauline Ezanno based on reviews by Rowland Raymond Kao, Arata Hidano and 1 anonymous reviewer
Scientific research can be seen by some as a competitive territory: competition of opinions, concepts, publications, competition for funding. Fortunately, it is above all a territory of sharing and cross-fertilization of ideas. It is gradually becoming a territory of productive interdisciplinary collaborations, despite persistent resistance to making borders more permeable . At the crossroads of worlds, many challenges must be met for communities to understand each other, to be able to communicate with one another, and to benefit mutually from scientific interactions .
Delphine Destoumieux-Garzon and co-authors  propose to stimulate a single Animal Research Kinship (OneARK) to promote the crossing of the scientific communities in animal production and animal ecology. These two communities share many concepts and methods, which, while they are based on marked specificities (natural versus artificial systems), also and above all have common points that need to be explored more closely. Seven concepts of shared interest to improve the resilience and sustainability of animal population systems were explored by the authors: selection, system viability, system management, animal adaptability, inter-individual diversity in systems, agroecology, and animal monitoring.
This foundation stone paves the way for a finer integration between these two communities, which are close and yet distant, and which are slowly getting to know, understand, and recognize each other.
 Ledford, H. (2015). How to solve the world’s biggest problems. Nature, 525, 308–311. doi: 10.1038/525308a
|OneARK: Strengthening the links between animal production science and animal ecology
|Delphine Destoumieux-Garzón, Pascal Bonnet, Céline Teplitsky, François Criscuolo, Pierre-Yves Henry, David Mazurais, Patrick Prunet, Gilles Salvat, Philippe Usseglio-Polatera, Etienne Verrier and Nicolas Friggens
|<p>1. Wild and farmed animals are key elements of natural and managed ecosystems that deliver functions such as pollination, pest control and nutrient cycling within the broader roles they play in contributing to biodiversity and to every category...
|Agricultural sustainability, Animal genetics, Animal welfare, Ecology, Precision livestock farming, Veterinary epidemiology