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.

Isabelle Veissier

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

Using sequence data in livestock genomics has often been regarded as a solution to revolutionize livestock breeding (Meuwissen & Goddard, 2010). The main expected benefits were to enhance the accuracy of breeding values, achieve better persistence of the accuracy over generations, and enable across populations or breed predictions (Hickey, 2013). Despite the promised benefits, whole-genome sequencing has not yet been implemented in livestock breeding programs, replacing SNP arrays for routine evaluation.

In this work, Johnsson (2023) thoroughly reviewed the literature regarding the implications of whole-genome sequencing and functional genomics for livestock breeding practice. The author discusses the potential applications and reasons for difficulties in their implementation. The author speculates that the main challenge for making using the sequence data profitable is to overcome the problem of the small dimensionality of the genetic data and proposes three potential ways to achieve this goal. The first approach is better modeling of genomic segments, the second inclusion of undetected genetic variation, and the third use of functional genomic information.  

The paper presents an original and interesting perspective on the current status of the use of sequence data in livestock breeding programs and perspectives for the future. 

References

Hickey,J.M.,2013.Sequencing millions of animals for genomic selection 2.0. Journal of Animal Breeding and Genetics 130:331–332. https://doi.org/10.1111/jbg.12054 

Johnsson, M., 2023. The big challenge for livestock genomics is to make sequence data pay. arXiv, 2302.01140, ver. 4 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.48550/arXiv.2302.01140 

Meuwissen, T., Goddard, M.,2010. Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics 185:623–631. https://doi.org/10.1534/genetics.110.116590 

The identification of reliable estimates of growth potential and resilience over the fattening period in large populations is a challenge in actual swine breeding conditions. To overcome this drawback, the study by Revilla et al. 2021 in the frame of precision livestock farming aimed to propose an innovative modelling approach, in addition to previous studies from the same group (Revilla et al. 2019), to enhance the quality of the quantification of pig resilience during the entire fattening period. 

The authors developed a model that quantifies an “individual pig resilience indicator” based on longitudinal data, for instance body weight, recorded routinely by a commercially available automatic feeding system. Revilla and co-workers considered in their study two mainly commercialised pure pig breeds these being Piétrain including Piétrain Français NN Axiom line (Pie NN) free from halothane-sensitivity (ryanodine receptor gene, RYR1) and Piétrain Français Axiom line positive to this gene and Duroc. Therefore, the authors investigated the potential of improving resilience of swine livestock through inclusion for the first time of an “individual pig resilience indicator” in breeding objectives. A database of 13 093 boars (approximately 11.1 million of weightings) belonging to Pie (n= 5 841), Pie NN (n = 5 032) and Duroc (n= 2 220) finished under ad libitum feeding, high sanitary level and controlled temperature was used to develop robust models.

The authors checked the three datasets (for each pig breed)​ independently to explore the variation and gaps (a data pre-treatment procedure) to ensure high quality data for the modelling approach. Then, they applied the Gompertz model and linear interpolation on body weight data to quantify individual deviations from the expected production, allowing the creation of the ABC index. For the modelling, the authors applied a two-step mathematical model approach by first establishing a theoretical growth curve of each animal, while the second step aimed to build the actual perturbed growth curve. The heritability of the index ranged from 0.03 to 0.04, with similar heritability between Piétrain and Duroc breeds. Moreover, moderate genetic relationships were computed between the proposed index and important phenotypic traits in swine production likely BF100: backfat thickness at 100kg; LD100: longissimus dorsi thickness at 100kg; ADG: average daily gain during control and FCR: feed conversion ratio.

Developing models able to capture perturbations during the fattening period is a challenge in swine breeding industry. The model and methodology proposed by the authors in this innovative work (although preliminary and with low heritabilities) would help overcome such limit and facilitate a real implementation at large scale in pig breeding system. The modelling approach further offers an opportunity to develop a selection criterion to improve resilience in swine breeding conditions. 

To explore the full potential of this modelling approach, a larger database and other factors such as breed, behaviour and feeding behaviour of the animals, rearing practices, management and environment conditions, age… etc. are worthy to consider. In the future, more in depth measurements of behaviour that can be computed for example using computer vision should be desirable to increase the robustness of the proposed model.

References

Revilla, M., Friggens, N.C., Broudiscou, L.P., Lemonnier, G., Blanc, F., Ravon, L., Mercat, M.J., Billon, Y., Rogel-Gaillard, C., Le Floch, N. and Estellé, J. (2019). Towards the quantitative characterisation of piglets’ robustness to weaning: a modelling approach. Animal, 13(11), 2536-2546. https://doi.org/10.1017/S1751731119000843 

Revilla M, Lenoir G, Flatres-Grall L, Muñoz-Tamayo R, Friggens NC (2021). Quantifying growth perturbations over the fattening period in swine via mathematical modelling. bioRxiv, 2020.10.22.349985, ver. 5 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2020.10.22.349985 

To limit the use of antibiotics in the few days after hatching, it is necessary to improve the robustness of chicks during the early post-hatch period. This can be achieved by ensuring immediate access to feeds, optimizing the implantation and maturation of the microbiota and immune system of each chick, and minimizing exposure of stressors such as transportation. The study conducted by Guilloteau and colleagues (2024) compared the performance and health of chicks raised in conventional hatching systems with those raised in on-farm hatching systems. The authors showed that both systems yielded similar hatching percentage of eggs. Chicks from on-farm hatching systems exhibited higher body weights during the post-hatch period compared to those from conventional hatching, whereas health parameters were not affected by the system. An originality of the study was the examination of the benefits of the presence of an adult hen in hatching systems. The effects on chick traits were interpreted in relation to the hen behavior at hatching and a classification according to maternal or agonistic activities towards the chicks. However, the experimental design did not allow to make statistical correlations between hen behavior pattern and chick traits. Importantly, the presence of a hen decreased the hatching percentage, and this was likely associated with hen aggressiveness in the pen. The presence of the hen deteriorated the quality scores of the chicks in the on-farm hatching system, and increased mortality of chicks at hatching, negatively impacting chick weight gain and feed efficiency during the few days after hatching in both conventional and on-farm hatching systems. Thereafter, the effect of the presence of a hen on chick body weight was different according to the sex of the chicks and the type of hatching system. The presence of a hen did not reduce the parasitic load of the chicks nor improved clinical signs. No specific characterization of the fecal microbiota of the chicks was conducted, preventing the testing whether or not the presence of the hen affected the early implantation and maturation of the chick microbiome. Altogether, the data indicate that on-farm hatching systems are at least equivalent (in terms of health traits, feed efficiency) or even favorable (for faster growth in the early period after hatching) for chicks. Training the hens (considered as foster adults) to the presence of eggs and chicks or selecting hens according to specific activity behavioral patterns could be ways to establish better interactions between hens and chicks. Although the number and type of environmental stressors tested in the experiment differ from those in commercial farms, the article opens new perspectives for alternative hatching and farming practices.

Reference

Guilloteau LA, Bertin A, Crochet S, Bagnard C, Hondelatte A, Ravon L, Schouler C, Germain K, Collin A (2024) On-farm hatching and contact with adult hen post hatch induce sex-dependent effects on performance, health and robustness in broiler chickens. bioRxiv, 2023.05.17.541117. ver. 3 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2023.05.17.541117. 

Naturally occurring compounds that can reduce methane production in anaerobic conditions have been studied for quite some time as feasible approaches to mitigate methane production in ruminant animals, especially those of commercial importance. Asparagopsis taxiformis (red algae) and Dictyota bartayresii (brown algae) are effective inhibitors of methane synthesis under in vitro anaerobic fermentation systems (Machado et al., 2014) likely because of their high concentration of secondary metabolites that are toxic to the typical rumen microbiota, including protozoa. In addition to phytoplankton (Palmer and Reason, 2009), Asparagopsis contains a high concentration of haloform compounds (e.g., bromoform, chloroform) while Dictyota has a high concentration of isoprenoid terpenes. Despite the economic and biological impact of diverse phytochemicals on reducing methane production in ruminant animals (Tedeschi et al., 2021), haloform compounds’ environmental impact and safety, in particular, are still unclear. In the present study, Munõz-Tamayo and collaborators (2021) listed relevant literature about the impact of A. taxiformis on ruminal methane production.

Concurrent to the understanding of mechanisms and biology behind the reduction of ruminal methane, mathematical models can lead the way to enhance the effectiveness of feeding A. taxiformis under commercial applications. Thus, in the present study, Munõz-Tamayo and collaborators (2021) sought to develop a mathematical model to understand the rumen fermentation changes in vitro experimentation containing extract of A. taxiformis by adapting a previously documented model by Muñoz-Tamayo et al. (2016).

Modeling development, calibration, and evaluation steps should be independent of each other, requiring complete, distinct, and separate databases (Tedeschi, 2006). However, in rare circumstances where such requirements cannot be met because data availability is scarce, the cross-validation technique, when possible, should be considered to assess data dispersion’s effects on model adequacy. In other situations, clear reasoning for failing to do so must be addressed in the paper. In the present paper, Munõz-Tamayo and collaborators (2021) explained the limitations in their modeling efforts were primarily due to the lack of ideal data: “experiments with simultaneous dynamic data of bromoform, volatile fatty acids, hydrogen, and methane.” Regardless of the availability of ideal data, improvements in the conceptual model are warranted to include amino acids and branched-chain fatty acids fermentation dynamics in the rumen and the fluctuations in ruminal pH.

References

Machado L, Magnusson M, Paul NA, Nys R de, Tomkins N (2014) Effects of Marine and Freshwater Macroalgae on In Vitro Total Gas and Methane Production. PLOS ONE, 9, e85289. https://doi.org/10.1371/journal.pone.0085289

Muñoz-Tamayo R, Chagas JC, Ramin M, Krizsan SJ (2021) Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production. bioRxiv, 2020.11.09.374330, ver. 4 peer-reviewed and recommended by PCI Animal Science. https://doi.org/10.1101/2020.11.09.374330

Muñoz-Tamayo R, Giger-Reverdin S, Sauvant D (2016) Mechanistic modelling of in vitro fermentation and methane production by rumen microbiota. Animal Feed Science and Technology, 220, 1–21. https://doi.org/10.1016/j.anifeedsci.2016.07.005

Palmer CJ, Reason CJ (2009) Relationships of surface bromoform concentrations with mixed layer depth and salinity in the tropical oceans. Global Biogeochemical Cycles, 23. https://doi.org/10.1029/2008GB003338

Tedeschi LO (2006) Assessment of the adequacy of mathematical models. Agricultural Systems, 89, 225–247. https://doi.org/10.1016/j.agsy.2005.11.004

Tedeschi LO, Muir JP, Naumann HD, Norris AB, Ramírez-Restrepo CA, Mertens-Talcott SU (2021) Nutritional Aspects of Ecologically Relevant Phytochemicals in Ruminant Production. Frontiers in Veterinary Science, 8. https://doi.org/10.3389/fvets.2021.628445