One of the achievements of animal genetics is that it finds solutions along with the emergence of new needs of the animal husbandry community or the adoption of new laws. Muir and Cheng (2013) research serves as a classic example of using the innovations of animal genetics to meet new legal challenges, such as the restriction of beak cutting in laying hens. Muir and Cheng (2013) investigated the genetic diversity to deal with the cannibalism of intact chickens. In 2021, the European Citizens' Initiative urged the European Commission to legislate against the use of cages for farm animals in the livestock industry. Chapuis et al., (2024) presented a successful solution to the poultry industry about this (future) law by presenting a cost-efficient assignment SNP panel.

In animal breeding, access to pedigree information is necessary for genetic progress. Since the 1970s, the development of genomic science and  molecular techniques has shown their ability in this field. Despite the substantial reduction of genotyping costs in the last 20 years, the practical use of genome-wide genotyping for thousands of SNPs remains challenging. Therefore, the search for a small, cost-effective SNP panel is ongoing, with objectives including genetic diversity (Viale et al., 2017), product traceability (Dominik et al., 2021), species and hybrid identification (Harmoinen et al., 2021) and pedigree construction in wild populations (Ekblom et al., 2021). Furthermore, especially in recent decades, small panels of markers have been proposed for parentage assignment in different animals. For example, Domínguez-Viveros et al., (2020) developed panels with 42 to 63 markers for different sheep breeds in Mexico. Similar panels for parentage assignment have been proposed for salmon (May et al., 2020), rainbow trout (Liu et al., 2016), French sheep (Tortereau et al., 2017), Spanish sheep (Calvo et al., 2021), and European bison (Wehrenberg et al., 2024), with marker numbers of 142, 95, 180, 173, and 96, respectively. Massault et al., (2021) showed by simulation that a panel with at least 50 markers is sufficient for progeny assignment in pearl oysters. These examples highlight that extracting a small panel of markers (usually less than 200) from the total genotyping introduced in different species, can open new horizons for applying genomic information in animal breeding.

Chapuis et al. (2024) addressed the challenge of finding an efficient set of markers that can be used in the hybridization of two species of the Pekin duck and the Muscovy duck. They used KASPar technology to setup a panel, with SNPs existing in both species and their hybrids. This panel has sufficient polymorphism to use in practice. Thus, it can be considered as a step forward compared to previous work done on microsatellites. A final list of SNPs was constructed from a reference set comprising 600 K genotyping of Anas platyrhynchos, Cairina moschata and mule duck. 

In addition to developing of a cost-efficient assignment panel, the work of Chapuis et al. (2024) presented a factorial design to maintain genetic diversity while considering specificities of duck production. The use of factorial design in avian pedigreed populations is relatively novel, making this research particularly innovative. The study's approach to factorial design in populations with limited size may be generalized to similar poultry species. Furthermore, sufficient effective size of population is selected. So, the panel can be used in other populations outside the tested populations. A notable feature of this panel is the use of neutral SNPs, which ensures that markers will not be lost due to future selection pressures over time.

The paper of Chapuis et al. (2024) exemplifies the application of molecular genetics to address challenges in the poultry industry.  The use of kinship matrix instead of relationship matrix, taking into account the unique characteristics of duck production, could be another novelty of the paper. According to the reviewers' comments, the results can be beneficial in the future, particularly with the introduction of the specific factorial design.

References

Calvo JH, Serrano M, Tortereau F, Sarto P, Iguacel LP, Jiménez MA, Folch J, Alabart JL, Fabre S and Lahoz B (2021). Development of a SNP parentage assignment panel in some North-Eastern Spanish meat sheep breeds. Spanish Journal of Agricultural Research 18, e0406. https://doi.org/10.5424/sjar/2020184-16805    

Chapuis H, Brard-Fudulea S, Hazard A, Vignal A, Demars J, Rouger R, Teissier M, Gilbert H (2024). Cost-efficient assignment panel for ducks. Setup of a cost-efficient assignment panel for duck populations.: An illustration with experimental data. HAL, hal-04542880, ver. 2 peer-reviewed and recommended by Peer Community in Animal Science. https://hal.inrae.fr/hal-04542880 

Domínguez-Viveros J, Rodríguez-Almeida FA, Jahuey-Martínez FJ, Martínez-Quintana JA, Aguilar-Palma GN, Ordoñez-Baquera P (2020). Definition of a SNP panel for paternity testing in ten sheep populations in Mexico, Small Ruminant Research ,193,106262. https://doi.org/10.1016/j.smallrumres.2020.106262

Dominik S, Duff CJ, Byrne AI, Daetwyler H, Reverter A (2021). Ultra-small SNP panels to uniquely identify individuals in thousands of samples. Animal Production Science 61, 1796–1800. https://doi.org/10.1071/AN21123

Ekblom R, Aronsson M, Elsner-Gearing F, Johansson M, Fountain T, Persson J (2021). Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples. Conservation Genetics Resources 13, 261–274. https://doi.org/10.1007/s12686-021-01208-5

Harmoinen J, von Thaden A, Aspi J, Kvist L, Cocchiararo B, Jarausch A, Gazzola A, Sin T, Lohi H, Hytönen MK, Kojola I, Stronen AV, Caniglia R, Mattucci F, Galaverni M, Godinho R, Ruiz-González A, Randi E, Muñoz-Fuentes V, Nowak C (2021). Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples. BMC Genomics 22, 473. https://doi.org/10.1186/s12864-021-07761-5

Liu S, Palti Y, Gao G, Rexroad CE (2016). Development and validation of a SNP panel for parentage assignment in rainbow trout. Aquaculture 452, 178–182. https://doi.org/10.1016/j.aquaculture.2015.11.001

Massault C, Jones DB, Zenger KR, Strugnell JM, Barnard R, Jerry DR (2021). A SNP parentage assignment panel for the silver lipped pearl oyster (Pinctada maxima). Aquaculture Reports 20, 100687. https://doi.org/10.1016/j.aqrep.2021.100687

May SA, McKinney GJ, Hilborn R, Hauser L, Naish KA (2020). Power of a dual-use SNP panel for pedigree reconstruction and population assignment. Ecology and Evolution 10, 9522–9531. https://doi.org/10.1002/ece3.6645

Muir WM, Cheng HW(2013). Genetics and the Behaviour of Chickens: Welfare and Productivity. In Genetics and the Behaviour of Domestic Animals. Vol. 2 (2nd ed.). pp. 1–30.ISBN: 9780128100165

Tortereau F, Moreno CR, Tosser-Klopp G, Servin B, Raoul J (2017). Development of a SNP panel dedicated to parentage assignment in French sheep populations. BMC Genetics 18, 50. https://doi.org/10.1186/s12863-017-0518-2

Viale E, Zanetti E, Özdemir D, Broccanello C, Dalmasso A, De Marchi M, Cassandro M (2017). Development and validation of a novel SNP panel for the genetic characterization of Italian chicken breeds by next-generation sequencing discovery and array genotyping. Poultry Science 96, 3858–3866. https://doi.org/10.3382/ps/pex238

Wehrenberg G, Tokarska M, Cocchiararo B, Nowak C (2024). A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison. Scientific Reports 14, 1875. https://doi.org/10.1038/s41598-024-51495-9

The study by Lagarde et al. (2025) is part of efforts aiming to meet the challenges of adapting livestock farming, and more specifically of aquaculture, to the effects of climate change. In fact, during heat waves, water temperatures rise and oxygen becomes scarce. Fish have to adapt to these conditions of hyperthermia and hypoxia. Studies have already shown that it is possible to genetically improve these resistances in salmonids (e.g. Debes et al., 2021). However, current methods for phenotyping these resistances rely on exposing fish to extreme conditions until they lose equilibrium, which indicates that the animal experiences severe conditions and raises ethical and animal welfare concerns.

From the aforementioned, there is then a strong interest in using and identifying less invasive phenotypes, such as behavioural changes, that could serve as indicators of fish responses to hyperthermia and hypoxia. Some behaviours show promise in both wild (Campos et al., 2018) and farmed fish (Van Raaij et al., 1996). A former study by the authors of this manuscript suggests that some of these behaviours are sufficiently heritable to consider applying selection on them (Lagarde et al., 2023). Therefore, the main aim of the present study was to test whether behaviour can be used as an indirect selection criterion to improve the adaptation of rainbow trout to heat waves. To achieve this lofty goal, the responses of different isogenic lines of trout to hyperthermia and hypoxia were investigated using new criteria based on behavioural responses and the reference measure of loss of equilibrium.

The results suggest that certain behavioural traits, such as distance travelled and frequency of zone changes, are associated with resistance to these stresses. Moreover, moderate correlations were observed between certain behavioural variables and resistance to hyperthermia. Indeed, lines that were more resistant to hyperthermia had lower distance travelled and frequency of zone changes during the behavioural test. Other significant and positive correlations were observed between acute hypoxia resistance and certain behavioural variables, likely distance travelled, frequency of zone change and percentage of time spent moving.

These results pave the way for less invasive methods in assessing hyperthermia and hypoxia resistance based on behavioural observations, which could improve the resistance of farmed fish in response to climate change. The study further allows refining the measurements carried out on candidates for selection in order to improve their welfare during evaluation tests.

In conclusion, this study is commendable for its thematic relevance, originality and the potential application of its results to genetic selection of farmed fish.

References

Campos DF, Val AL, Almeida-Val VMF. 2018. The influence of lifestyle and swimming behavior on metabolic rate and thermal tolerance of twelve Amazon forest stream fish species. Journal of Thermal Biology 72:148–154. https://doi.org/10.1016/j.jtherbio.2018.02.002

Debes P V., Solberg MF, Matre IH, Dyrhovden L, Glover KA. 2021. Genetic variation for upper thermal tolerance diminishes within and between populations with increasing acclimation temperature in Atlantic salmon. Heredity 127:455–466. https://doi.org/10.1038/s41437-021-00469-y

Lagarde H, Phocas F, Pouil S, Goardon L, Bideau M, Guyvarc’h F, Labbé L, Dechamp N, Prchal M, Dupont-Nivet M, Lallias D. 2023. Are resistances to acute hyperthermia or hypoxia stress similar and consistent between early and late ages in rainbow trout using isogenic lines? Aquaculture 562:738800. https://doi.org/10.1016/j.aquaculture.2022.738800

Lagarde H, Lallias D, Phocas F, Goardon L, Bideau M, Guyvarc'h F, Labbé L, Dupont-Nivet M, Cousin X. 2025. Screening for links between behaviour and acute hyperthermia and hypoxia resistance in rainbow trout using isogenic lines. bioRxiv, ver.4 peer-reviewed and recommended by PCI Animal Science https://doi.org/10.1101/2023.10.19.563047

Van Raaij MTM, Pit DSS, Balm PHM, Steffens AB, Van Den Thillart GEEJM. 1996. Behavioral strategy and the physiological stress response in rainbow trout exposed to severe hypoxia. Hormones and Behavior 30:85–92. https://doi.org/10.1006/hbeh.1996.0012