Large-scale phenotyping of livestock welfare in commercial production systems: a new frontier in animal breeding

Authors: BRITO, LUIZ - Purdue University; OLIVEIRA, H - Purdue University; MCCONN, BETTY - Orise Fellow; Marchant, Jeremy; SCHINCKEL, ALLAN - Purdue University; Johnson, Jay

Submitted to: Frontiers in Genetics
Publication Type: Review Article
Publication Acceptance Date: 7/3/2020
Publication Date: 7/31/2020
Citation: Brito, L.F., Oliveira, H.R., Mcconn, B., Marchant Forde, J.N., Schinckel, A.P., Johnson, J.S. 2020. Large-scale phenotyping of livestock welfare in commercial production systems: a new frontier in animal breeding. Frontiers in Genetics. https://doi.org/10.3389/fgene.2020.00793.
DOI: https://doi.org/10.3389/fgene.2020.00793

Interpretive Summary: Animal welfare has increasingly important ethical, legal and economic implications in livestock production around the world. Animal product consumers and the society in general are becoming more interested in ensuring the best welfare practices at all stages of the animal production chain, which results in direct implications to the whole industry. In addition, compromised welfare is associated to reduced animal productivity, longevity, poorer meat quality, lower reproductive performance, greater incidence of diseases in the herds or flocks. Animal welfare can be broadly expressed based on the five freedoms of the animals, which consists on the absence of negative symptoms of welfare, as well as positive welfare. Despite the fact that various countries have implemented regulations and legislation to ensure ethical treatment of animals from birth to slaughter, completely eliminating welfare issues is very challenging. This is due to various factors, including climate change effects, growing intensification in commercial production facilities, group housed animals, antibiotic resistance, greater disease incidence, and to a lesser extent, genetic selection for a limited number of production traits in some breeding programs or indirect genetic responses. In this context, the implementation of selective breeding schemes to genetically modify the animals’ bodies and/or behaviors in ways that improve welfare in commercial systems is a promising route.

Technical Abstract: Genomic breeding programs have been paramount for improving the rates of genetic progress for productive efficiency traits in livestock. This has been accompanied by the intensification of production systems, use of a wide range of precision technologies for routine management practices and high-throughput phenotyping. Simultaneously, a greater societal awareness of animal welfare issues has influenced animal producers to consider improved welfare over some production traits. Therefore, several animal management practices and breeding technologies have been developed in recent years to promote positive animal welfare states. In particular, genomic selection can be used to improve livestock social behavior, increase stress and disease tolerance, and ease adaptation to production system changes. The main requirements for including novel behavioral and welfare traits in genomic breeding schemes are: 1) to identify traits that fully represent the biological mechanisms of the industry breeding goals, 2) the availability of individual phenotypic records measured on a large number of animals; 3) phenotypes that are easily and relatively inexpensive to collect and can be analyzed/processed in a short timeframe, and 4) the derived traits are heritable. In this review, we will summarize key indicator variables of livestock behavior and welfare, identify major advancements, challenges, and opportunities to generate high-throughput datasets to enable genomic selection for improved welfare in livestock, and describe the primary statistical and bioinformatic methods available for large-scale data analyses. A wide variety of novel welfare indicator traits can be derived based on information captured by modern technology, including sensors, automatic feeding systems, milking robots, activity collars, video cameras and indirect biomarkers (e.g., physiological status defined based on milk mid-infrared spectra). The development of novel traits coupled with genomic selection schemes for improved welfare in livestock appear to be feasible and can be optimized based on recently developed technologies.