Areas of ATOL

“Welfare” aim (M.C. Salaün, curator)

This aim lies in the acknowledgment of the sensitivity of livestock, which is expressed by perceptual, emotional and cognitive abilities. Acknowledging the fundamental needs of animals, whether they are nutritional, physical or social, seems decisive to allow for the expression of species-specific behaviours. The “welfare” aim represents an agronomic and societal challenge. Indeed, living standards of animals are sometimes associated to violations of animal welfare. The reassessment of productions systems, intensive ones especially, represents a factor for their evolution towards animal maintenance conditions more respectful of their well-being. Animal welfare assessment is based on five liberties (Farm Animal Welfare Council, 1995):

  1. Freedom from pain, injury or disease
  2. Freedom from fear and distress
  3. Freedom from hunger or thirst
  4. Freedom from discomfort by providing sufficient space
  5. Freedom to express (most) normal behaviour

This assessment makes use of behavioural, physiological, zootechnical and health-related criteria. The “welfare” aim of this ontology takes these criteria into account, thanks to a three-branched structure:

  • “Animal performance traits”
  • “Health traits”
  • “Psychoneuroendocrinological state traits”

The “Psychoneuroendocrinological state traits” branch is divided into nine subsections:

  • behavioural traits
  • biological rhythm traits
  • cognitive function traits
  • emotional function traits
  • metabolism traits
  • pain responses traits
  • reflex responses traits
  • sensory capacity traits
  • stress response traits.
Experts:

The group of experts includes 11 people for each species studied, and for each approach of animal welfare: behaviour, health, physiology, zootechnics: A. Boissy (URH, bovine), MM Mialon-Richard (URH, ovine), C. Duvaux-Ponter (UMR 0791, caprine), L Lansade (UMR 0085, equine), C Arnould (UMR 0085, poultry), L Fortun-Lamothe (UMR 1289, rabbit), P.Prunet – V Colson (UR 1037, fish), M Keller (UMR 0085, rodent), P Mormède (UMR 0444, multispecies), J Servière (UMR 0791, multispecies), E. Merlot (UMR 1348, swine).

Growth and meat production (J. Bugeon, curator)

This part of the ontology includes all traits related to animal growth, carcass quality in terms of state of fattening, muscular development (from its embryonic formation to a commercial state), as well as meat and adipose tissue quality on a technological, nutritional and sensory viewpoint. Livestock species represented are bovines, ovines, the trout, the rabbit, poultry, the turkey, swine, and two model species, the mouse and the zebrafish. When building the ontology, each expert validated and added traits relevant to their species of interest. Hierarchisation helped create five main branches:

  1. Adipose tissue trait
  2. Carcass quality trait
  3. Growth trait
  4. Meat quality trait
  5. Muscular system trait
Experts:

Quality of growth: Elisabeth Baeza (UMR BOA, poultry), Jean-Paul Brun (UMRH, bovines), Arnaud Chatonnet (UMR DMEM, zebrafish), Michel Duclos (UMR BOA, poultry), Xavier Fernandez (UMR TANDEM, rabbit), Florence Gondret (UMR PEGASE, swine), Catherine Jurie (UMRH, bovines), Serge Leibovitch (UMR DMEM, mouse), Brigitte Picard (UMRH, bovines), Sophie Prache (UMRH, ovines)

Development led by Isabelle Hue: Isabelle Cassar-Malek (UMRH, bovines), Pierre-Yves Rescan (LPGP, trout), Elisabeth Baeza (UMR BOA, poultry)

Fatty liver (J. Bugeon, curator)

This part of the ontology includes all of the traits related to liver physiology, fatty liver production and its technological, nutritional and sensory qualities. The concerned species are the duck and the goose.

Expert:

Xavier Fernandez (UMR GenPhySE, Toulouse, Duck)

Mammary gland and milk production trait (C. Hurtaud, curator)

This part of the ontology includes all traits associated to the morphological description of the mammary gland (globally or at tissue level), its physiology (mammogenesis, metabolic and synthesis activity), and all traits concerning milk and colostrum production: ejection, quantity, milk and colostrum composition, technological aptitude, milk sensory properties and physical structure.

The following experts from the PHASE, CEPIA and MICA divisions have participated in building this ontology:

  • Laurence BERNARD (UMR 1213 Herbivores)
  • Frédéric DESSAUGE (UMR 1348 PEGASE Physiology, Environment, and Genetics for the Animal and Livestock Systems)
  • Eve DEVINOY (UR 1313 GABI Animal Genetics and Integrative Biology)
  • Yves LE LOIR (UMR 1253 Science and Technology of Milk and Eggs)
  • Pierre-Guy MARNET (Agrocampus Ouest UMR 1348 PEGASE Physiology, Environment, and Genetics for the Animal and Livestock Systems)
  • Marie-Christine MONTEL (UMR 0545 Cheese research)
  • Hélène QUESNEL (UMR 1348 PEGASE Physiology, Environment, and Genetics for the Animal and Livestock Systems)
  • Isabelle VERDIER-METZ (UMR 0545 Cheese research)

Egg (C. Hurtaud, curator)

This part of the ontology includes all traits associated to egg formation, its morphological description, its composition (egg shell, egg yolk and white and vitelline membrane composition), its production and quality (technological, organoleptic and mecanical).

The following experts from the PHASE and CEPIA divisions have participated in building this ontology:

  • Joël GAUTRON (UMR BOA Avian Biology & Poultry Research)
  • Françoise NAU (Agrocampus Ouest UMR 1253 Science and Technology of Milk and Eggs)
  • Marc ANTON (UR 1268 BIA Biopolymers Interactions Assemblies)

Nutrition (J. Vernet, curator)

This part deals with all measurable or observable traits associated to all functions used by animals to transform food into nutrients, and how they use them for their maintenance and productions.

To this day, the “Nutrition” branch of the ontology, with the aim of understanding feed efficiency, is made up of six subsections:

  1. digestive system morphology which presents the anatomical description of digestive compartments
  2. digestive system physiology which addresses the working of digestion and the absorption of nutrients
  3. ingestion which describes the traits associated to the quantity of feed and water ingested by the animal
  4. animal efficiency, supplementation and animal requirement, that can be described through the following definitions:
    • “animal efficiency” is equal to production output (kg of meat or milk) divided by feed input (kg)
    • “supplementation” describes the link between the quantity of nutrients found in productions and the quantity of nutrients given to the animal
    • “animal requirement” describes the quantity of nutrients given to the animal to be able to certainly attend to its needs
Experts:

The following group of experts has participated in building this ontology: Jacques Agabriel (UMRH, bovine), Jocelyne Aufrère (UMRH, ovine, bovine), Philippe Lescoat (UMR BOA, swine, poultry), Didier Micol (UMRH, bovine), Françoise Médale (UMR NuMeA, fish), Diego Morgavi (UMRH, bovine), Agnes Narcy (UMR BOA, poultry), Pierre Nozière (UMRH, ovine, bovine), Stéphane Panserat (UMR NuMaA, fish), Jaap van Milgen (UMR PEGASE, swine, bovine).

Reproduction (A. Fatet, curator)

This part of the ontology includes all traits associated to animal reproduction and fertility evaluation, endocrinology, male and female specificities (anatomy, gamete production…), conception (gamete maturation, early development of the embryo…) and sexual differentiation.

Hierarchisation helped create five main branches:

  1. endocrine reproductive system trait
  2. female reproductive feature
  3. male reproductive feature
  4. conception physiology
  5. sex determination
Experts:

The following group of experts have participated in building the “reproduction” branch of this ontology: Elisabeth Blesbois and Joël Gautron (UMR BOA, poultry), Nadine Gérard and Marianne Vidament (UMR PRC, equin), Michèle Theau-Clement (UMR GenPhySE, rabbit), Florence Le Gac (LPGP, fish), Fabrice Télétchéa (UR AFPA, fish), Florian Guillon (UMR PRC, mouse), Rex Scaramuzzi (UMR PRC, ovines – retired), Bernard Leboeuf (UEICP, goat – retired).

The following experts have worked on the interaction “reproduction*development”, co-animated by Isabelle Hue: Olivier Sandra, Béatrice Mandon-Pepin, Eric Pailhoux, Véronique Duranthon (UMR BDR), Marc-André Sirard (Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Canada).