Biological resources for functional annotation of animal genomes.

In order to generate an atlas of the functional elements driving genome expression in domestic animals, the FAANG (Functional Annotation of Animal Genome) strategy consisted of sampling a large number of tissues from a few animals of different species, sexes, ages and stages of production.

This paper presents the collection of tissue samples from four species produced by two pilot projects, at INRAE (Institut national de recherche sur l'agriculture, l'alimentation et l'environnement) and at the University of California, Davis. These are three mammals (cattle, goats and pigs) and one bird (chicken). He describes the metadata characterising these reference sets :

• (1) for animals with origin and breeding history, physiological status and environmental conditions;
• (2) for samples with collection site and tissue/cell processing;
• (3) for quality control; and
• (4) for storage and subsequent distribution.

Three sets are identified: Set 1 includes tissues for which collection can be standardised and for which representative aliquots can be easily distributed (liver, spleen, lung, heart, fat deposits, skin, muscle and peripheral blood mononuclear cells); Set 2 includes tissues requiring special protocols due to their cellular heterogeneity (brain, digestive tract, secretory organs, gonads and gametes, reproductive system, immune tissues, cartilage); Set 3 includes specific cell preparations (immune cells, tracheal epithelial cells). Dedicated sampling protocols have been established and uploaded to https://data.faang.org/protocol/samples. Specificities between mammals and chicken are described where relevant. A total of 73 different tissues or tissue sections were collected, 21 of which are common to all four species.

Having a common set of tissues will facilitate the transfer of knowledge within and between species and help to reduce animal testing. Combining data on the same samples will facilitate data integration. Quality control was performed on some tissues with RNA extraction and RNA quality control. Over 5,000 samples were stored with unique identifiers, and over 4,000 were uploaded to the Biosamples database, provided that standard ontologies were available to describe the sample. Many tissues have already been used to implement the FAANG tests, with published results. All samples are available without restriction for further testing. The application procedure is described. FAANG members are encouraged to apply a range of molecular tests to characterise the functional status of collected samples and to share their results, in accordance with the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

Contact :

• Michèle Tixier-Boichard