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KEY-WORDS: genome annotation; domestic animals; genomic selection; fundamental research

However, the availability of such data only has a limited usefulness for other species, since understanding important phenotypes in their authentic biological context necessitates specific information for each organism. The international intitiative FAANG (Functional Annotation of Animal Genomes) was formally launched in 2015 by a white paper ¹.The main objective of FAANG is to provide support and coordination for the international community through the creation of reference functional maps for domestic animal genomes, with an intitial accent on farm species and companion animals. As with humans and model animals, such maps can determine which regions of each genome are functional, with what temporality, in which contexte, in which cells and tissues; they therefore contribute to predictive biology. The functional annotation provided by the FAANG initiative will give an added value and usefulness to reference genomes of domestic animal species.

This review, which was requested by the journal "Annual Review of Animal Biosciences", is aimed at evaluating the results acquired by FAANG since its beginning, and to trace the future direction of the initiative. In addition to E. Giuffra (INRA) and C.K. Tuggle (Iowa State University, USA) who coordinate the Steering Committee of FAANG (www.faang.org), this review associates 24 co-authors who represent the main institutions of the consortium amongst which figure three INRA members (H. Acloque, S. Djebali and S. Foissac).

The collaborative "OpenScience" approach is essential for the development of an environment favoring success of research and it has therefore been one of the central themes since the beginning of FAANG. A limited number of international institutes, including INRA, has been working at the heart of the different activities that preceded the launching of the intitiative, and which support it today. For INRA, the metaprogram SELGEN financed the pilot project (FR-AgENCODE) with the participation of scientists from the Animal Genetics Division in the INRA research centers of Jouy (UMR1313 GABI), Toulouse (UMR1388 GenPhySE) and Rennes (UMR1348 PEGASE) ^2,3. This working group involved several research and experimental units along with a contribution from the national infrastructure CRB-Anim (https://www.crb-anim.fr), and the core facilities GeT-PlaGe (https://get.genotoul.fr/) and @BRIDGe (http://abridge.inra.fr/). Today, in addition to the diversity of the research projects underway in several countries, FAANG scientists created a coordinated organization to collect and analyze data, which is crutial to the success of the intitiative, consolidated by two networking projects in Europe (COST Action FAANG Europe : http://www.faang-europe.org) and in the United States (le « AG2P RCN », http://ag2p.org/), and by the EMBL-EBI project, currently underway for the creation of the DCC (Data Coordination Centre)⁴ (Figure 1).  

FAANG has now entered a growing phase, highlighted in this review. An approximately 20 million dollar financing was obtained in the United States for threee projects that have been underway since 2018 and which concern cattle, chickens and pigs. The European SC2-SFS30 call-for-projects will support three projects beginning in 2019 for a total of approximately 18 million euros. The competing EU projects are focused on cattle, on different fish species in aquaculture, on the pig and chicken. INRA will be a major partner in at least two of the selected projects.

Data annotation will be used both to better understand the functionning of animal genomes, including an epigenetic dimension, and to improve the precision and sensitivity of genomic selection. However, as with projects on man and model organisms, the FAANG data will allow identifying an important number of elements from candidate sequences. FAANG therefore represents a starting point to test the link between the different genetic variants present in these genomes and their relation with molecular, cellular phenotypes along with the whole organism scale. Annotation of the most pertinent tissues and development stages for each domestic species will provide enough reference information to perform, more efficiently, "genotype-to-phenotype" research. These techniques will include amongst others, genome editing for the modification of important sequences and testing of the underlying phenotypes along with the availability of biological systems (3D cell cultures such as organoids, for in vitro phentoyping) in which the effects of these modifications can be measured on the molecular level, as intermediate phentoypes.