FR-AgENCODE: A Pilot Project to Improve the Functional Annotation of Livestock Genomes

Deciphering the network of functional connections between genotype and quantitative phenotype is probably the most significant challenge of the post-genomic era. However, while most livestock genomes have been sequenced, their sequences exhibit various degrees of completeness and reliability. Moreover, much remains to be done to improve their functional annotation. In human and model species, ENCODE projects have shown that a genome-wide identification of functional elements in multiple species is an invaluable resource for the dissection of genotype to phenotype relationships. Consequently, the FAANG consortium (Functional Annotation of ANimal Genomes) initiated a worldwide action for the characterization of all functional elements in genomes of domesticated animals.

In this context, the French National Institute of Agronomic Research (INRA) is launching the FR-AgENCODE pilot project to improve the functional annotation of 4 animal genomes (pig, goat, chicken and cattle). In collaboration with FAANG partners worldwide, the FR-AgENCODE consortium aims to:

- build a biorepository of tissue samples from several animals in each species.
- perform a series of high-throughput molecular assays (RNA-seq and Hi-C) to characterize the transcriptome and the chromatin structure of several tissue samples per animal.
- store, analyze and share both data and results via an integrative platform.
- define a set of Standard Operative Procedures for the production and the analysis of the data.

In this presentation we will give an overview of the FAANG initiative and illustrate how the FR-AgENCODE pilot project can contribute to the international effort with expected outcomes in agriculture, biomedical science and the environment.