The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era.

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Published in Genes, v. 12, issue 11, 1707.

© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Portions of this work were supported by Animal Breeding and Functional Annotation of Genomes (A1201) Grant 2019-67015-29340/Project Accession 1018854 from the USDA National Institute of Food and Agriculture, the Grayson Jockey Club Foundation, USDA NRSP-8 and the UC Davis Center for Equine Health, Italian Ministry of Education, University and Research (MIUR) [Dipartimenti di Eccellenza Program (2018–2022)—Dept. of Biology and Biotechnology “L. Spallanzani”, University of Pavia]. Support for C.J.F was provided by the National Institutes of Health (NIH) (L40 TR001136).

Related Content

All FAANG data discussed in this manuscript can be accessed from Sequence Read Archive (SRA), European Nucleotide Archive (ENA), or faang.org/dataset using accession numbers listed in Table 1.