Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2021 Oct 27;12(11):1707.
doi: 10.3390/genes12111707.

Decoding the Equine Genome: Lessons from ENCODE

Sichong Peng  1 , Jessica L Petersen  2 , Rebecca R Bellone  1   3 , Ted Kalbfleisch  4 , N B Kingsley  1   3 , Alexa M Barber  2 , Eleonora Cappelletti  5 , Elena Giulotto  5 , Carrie J Finno  1
Affiliations
Review

Decoding the Equine Genome: Lessons from ENCODE

Sichong Peng et al. Genes (Basel). .

Abstract

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.

Keywords: FAANG; epigenetics; functional annotation; gene regulation; health; horse; transcriptome; welfare.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

References

    1. Wade C.M., Giulotto E., Sigurdsson S., Zoli M., Gnerre S., Imsland F., Lear T.L., Adelson D.L., Bailey E., Bellone R.R., et al. Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse. Science. 2009;326:865–867. doi: 10.1126/science.1178158. - DOI - PMC - PubMed
    1. Kalbfleisch T.S., Rice E.S., DePriest M.S., Walenz B.P., Hestand M.S., Vermeesch J.R., O′Connell B.L., Fiddes I.T., Vershinina A.O., Saremi N.F., et al. Improved Reference Genome for the Domestic Horse Increases Assembly Contiguity and Composition. Commun. Biol. 2018;1:197. doi: 10.1038/s42003-018-0199-z. - DOI - PMC - PubMed
    1. Raudsepp T., Finno C.J., Bellone R.R., Petersen J.L. Ten Years of the Horse Reference Genome: Insights into Equine Biology, Domestication and Population Dynamics in the Post-genome Era. Anim. Genet. 2019;50:569–597. doi: 10.1111/age.12857. - DOI - PMC - PubMed
    1. Hack Y.L., Crabtree E.E., Avila F., Sutton R.B., Grahn R., Oh A., Gilger B., Bellone R.R. Whole-genome Sequencing Identifies Missense Mutation in GRM6 as the Likely Cause of Congenital Stationary Night Blindness in a Tennessee Walking Horse. Equine Vet. J. 2021;53:316–323. doi: 10.1111/evj.13318. - DOI - PubMed
    1. Rivas V.N., Magdesian K.G., Fagan S., Slovis N.M., Luethy D., Javsicas L.H., Caserto B.G., Miller A.D., Dahlgren A.R., Peterson J., et al. A Nonsense Variant in Rap Guanine Nucleotide Exchange Factor 5 (RAPGEF5) Is Associated with Equine Familial Isolated Hypoparathyroidism in Thoroughbred Foals. PLoS Genet. 2020;16:e1009028. doi: 10.1371/journal.pgen.1009028. - DOI - PMC - PubMed

Publication types