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Genes2021; 12(11); doi: 10.3390/genes12111707

Decoding the Equine Genome: Lessons from ENCODE.

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.
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Publication Date: 2021-10-27 PubMed ID: 34828313PubMed Central: PMC8625040DOI: 10.3390/genes12111707Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't
  • Review

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research study explores the efforts to address gaps in knowledge about the function of the horse genome, aiming to deepen understanding of complex traits in horses. The equine Functional Annotation of Animal Genome (FAANG) initiative attempts to connect genome and gene expression, using the Encyclopedia of DNA Elements (ENCODE) project as an inspiration.

Equine Genome Studies

For years, the equine genomics field has significantly advanced largely due to the reference genome assemblies, EquCab2.0 and EquCab3.0. These tools have facilitated:

  • Creation of new tools specifically designed for studying horse genetics.
  • The discovery of novel genetic characteristics within horses.

Despite these advancements, substantial gaps remain in the understanding of the functional aspects of the horse genome. This lack of knowledge prevents comprehensive study of complex traits within horses.

FAANG Initiative

In response to the limited understanding of genome function, the equine Functional Annotation of Animal Genome (FAANG) initiative was created. This project’s goal is to bridge the gap between basic genetic information (the genome) and the expression of those genes within organism tissues. The initiative draws inspiration from the Encyclopedia of DNA Elements (ENCODE) project, applying its principles to expand on equine genetics.

Data Generation and Current State

Three years into the FAANG initiative, the project has yielded plenty of data. The project’s scope is considerable, with:

  • Data from more than 400 experiments conducted using over 50 tissues.
  • A focused study of several regulatory features of the equine genome.

The authors review how lessons learned from the ENCODE project have guided the FAANG project’s approach and decision-making processes.

The Significance of FAANG for Future Research

The researchers discuss the potential of the FAANG initiative as a blueprint for future expansion of functional annotation (the process of identifying the functions of genes and determining the roles they play in an organism’s biology) in horse genetics. This research could provide a reference point for future studies of complex traits in horses. A fully annotated reference “Functional Atlas” of the horse genome will likely prove instrumental in pushing forward equine genetics research.

Cite This Article

APA
Peng S, Petersen JL, Bellone RR, Kalbfleisch T, Kingsley NB, Barber AM, Cappelletti E, Giulotto E, Finno CJ. (2021). Decoding the Equine Genome: Lessons from ENCODE. Genes (Basel), 12(11). https://doi.org/10.3390/genes12111707

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 12
Issue: 11

Researcher Affiliations

Peng, Sichong
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USA.
Bellone, Rebecca R
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
Kalbfleisch, Ted
  • Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40503, USA.
Kingsley, N B
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
Barber, Alexa M
  • Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USA.
Cappelletti, Eleonora
  • Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.
Giulotto, Elena
  • Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.
Finno, Carrie J
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.

MeSH Terms

  • Animals
  • Gene Expression Profiling / veterinary
  • Genome
  • Genomics / methods
  • Horses / genetics
  • Molecular Sequence Annotation

Conflict of Interest Statement

The authors declare no conflict of interest.

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