Scientists are creating an equine genetic map like no other, providing unprecedented insights into the way horses function.
Researchers, writing in the journal Genes, have provided an update on progress with the equine Functional Annotation of Animal Genome (FAANG) initiative.
The study team, in their review, said 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,” they said.
Looking to fill these knowledge gaps, the researchers were inspired by the phenomenal success of the Encyclopedia of DNA Elements (ENCODE) project in humans.
ENCODE was proposed in 2003 as an ambitious effort to identify all functional elements in the human genome sequence.
By 2017, ENCODE had concluded its third phase, delivering an integrated set of DNA transcription, regulation, and epigenetic modifications from a total of 7495 experiments in more than 500 cell types and tissues.
The project has improved the understanding of gene regulation and delivered a wide range of computational tools, as well as a rich deposit of well-documented, publicly available experimental datasets.
An international group of researchers proposed a similar, coordinated effort to systematically annotate a range of animal genomes — the FAANG project.
As part of the FAANG initiative, the equine FAANG group has been actively working with the larger FAANG community and ENCODE researchers to lead the annotation efforts for the horse genome.
Since launching three years ago, the equine FAANG group has generated data from more than 400 experiments using more than 50 tissues, targeting a variety of regulatory features of the equine genome.
The experimental results are being made publicly available as they are generated and evaluated for quality control. They have, and continue to be used, in unrelated research projects.
The review team said more than 80 tissues collected from four healthy and comprehensively phenotyped horses are being used in the FAANG initiative.
“We will be able to generate a map of gene expression and regulation throughout the horse body, providing unique opportunities to investigate tissue-specific gene expression and gene networks.”
The authors noted that while the equine FAANG biobank represents a wide variety of tissue types, the four horses from which these tissues were collected represent only a narrow subset of the horse population, as well as developmental stages.
“These horses were intentionally selected to be of the same breed as the reference genome assembly in order to better annotate the reference genome assembly.
“However, caution should be taken with interpretation and extrapolation of these data to other breeds or developmental stages,” they said.
“Regardless, this initiative will serve as a template and reference point for the future expansion of the transcriptome and epigenome of equids.”
The researchers said FAANG represents a notable international collaborative effort in the equine community that has brought together equine researchers and practitioners from around the globe.
“Most importantly,” they continued, “FAANG collaborators have been vocal proponents of open science and broad data accessibility within the equine community.
“The growing number of publicly available datasets is accelerating discoveries and powering large-scale analyses.
“Well-annotated and carefully documented FAANG data with accompanying comprehensive metadata will serve as a reference point for many future discoveries in the horse.”
The review team comprised Sichong Peng, Rebecca Bellone, N.B. Kingsley and Carrie Finno, all with the School of Veterinary Medicine at the University of California-Davis; Jessica Petersen and Alexa Barber, with the Department of Animal Science at the University of Nebraska; Ted Kalbfleisch, with the Gluck Equine Research Center at the University of Kentucky; and Eleonora Cappelletti and Elena Giulotto, with the Department of Biology and Biotechnology “L. Spallanzani”, with the University of Pavia in Italy.
Peng, S.; Petersen, J.L.; Bellone, R.R.; Kalbfleisch, T.; Kingsley, N.B.; Barber, A.M.; Cappelletti, E.; Giulotto, E.; Finno, C.J. Decoding the Equine Genome: Lessons from ENCODE. Genes 2021, 12, 1707. https://doi.org/10.3390/genes12111707