Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research

Authors: KERN, COLIN - University Of California, Davis; YING, WANG - University Of California, Davis; XU, XIAOQIN - University Of California, Davis; PAN, ZHANGYUAN - University Of California, Davis; HALSTEAD, MICHELLE - University Of California, Davis; CHANTHAVIXAY, GANREA - University Of California; SAELAO, PEROT - University Of California, Davis; WATERS, SUSAN - University Of California, Davis; XIANG, RUIDONG - Agriculture Victoria; CHAMBERLAIN, AMANDA - Agriculture Victoria; KORF, IAN - University Of California, Davis; DELANY, MARY - University Of California, Davis; Cheng, Hans; MEDRANO, JUAN - University Of California, Davis; VAN EENENNAAM, ALISON - University Of California, Davis; TUGGLE, CHRIS - Iowa State University; ERNST, CATHERINE - Michigan State University; FLICEK, PAUL - European Bioinformatics Institute; QUON, GERALD - University Of California, Davis; ROSS, PABLO - University Of California, Davis; ZHOU, HUAIJUN - University Of California, Davis

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2021
Publication Date: 3/23/2021
Citation: Kern, C., Ying, W., Xu, X., Pan, Z., Halstead, M., Chanthavixay, G., Saelao, P., Waters, S., Xiang, R., Chamberlain, A., Korf, I., Delany, M.E., Cheng, H.H., Medrano, J.F., Van Eenennaam, A.L., Tuggle, C.K., Ernst, C., Flicek, P., Quon, G., Ross, P., Zhou, H. 2021. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nature Communications. 12:1821. https://doi.org/10.1038/s41467-021-22100-8.
DOI: https://doi.org/10.1038/s41467-021-22100-8

Interpretive Summary: Connecting genotype to phenotype has been a major goal for animal genetics. Despite complete genome assemblies for many species including all farm animals, it has become clear that much of the driving force for variation in observed traits is genetic variation for regulatory elements that determine when and where a gene is expressed. This submission is the first comprehensive catalog of regulatory elements for farm animals, which greatly aids the identification of causative genetic variation for complex traits such as growth, reproduction, disease resistance, etc. This resource greatly aids commercial breeders to select for superior animals as well as providing fundamental knowledge for academic scientists.

Technical Abstract: Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.