Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits

Ruidong Xiang, Irene Van Den Berg, Iona M. MacLeod, Benjamin J. Hayes, Claire P. Prowse-Wilkins, Min Wang, Sunduimijid Bolormaa, Zhiqian Liu, Simone J. Rochfort, Coralie M. Reich, Brett A. Mason, Christy J. Vander Jagt, Hans D. Daetwyler, Mogens S. Lund, Amanda J. Chamberlain, Michael E. Goddard
doi: https://doi.org/10.1101/601658
Ruidong Xiang
1Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville 3052, Victoria, Australia
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: ruidong.xiang@unimelb.edu.au
Irene Van Den Berg
1Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville 3052, Victoria, Australia
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Iona M. MacLeod
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Benjamin J. Hayes
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
3Centre for Animal Science, The University of Queensland, St Lucia 4067, Queensland, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Claire P. Prowse-Wilkins
1Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville 3052, Victoria, Australia
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Min Wang
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
4School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sunduimijid Bolormaa
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Zhiqian Liu
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Simone J. Rochfort
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
4School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Coralie M. Reich
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Brett A. Mason
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christy J. Vander Jagt
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hans D. Daetwyler
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
4School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mogens S. Lund
5Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, PO Box 50, DK-8830 Tjele, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Amanda J. Chamberlain
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michael E. Goddard
1Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville 3052, Victoria, Australia
2Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria 3083, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Many genome variants shaping mammalian phenotype are hypothesized to regulate gene transcription and/or to be under selection. However, most of the evidence to support this hypothesis comes from human studies. Systematic evidence for regulatory and evolutionary signals contributing to complex traits in a different mammalian model is needed. Sequence variants associated with gene expression (eQTLs) and concentration of metabolites (mQTLs), and under histone modification marks in several tissues were discovered from multi-omics data of over 400 cattle. Variants under selection and evolutionary constraint were identified using genome databases of multiple species. These analyses defined 30 sets of variants and for each set we estimated the genetic variance the set explained across 34 complex traits in 11,923 bulls and 32,347 cows with 17,669,372 imputed variants. The per-variant trait heritability of these sets across traits was highly consistent (r>0.94) between bulls and cows. Based on the per-variant heritability, conserved sites across 100 vertebrate species and mQTLs ranked the highest, followed by eQTLs, young variants, those under histone modification marks and selection signatures. From these results, we defined a Functional-And-Evolutionary Trait Heritability (FAETH) score indicating the functionality and predicted heritability of each variant. In 7,551 Danish cattle, the high FAETH-ranking variants had significantly increased genetic variances and genomic prediction accuracies in 3 production traits compared to the low FAETH-ranking variants. The FAETH framework combines the information of gene regulation, evolution and trait heritability to rank variants and the publicly available FAETH data provides a set of biological priors for cattle genomic selection worldwide.

Footnotes

  • The genome sites under evolutionary constraint was further analysed with 100 vertebrate species and they showed strong enrichment of heritability. The FAETH score has been updated, including detailed annotation categories of each sequence variant The robustness of FAETH score is further validated with more traits and cattle breeds, including beef breeds.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted July 09, 2019.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits
Ruidong Xiang, Irene Van Den Berg, Iona M. MacLeod, Benjamin J. Hayes, Claire P. Prowse-Wilkins, Min Wang, Sunduimijid Bolormaa, Zhiqian Liu, Simone J. Rochfort, Coralie M. Reich, Brett A. Mason, Christy J. Vander Jagt, Hans D. Daetwyler, Mogens S. Lund, Amanda J. Chamberlain, Michael E. Goddard
bioRxiv 601658; doi: https://doi.org/10.1101/601658
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits
Ruidong Xiang, Irene Van Den Berg, Iona M. MacLeod, Benjamin J. Hayes, Claire P. Prowse-Wilkins, Min Wang, Sunduimijid Bolormaa, Zhiqian Liu, Simone J. Rochfort, Coralie M. Reich, Brett A. Mason, Christy J. Vander Jagt, Hans D. Daetwyler, Mogens S. Lund, Amanda J. Chamberlain, Michael E. Goddard
bioRxiv 601658; doi: https://doi.org/10.1101/601658

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4682)
  • Biochemistry (10360)
  • Bioengineering (7672)
  • Bioinformatics (26335)
  • Biophysics (13526)
  • Cancer Biology (10686)
  • Cell Biology (15438)
  • Clinical Trials (138)
  • Developmental Biology (8497)
  • Ecology (12821)
  • Epidemiology (2067)
  • Evolutionary Biology (16857)
  • Genetics (11399)
  • Genomics (15478)
  • Immunology (10617)
  • Microbiology (25216)
  • Molecular Biology (10222)
  • Neuroscience (54466)
  • Paleontology (401)
  • Pathology (1668)
  • Pharmacology and Toxicology (2897)
  • Physiology (4342)
  • Plant Biology (9247)
  • Scientific Communication and Education (1586)
  • Synthetic Biology (2558)
  • Systems Biology (6781)
  • Zoology (1466)