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Professor Ben Hayes
Professor

Ben Hayes

Email: 
Phone: 
+61 7 334 62173

Overview

Background

Professor Hayes has extensive research experience in genetic improvement of livestock, crop, pasture and aquaculture species, with a focus on integration of genomic information into breeding programs, including leading many large scale projects which have successfully implemented genomic technologies in livestock and cropping industries. Author of more than 300 journal papers, including in Nature Genetics, Nature Reviews Genetics, and Science, contributing to statistical methodology for genomic, microbiome and metagenomic profile predictions, quantitative genetics including knowledge of genetic mechanisms underlying complex traits, and development of bioinformatics pipelines for sequence analysis. Thomson Reuters highly cited researcher in 2015, 2016, 2017 and 2018.

Availability

Professor Ben Hayes is:
Available for supervision

Qualifications

  • Doctor of Philosophy, Central Queensland University

Research impacts

Genomic prediction, of which Ben Hayes was a co-inventor, and first described in the seminal publication [Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157, 1819-1829] is now being used very widely in livestock and crops to predict future trait outcomes. The technology is also being used increasingly in human disease research.

In dairy cattle, the technology has been actively used by the industry for the past five years, and increases in genetic gain for key economic traits can be demonstrated. Nearly every dairy bull worldwide chosen for widespread use in the industry is now selected on the basis of genomic predictions. Dr Hayes has been an invited speaker at numerous high profile conferences, including the Biology of Genomes conference at Cold Spring Harbor May 2015, and also has a number of youtube videos explaining complex trait prediction for a general audience, one of which has been viewed more than 5000 times (https://www.youtube.com/watch?v=RovnCsda-zQ).

Ben Hayes led the program on animal improvement of the Dairy Futures CRC, which concluded June 2016. The animal improvement program in the Dairy Futures CRC is a successful research and utilisation program which has a very high level of industry input and collaboration. The value of the program was recognised recently when it was awarded a Cooperative Research Centres Association (CRCA) Award for Excellence in Innovation. The Dairy Futures CRC under the leadership of Dr. Hayes successfully developed and implemented a genomic breeding value for feed efficiency, which has been widely adopted by the industry.

Dr. Hayes established the 1000 bull genomes project, a consortium of over 30 institutes across the globe, which has assembled whole genome sequences of 1682 cattle of 55 breeds. The consortium has published a widely cited paper in Nature Genetics (Daetwyler et al. 2014), and has already led to more than 50 companion papers.

Works

Search Professor Ben Hayes’s works on UQ eSpace

386 works between 2000 and 2024

341 - 360 of 386 works

2009

Journal Article

An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic ca

MacEachern, Sean, Hayes, Ben, McEwan, John and Goddard, Mike (2009). An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic ca. BMC Genomics, 10 181. doi: 10.1186/1471-2164-10-181

An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic ca

2009

Journal Article

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

Gibbs, Richard A., Taylor, Jeremy F., Van Tassell, Curtis P., Barendse, William, Eversoie, Kallye A., Gill, Clare A., Green, Ronnie D., Hamernik, Debora L., Kappes, Steven M., Lien, Sigbjorn, Matukumalli, Lakshmi K., McEwan, John C., Nazareth, Lynne V., Schnabel, Robert D., Taylor, Jeremy F., Weinstock, George M., Wheeler, David A., Ajmone-Marsan, Paolo, Barendse, William, Boettcher, Paul J., Caetano, Alexandre R., Garcia, Jose Fernando, Hanotte, Olivier, Mariani, Paola, Skow, Loren C., Williams, John L., Caetano, Alexandre R., Diallo, Boubacar, Green, Ronnie D. ... Dodds, Ken G. (2009). Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science, 324 (5926), 528-532. doi: 10.1126/science.1167936

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

2009

Journal Article

Increased accuracy of artificial selection by using the realized relationship matrix. (vol 91, pg 47, 2009)

Hayes, B. J., Visscher, P. M. and Goddard, M. E. (2009). Increased accuracy of artificial selection by using the realized relationship matrix. (vol 91, pg 47, 2009). Genetics Research, 91 (2), 143-143. doi: 10.1017/S0016672309000111

Increased accuracy of artificial selection by using the realized relationship matrix. (vol 91, pg 47, 2009)

2009

Journal Article

A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle

Hayes, B. J., Chamberlain, A. J., Maceachern, S., Savin, K., McPartlan, H., MacLeod, I., Sethuraman, L. and Goddard, M. E. (2009). A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Animal Genetics, 40 (2), 176-184. doi: 10.1111/j.1365-2052.2008.01815.x

A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle

2009

Journal Article

Casein haplotypes and their association with milk production traits in Norwegian Red cattle

Nilsen, Heidi, Olsen, Hanne Gro, Hayes, Ben, Sehested, Erling, Svendsen, Morten, Nome, Torfinn, Meuwissen, Theo and Lien, Sigbjorn (2009). Casein haplotypes and their association with milk production traits in Norwegian Red cattle. Genetics Selection Evolution, 41 (1) 24. doi: 10.1186/1297-9686-41-24

Casein haplotypes and their association with milk production traits in Norwegian Red cattle

2009

Journal Article

Invited review: genomic selection in dairy cattle: progress and challenges

Hayes, B. J., Bowman, P. J., Chamberlain, A. J. and Goddard, M. E. (2009). Invited review: genomic selection in dairy cattle: progress and challenges. Journal of Dairy Science, 92 (2), 433-443. doi: 10.3168/jds.2008-1646

Invited review: genomic selection in dairy cattle: progress and challenges

2009

Journal Article

Increased accuracy of artificial selection by using the realized relationship matrix

Hayes, B. J., Visscher, P. M. and Goddard, M. E. (2009). Increased accuracy of artificial selection by using the realized relationship matrix. Genetics Research, 91 (1), 47-60. doi: 10.1017/S0016672308009981

Increased accuracy of artificial selection by using the realized relationship matrix

2008

Journal Article

Modelling the use of gene expression profiles with selective breeding for improved disease resistance in Atlantic salmon (Salmo salar)

Robinson, Nick and Hayes, Ben (2008). Modelling the use of gene expression profiles with selective breeding for improved disease resistance in Atlantic salmon (Salmo salar). Aquaculture, 285 (1-4), 38-46. doi: 10.1016/j.aquaculture.2008.08.016

Modelling the use of gene expression profiles with selective breeding for improved disease resistance in Atlantic salmon (Salmo salar)

2008

Journal Article

Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling

Baranski, M., Rourke, M., Loughnan, S., Hayes, B., Austin, C. and Robinson, N. (2008). Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling. Animal Genetics, 39 (6), 606-614. doi: 10.1111/j.1365-2052.2008.01773.x

Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling

2008

Journal Article

Predicting unobserved phenotypes for complex traits from whole-genome SNP data

Lee, Sang Hong, van der Werf, Julius H. J., Hayes, Ben J., Goddard, Michael E. and Visscher, Peter M. (2008). Predicting unobserved phenotypes for complex traits from whole-genome SNP data. PLoS Genetics, 4 (10) e1000231, e1000231. doi: 10.1371/journal.pgen.1000231

Predicting unobserved phenotypes for complex traits from whole-genome SNP data

2008

Journal Article

Use of gene expression data for predicting continuous phenotypes for animal production and breeding

Robinson, N., Goddard, M. and Hayes, B. (2008). Use of gene expression data for predicting continuous phenotypes for animal production and breeding. Animal, 2 (10), 1413-1420. doi: 10.1017/S1751731108002632

Use of gene expression data for predicting continuous phenotypes for animal production and breeding

2008

Journal Article

Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle

de Roos, A. P. W., Hayes, B. J., Spelman, R. J. and Goddard, M. E. (2008). Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics, 179 (3), 1503-1512. doi: 10.1534/genetics.107.084301

Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle

2008

Journal Article

A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers

Moen, Thomas, Hayes, Ben, Baranski, Matthew, Berg, Paul R., Kjoglum, Sissel, Koop, Ben F., Davidson, Willie S., Omholt, Stig W. and Lien, Sigbjorn (2008). A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics, 9 223. doi: 10.1186/1471-2164-9-223

A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers

2008

Journal Article

Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence

Nilsen, H., Hayes, B., Berg, P. R., Roseth, A., Sundsaasen, K. K., Nilsen, K. and Lien, S. (2008). Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence. Animal Genetics, 39 (2), 97-104. doi: 10.1111/j.1365-2052.2007.01686.x

Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence

2008

Journal Article

The origin of selection signatures on bovine chromosome 6

Hayes, B. J., Lien, S., Nilsen, H., Olsen, H. G., Berg, P., Maceachern, S., Potter, S. and Meuwissen, T. H. E. (2008). The origin of selection signatures on bovine chromosome 6. Animal Genetics, 39 (2), 105-111. doi: 10.1111/j.1365-2052.2007.01683.x

The origin of selection signatures on bovine chromosome 6

2008

Journal Article

Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection

Moen, Thomas, Hayes, Ben, Nilsen, Frank, Delghandi, Madjid, Fjalestad, Kjersti T., Fevolden, Svein-Erik, Berg, Paul R. and Lien, Sigbjorn (2008). Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection. BMC Genetics, 9 (1) 18. doi: 10.1186/1471-2156-9-18

Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection

2008

Journal Article

Comparison of casein haplotypes between two geographically distant European dairy goat breeds

Finocchiaro, R., Hayes, B. J., Siwek, M., Spelman, R. J., van Kaam, J. B. C. H. M., Adnoy, T. and Portolano, B. (2008). Comparison of casein haplotypes between two geographically distant European dairy goat breeds. Journal of Animal Breeding and Genetics, 125 (1), 68-72. doi: 10.1111/j.1439-0388.2007.00687.x

Comparison of casein haplotypes between two geographically distant European dairy goat breeds

2008

Journal Article

Technical note: prediction of breeding values using marker-derived relationship matrices

Hayes, B. J. and Goddard, M. E. (2008). Technical note: prediction of breeding values using marker-derived relationship matrices. Journal of Animal Science, 86 (9), 2089-2092. doi: 10.2527/jas.2007-0733

Technical note: prediction of breeding values using marker-derived relationship matrices

2007

Journal Article

Genomic selection

Goddard, M. E. and Hayes, B. J. (2007). Genomic selection. Journal of Animal Breeding and Genetics, 124 (6), 323-330. doi: 10.1111/j.1439-0388.2007.00702.x

Genomic selection

2007

Journal Article

Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): comparing survival analysis with analysis on affected/resistant data

Moen, Thomas, Sonesson, Anna K., Hayes, Ben, Lien, Sigbjorn, Munck, Hege and Meuwissen, Theo H. E. (2007). Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): comparing survival analysis with analysis on affected/resistant data. BMC Genetics, 8 (1) 53. doi: 10.1186/1471-2156-8-53

Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): comparing survival analysis with analysis on affected/resistant data

Funding

Current funding

  • 2024 - 2029
    ARC Training Centre in Predictive Breeding for Agricultural Futures
    ARC Industrial Transformation Training Centres
    Open grant
  • 2024 - 2028
    Program 2 - Resistance Sources: Using 'FastStack' to develop effective durable net blotch resistance gene stacks
    Grains Research & Development Corporation
    Open grant
  • 2024 - 2028
    Fast tracking deployment of chickpea heat tolerance
    GRDC - PROC-9176886 - Fast tracking deployment of chickpea heat tolerance to develop chickpea varieties with improved high temperature tolerance
    Open grant
  • 2023 - 2027
    RustHapSelect: Fast-tracking rust resistance haplotypes into high-yielding germplasm (GRDC grant administered by CSIRO)
    CSIRO
    Open grant
  • 2023 - 2027
    Analytics for the Australian Grains Industry (AAGI)
    Grains Research & Development Corporation
    Open grant
  • 2022 - 2025
    Northern Genomics commercialisation scoping study
    Meat & Livestock Australia
    Open grant
  • 2022 - 2027
    Reducing methane emissions and improving profitability in Northern Australian beef
    Meat & Livestock Australia
    Open grant
  • 2022 - 2026
    Scaling Genomic Selection Across the Indian Smallholder Dairy Sector (BMGF grant administered by BAIF Development Research Foundation)
    BAIF Development Research Foundation
    Open grant
  • 2022 - 2027
    Facilitating Innovations for Resilient Livestock Farming Systems (Re-Livestock) (Horizon Europe grant administered by the Spanish National Research Council)
    Spanish National Research Council (Agencia Estatal Consejo Superior de Investigaciones Científicas)
    Open grant
  • 2022 - 2026
    Balancing polled and profit: demonstration of breeding strategies to replace dehorning in a large integrated beef and cattle operation
    A. A. COMPANY PTY. LTD.
    Open grant
  • 2022 - 2026
    On-farm genomics: genomic solutions for Northern beef cattle management and breeding
    Meat & Livestock Australia
    Open grant
  • 2022 - 2026
    Digging deeper to improve yield stability
    ARC Linkage Projects
    Open grant
  • 2022 - 2026
    LESTR Low Emission Saliva Test for Ruminants
    Meat & Livestock Australia
    Open grant
  • 2021 - 2026
    ARC Research Hub for Supercharging Tropical Aquaculture Through Genetic Solutions - externally administered by James Cook University (JCU)
    James Cook University
    Open grant
  • 2021 - 2026
    NB2: Assessing practical interventions to reduce calf wastage and herd mortality in northern systems
    Meat & Livestock Australia
    Open grant

Past funding

  • 2023 - 2024
    Genomic prediction of ratoon yield robustness
    Sugar Research Australia Limited
    Open grant
  • 2022 - 2024
    Development of genomic multi-breed eating quality trait estimates using shared global data (Meat & Livestock Australia project administered by University of New England)
    University of New England
    Open grant
  • 2021 - 2022
    DNA as the ultimate identifier in blockchain traceability systems
    Innovation Connections
    Open grant
  • 2020 - 2024
    Screening of diverse barley germplasm for rapid discovery and utilisation of novel disease resistance in barley using R-HapSelect : A haplotype-based toolkit
    Grains Research & Development Corporation
    Open grant
  • 2020 - 2023
    FY20 Postgraduate Scholarships - Harrison Lamb
    Meat & Livestock Australia
    Open grant
  • 2019 - 2021
    Bull fertility update: historical data, new cohort and advanced genomics (Meat & Livestock Australia grant administered by CSIRO)
    CSIRO
    Open grant
  • 2018 - 2023
    India Dairy Genetic Gain: Array designs for Indian Cattle and Buffalo
    Bill & Melinda Gates Foundation
    Open grant
  • 2018 - 2024
    National Tree Genomics Program - Genomics Toolbox
    Horticulture Innovation Australia Limited
    Open grant
  • 2018 - 2021
    Predicting age of livestock from DNA samples
    Meat & Livestock Australia
    Open grant
  • 2018 - 2023
    National Tree Genomics Program - Phenotype Prediction
    Horticulture Innovation Australia Limited
    Open grant
  • 2018 - 2023
    FastStack - evolutionary computing to stack desirable alleles in wheat
    ARC Linkage Projects
    Open grant
  • 2018 - 2021
    Female Reproduction Phenobank and Validation Herds
    Meat & Livestock Australia
    Open grant
  • 2017 - 2020
    Novel genomic technologies to improve fertility in Northern Beef Cattle
    ARC Linkage Projects
    Open grant
  • 2017 - 2024
    Improving fertility in northern cattle through host and pathogen molecular diagnosis
    Meat & Livestock Australia
    Open grant
  • 2017 - 2023
    Implementing and validating genomic selection in SRA breeding programs to accelerate improvements in yield, commercial cane sugar, and other key traits
    Sugar Research Australia Limited
    Open grant
  • 2017 - 2019
    Genetics R&D: Characterisation of the Brahman Genome
    Meat & Livestock Australia
    Open grant
  • 2017 - 2023
    Improving bovine respiratory disease control through the characterisation of pathogen genomics and host interactions
    Meat & Livestock Australia
    Open grant
  • 2017 - 2018
    Expression of genes and proteins related to meat quality in Bos indicus cattle
    UQ-FAPESP Strategic Research Fund SPRINT
    Open grant
  • 2017 - 2022
    Accelerating genetic gain for productivity and profitability in Northern beef cattle with genomic technologies
    Meat & Livestock Australia
    Open grant
  • 2017 - 2024
    Cattle tick and Buffalo fly host genetics, susceptibility to buffalo fly lesions and biomarkers for resistance
    Meat & Livestock Australia
    Open grant

Supervision

Availability

Professor Ben Hayes is:
Available for supervision

Before you email them, read our advice on how to contact a supervisor.

Supervision history

Current supervision

  • Doctor Philosophy

    Reducing methane emissions and improving profitability in Northern Australian beef

    Principal Advisor

    Other advisors: Dr Kieren McCosker

  • Doctor Philosophy

    Genomic selection for finfish Breeding Programs

    Principal Advisor

    Other advisors: Dr Owen Powell

  • Doctor Philosophy

    AI-accelerated breeding of high-protein mungbean

    Principal Advisor

    Other advisors: Professor Lee Hickey, Dr Eric Dinglasan, Dr Millicent Smith

  • Doctor Philosophy

    New mate allocation strategies to accelerate genetic gain in agricultural species.

    Principal Advisor

    Other advisors: Dr Eric Dinglasan, Dr Elizabeth Ross, Dr Owen Powell

  • Doctor Philosophy

    On farm genomics for selection and management in aquaculture: tank-side genotyping

    Principal Advisor

    Other advisors: Dr Hannah Siddle

  • Doctor Philosophy

    Molecular genetic analysis of rust disease resistance in wheat using cutting-edge technologies

    Principal Advisor

    Other advisors: Professor Lee Hickey, Dr Eric Dinglasan

  • Doctor Philosophy

    Molecular genetic analysis of multi-disease resistance in barley using cutting-edge technologies

    Associate Advisor

    Other advisors: Professor Lee Hickey, Dr Eric Dinglasan

Completed supervision

Media

Enquiries

For media enquiries about Professor Ben Hayes's areas of expertise, story ideas and help finding experts, contact our Media team:

communications@uq.edu.au