Skip to menu Skip to content Skip to footer
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

385 works between 2000 and 2024

61 - 80 of 385 works

2021

Conference Publication

PHENOBANK: A platform to facilitate collaboration and genomic selection for female fertility in beef cattle

Wockner, K. B., Tahir, M. S., Kour, J., Tan, W. L. A., Olasege, B. S., Porto-Neto, L. R., Little, B. A., Wilson, C. R., Dollemore, W., Reverter, A., Hayes, B. and Fortes, M. R. S. (2021). PHENOBANK: A platform to facilitate collaboration and genomic selection for female fertility in beef cattle. Association for the Advancement of Animal Breeding and Genetics, Adelaide, SA, Australia, 2 - 4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.

PHENOBANK: A platform to facilitate collaboration and genomic selection for female fertility in beef cattle

2021

Journal Article

Challenges and opportunities in applying genomic selection to ruminants owned by smallholder farmers

Burrow, Heather M., Mrode, Raphael, Mwai, Ally Okeyo, Coffey, Mike P. and Hayes, Ben J. (2021). Challenges and opportunities in applying genomic selection to ruminants owned by smallholder farmers. Agriculture, 11 (11) 1172, 1172. doi: 10.3390/AGRICULTURE11111172

Challenges and opportunities in applying genomic selection to ruminants owned by smallholder farmers

2021

Journal Article

A linkage disequilibrium-based approach to position unmapped SNPs in crop species

Yadav, Seema, Ross, Elizabeth M., Aitken, Karen S., Hickey, Lee T., Powell, Owen, Wei, Xianming, Voss-Fels, Kai P. and Hayes, Ben J. (2021). A linkage disequilibrium-based approach to position unmapped SNPs in crop species. BMC Genomics, 22 (1) 773, 1-9. doi: 10.1186/s12864-021-08116-w

A linkage disequilibrium-based approach to position unmapped SNPs in crop species

2021

Book Chapter

Cattle genomics

Hayes, B. J. and Cocks, B. (2021). Cattle genomics. Encyclopedia of dairy sciences. (pp. 620-625) edited by John W. Fuquay. Amsterdam, Netherlands: Elsevier. doi: 10.1016/B978-0-12-818766-1.00338-X

Cattle genomics

2021

Journal Article

Genomic diversity and breed composition of Vietnamese smallholder dairy cows

Bang, Nguyen N., Hayes, Ben J., Lyons, Russell E., Randhawa, Imtiaz A. S., Gaughan, John B. and McNeill, David M. (2021). Genomic diversity and breed composition of Vietnamese smallholder dairy cows. Journal of Animal Breeding and Genetics, 139 (2), 1-16. doi: 10.1111/jbg.12651

Genomic diversity and breed composition of Vietnamese smallholder dairy cows

2021

Journal Article

Prowler: a novel trimming algorithm for Oxford Nanopore sequence data

Lee, Simon, Nguyen, Loan T., Hayes, Ben J. and Ross, Elizabeth (2021). Prowler: a novel trimming algorithm for Oxford Nanopore sequence data. Bioinformatics, 37 (21), 3936-3937. doi: 10.1093/bioinformatics/btab630

Prowler: a novel trimming algorithm for Oxford Nanopore sequence data

2021

Journal Article

Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle

Olasege, Babatunde S., Tahir, Muhammad S., Gouveia, Gabriela C., Kour, Jagish, Porto-Neto, Laercio R., Hayes, Ben J. and Fortes, Marina R. S. (2021). Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle. Animal Production Science, 61 (18), 1863-1872. doi: 10.1071/an21097

Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle

2021

Conference Publication

Genome-wide analysis of transcription start sites across Bos indicus tissues

Forutan, Mehrnush, Ross, Elizabeth, Nguyen, Loan and Hayes, Ben (2021). Genome-wide analysis of transcription start sites across Bos indicus tissues. 38th International Conference on Animal Genetics, Online, 26 - 30 July 2021.

Genome-wide analysis of transcription start sites across Bos indicus tissues

2021

Conference Publication

Genomic prediction using low-coverage Nanopore sequencing

Lamb, Harrison, Nguyen, Loan T., Hayes, Ben J., Randhawa, Imtiaz A. S. and Ross, Elizabeth M. (2021). Genomic prediction using low-coverage Nanopore sequencing. 38th International Society of Animal Genetics, Virtual, 26 - 30 July 2021.

Genomic prediction using low-coverage Nanopore sequencing

2021

Conference Publication

A Bos indicus epigenetic clock predicts age from tail hair

Nguyen, Loan T., Forutan, Mehrnush, Hayes, Ben J. and Ross, Elizabeth M. (2021). A Bos indicus epigenetic clock predicts age from tail hair. 38th International Society of Animal Genetics (ISAG), Virtual, 26 - 30 July 2021.

A Bos indicus epigenetic clock predicts age from tail hair

2021

Conference Publication

The genetic complexity of scurs development in cattle

Randhawa, Imtiaz A. S., Lyons, Russell E., Hayes, Ben J. and McGowan, Michael R. (2021). The genetic complexity of scurs development in cattle. 38th International Society of Animal Genetics (ISAG), Virtual, 26-30 July 2021.

The genetic complexity of scurs development in cattle

2021

Journal Article

Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus

Forutan, Mehrnush, Ross, Elizabeth, Chamberlain, Amanda J., Nguyen, Loan, Mason, Brett, Moore, Stephen, Garner, Josie B., Xiang, Ruidong and Hayes, Ben J. (2021). Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus. Communications Biology, 4 (1) 829, 1-14. doi: 10.1038/s42003-021-02340-6

Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus

2021

Journal Article

Multiple country and breed genomic prediction of tick resistance in beef cattle

Cardoso, Fernando Flores, Matika, Oswald, Djikeng, Appolinaire, Mapholi, Ntanganedzeni, Burrow, Heather M., Yokoo, Marcos Jun Iti, Campos, Gabriel Soares, Gulias-Gomes, Claudia Cristina, Riggio, Valentina, Pong-Wong, Ricardo, Engle, Bailey, Porto-Neto, Laercio, Maiwashe, Azwihangwisi and Hayes, Ben J. (2021). Multiple country and breed genomic prediction of tick resistance in beef cattle. Frontiers in Immunology, 12 620847, 1-11. doi: 10.3389/fimmu.2021.620847

Multiple country and breed genomic prediction of tick resistance in beef cattle

2021

Journal Article

Interrogating the bovine reproductive tract metagenomes using culture-independent approaches: a systematic review

Ong, Chian Teng, Turni, Conny, Blackall, Patrick J., Boe-Hansen, Gry, Hayes, Ben J. and Tabor, Ala E. (2021). Interrogating the bovine reproductive tract metagenomes using culture-independent approaches: a systematic review. Animal Microbiome, 3 (1) 41, 41. doi: 10.1186/s42523-021-00106-3

Interrogating the bovine reproductive tract metagenomes using culture-independent approaches: a systematic review

2021

Journal Article

Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population

O’Connor, Katie M., Hayes, Ben J., Hardner, Craig M., Alam, Mobashwer, Henry, Robert J. and Topp, Bruce L. (2021). Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population. BMC Genomics, 22 (1) 370, 1-12. doi: 10.1186/s12864-021-07694-z

Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population

2021

Journal Article

Analysis of polycerate mutants reveals the evolutionary co-option of HOXD1 for horn patterning in Bovidae

Allais-Bonnet, Aurélie, Hintermann, Aurélie, Deloche, Marie-Christine, Cornette, Raphaël, Bardou, Philippe, Naval-Sanchez, Marina, Pinton, Alain, Haruda, Ashleigh, Grohs, Cécile, Zakany, Jozsef, Bigi, Daniele, Medugorac, Ivica, Putelat, Olivier, Greyvenstein, Ockert, Hadfield, Tracy, Jemaa, Slim Ben, Bunevski, Gjoko, Menzi, Fiona, Hirter, Nathalie, Paris, Julia M., Hedges, John, Palhiere, Isabelle, Rupp, Rachel, Lenstra, Johannes A., Gidney, Louisa, Lesur, Joséphine, Schafberg, Renate, Stache, Michael, Wandhammer, Marie-Dominique ... Capitan, Aurélien (2021). Analysis of polycerate mutants reveals the evolutionary co-option of HOXD1 for horn patterning in Bovidae. Molecular Biology and Evolution, 38 (6), 2260-2272. doi: 10.1093/molbev/msab021

Analysis of polycerate mutants reveals the evolutionary co-option of HOXD1 for horn patterning in Bovidae

2021

Journal Article

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

Trigo, Beatriz B., Utsunomiya, Adam T. H., Fortunato, Alvaro A. A. D., Milanesi, Marco, Torrecilha, Rafaela B. P., Lamb, Harrison, Nguyen, Loan, Ross, Elizabeth M., Hayes, Ben, Padula, Romulo C. M., Sussai, Thayla S., Zavarez, Ludmilla B., Cipriano, Rafael S., Caminhas, Maria M. T., Lopes, Flavia L., Pelle, Cassiano, Leeb, Tosso, Bannasch, Danika, Bickhart, Derek, Smith, Timothy P. L., Sonstegard, Tad S., Garcia, Jose F. and Utsunomiya, Yuri T. (2021). Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genetics Selection Evolution, 53 (1) 40, 40. doi: 10.1186/s12711-021-00633-2

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

2021

Journal Article

Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects

Yadav, Seema, Wei, Xianming, Joyce, Priya, Atkin, Felicity, Deomano, Emily, Sun, Yue, Nguyen, Loan T., Ross, Elizabeth M., Cavallaro, Tony, Aitken, Karen S., Hayes, Ben J. and Voss-Fels, Kai P. (2021). Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects. Theoretical and Applied Genetics, 134 (7), 2235-2252. doi: 10.1007/s00122-021-03822-1

Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects

2021

Journal Article

Comparison of genetic merit for weight and meat traits between the polled and horned cattle in multiple beef breeds

Randhawa, Imtiaz A. S., McGowan, Michael R., Porto-Neto, Laercio R., Hayes, Ben J. and Lyons, Russell E. (2021). Comparison of genetic merit for weight and meat traits between the polled and horned cattle in multiple beef breeds. Animals, 11 (3) 870, 1-21. doi: 10.3390/ani11030870

Comparison of genetic merit for weight and meat traits between the polled and horned cattle in multiple beef breeds

2021

Journal Article

Imputation accuracy to whole-genome sequence in Nellore cattle

Fernandes Junior, Gerardo A., Carvalheiro, Roberto, de Oliveira, Henrique N., Sargolzaei, Mehdi, Costilla, Roy, Ventura, Ricardo V., Fonseca, Larissa F. S., Neves, Haroldo H. R., Hayes, Ben J. and de Albuquerque, Lucia G. (2021). Imputation accuracy to whole-genome sequence in Nellore cattle. Genetics Selection Evolution, 53 (1) 27. doi: 10.1186/s12711-021-00622-5

Imputation accuracy to whole-genome sequence in Nellore cattle

Funding

Current funding

  • 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

  • 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