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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

385 works between 2000 and 2024

1 - 20 of 385 works

2024

Journal Article

Expression network analysis of bovine skin infested with Rhipicephalus australis identifies pro-inflammatory genes contributing to tick susceptibility

Mantilla Valdivieso, Emily F., Ross, Elizabeth M., Raza, Ali, Nguyen, Loan, Hayes, Ben J., Jonsson, Nicholas N., James, Peter and Tabor, Ala E. (2024). Expression network analysis of bovine skin infested with Rhipicephalus australis identifies pro-inflammatory genes contributing to tick susceptibility. Scientific Reports, 14 (1) 4419, 1-14. doi: 10.1038/s41598-024-54577-w

Expression network analysis of bovine skin infested with Rhipicephalus australis identifies pro-inflammatory genes contributing to tick susceptibility

2024

Journal Article

Genome-wide atlas of rust resistance loci in wheat

Tong, Jingyang, Zhao, Cong, Liu, Dan, Jambuthenne, Dilani T., Sun, Mengjing, Dinglasan, Eric, Periyannan, Sambasivam K., Hickey, Lee T. and Hayes, Ben J. (2024). Genome-wide atlas of rust resistance loci in wheat. Theoretical and Applied Genetics, 137 (8) 179, 179. doi: 10.1007/s00122-024-04689-8

Genome-wide atlas of rust resistance loci in wheat

2024

Journal Article

Dissecting loci that underpin the genetic correlations between production, fertility, and urea traits in Australian Holstein cattle

Olasege, Babatunde S., van den Berg, Irene, Haile‐Mariam, Mekonnen, Ho, Phuong N., Yin Oh, Zhen, Porto‐Neto, Laercio R., Hayes, Ben J., Pryce, Jennie E. and Fortes, Marina R. S. (2024). Dissecting loci that underpin the genetic correlations between production, fertility, and urea traits in Australian Holstein cattle. Animal Genetics, 55 (4), 540-558. doi: 10.1111/age.13455

Dissecting loci that underpin the genetic correlations between production, fertility, and urea traits in Australian Holstein cattle

2024

Journal Article

Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility

Forutan, Mehrnush, Engle, Bailey N., Chamberlain, Amanda J., Ross, Elizabeth M., Nguyen, Loan T., D’Occhio, Michael J., Snr, Alf Collins, Kho, Elise A., Fordyce, Geoffry, Speight, Shannon, Goddard, Michael E. and Hayes, Ben J. (2024). Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility. Communications Biology, 7 (1) 724, 724. doi: 10.1038/s42003-024-06403-2

Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility

2024

Journal Article

Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain

Villiers, Kira, Voss‐Fels, Kai P., Dinglasan, Eric, Jacobs, Bertus, Hickey, Lee and Hayes, Ben J. (2024). Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain. The Plant Genome, 17 (2) e20467, e20467. doi: 10.1002/tpg2.20467

Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain

2024

Journal Article

Genetic influence on within-person longitudinal change in anthropometric traits in the UK Biobank

Kemper, Kathryn E., Sidorenko, Julia, Wang, Huanwei, Hayes, Ben J., Wray, Naomi R., Yengo, Loic, Keller, Matthew C., Goddard, Michael and Visscher, Peter M. (2024). Genetic influence on within-person longitudinal change in anthropometric traits in the UK Biobank. Nature Communications, 15 (1) 3776, 3776. doi: 10.1038/s41467-024-47802-7

Genetic influence on within-person longitudinal change in anthropometric traits in the UK Biobank

2024

Journal Article

Epidemiological Risk Factors and Modelling Approaches for Risk Assessment of Lumpy Skin Disease Virus Introduction and Spread: Methodological Review and Implications for Risk-Based Surveillance in Australia

Owada, Kei, Mahony, Timothy J., Ambrose, Rebecca K., Hayes, Ben J. and Soares Magalhães, Ricardo J. (2024). Epidemiological Risk Factors and Modelling Approaches for Risk Assessment of Lumpy Skin Disease Virus Introduction and Spread: Methodological Review and Implications for Risk-Based Surveillance in Australia. Transboundary and Emerging Diseases, 2024 ARTN 3090226, 1-16. doi: 10.1155/2024/3090226

Epidemiological Risk Factors and Modelling Approaches for Risk Assessment of Lumpy Skin Disease Virus Introduction and Spread: Methodological Review and Implications for Risk-Based Surveillance in Australia

2024

Journal Article

Genomic prediction for sugarcane diseases including hybrid Bayesian-machine learning approaches

Chen, Chensong, Bhuiyan, Shamsul A., Ross, Elizabeth, Powell, Owen, Dinglasan, Eric, Wei, Xianming, Atkin, Felicity, Deomano, Emily and Hayes, Ben (2024). Genomic prediction for sugarcane diseases including hybrid Bayesian-machine learning approaches. Frontiers in Plant Science, 15 1398903. doi: 10.3389/fpls.2024.1398903

Genomic prediction for sugarcane diseases including hybrid Bayesian-machine learning approaches

2024

Journal Article

Short Communication: Genomic estimated breeding values for bovine respiratory disease resistance in Angus feedlot cattle

Hayes, B J, Duff, C J, Hine, B C and Mahony, T J (2024). Short Communication: Genomic estimated breeding values for bovine respiratory disease resistance in Angus feedlot cattle. Journal of Animal Science, 102 skae113. doi: 10.1093/jas/skae113

Short Communication: Genomic estimated breeding values for bovine respiratory disease resistance in Angus feedlot cattle

2024

Journal Article

Pleomorphic adenoma gene (<i>PLAG1</i>) in reproduction and implication for embryonic survival in cattle: A review

D’Occhio, Michael J, Campanile, Giuseppe, Baruselli, Pietro S, Porto Neto, Laercio R, Hayes, Ben J, Collins, Alf and Fortes, Marina R S (2024). Pleomorphic adenoma gene (PLAG1) in reproduction and implication for embryonic survival in cattle: A review. Journal of Animal Science, 102 ARTN skae103. doi: 10.1093/jas/skae103

Pleomorphic adenoma gene (<i>PLAG1</i>) in reproduction and implication for embryonic survival in cattle: A review

2024

Journal Article

Genomic regions and biological pathways associated with sex-limited reproductive traits in bovine species

Olasege, Babatunde S, Oh, Zhen Yin, Tahir, Muhammad S, Porto-Neto, Laercio R, Hayes, Ben J and Fortes, Marina R S (2024). Genomic regions and biological pathways associated with sex-limited reproductive traits in bovine species. Journal of Animal Science, 102 ARTN skae085. doi: 10.1093/jas/skae085

Genomic regions and biological pathways associated with sex-limited reproductive traits in bovine species

2023

Journal Article

Imputation strategies for genomic prediction using nanopore sequencing

Lamb, H. J., Nguyen, L. T., Copley, J. P., Engle, B. N., Hayes, B. J. and Ross, E. M. (2023). Imputation strategies for genomic prediction using nanopore sequencing. BMC Biology, 21 (1) 286, 1-18. doi: 10.1186/s12915-023-01782-0

Imputation strategies for genomic prediction using nanopore sequencing

2023

Journal Article

Use of continuous genotypes for genomic prediction in sugarcane

Yadav, Seema, Ross, Elizabeth M., Wei, Xianming, Liu, Shouye, Nguyen, Loan To, Powell, Owen, Hickey, Lee T., Deomano, Emily, Atkin, Felicity, Voss‐Fels, Kai P. and Hayes, Ben J. (2023). Use of continuous genotypes for genomic prediction in sugarcane. The Plant Genome, 17 (1) e20417, e20417. doi: 10.1002/tpg2.20417

Use of continuous genotypes for genomic prediction in sugarcane

2023

Journal Article

Developing flexible models for genetic evaluations in smallholder crossbred dairy farms

Costilla, R., Zeng, J., Al Kalaldeh, M., Swaminathan, M., Gibson, J.P., Ducrocq, V. and Hayes, B.J. (2023). Developing flexible models for genetic evaluations in smallholder crossbred dairy farms. Journal of Dairy Science, 106 (12), 9125-9135. doi: 10.3168/jds.2022-23135

Developing flexible models for genetic evaluations in smallholder crossbred dairy farms

2023

Journal Article

Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategies

Yadav, Seema, Ross, Elizabeth M., Wei, Xianming, Powell, Owen, Hivert, Valentin, Hickey, Lee T., Atkin, Felicity, Deomano, Emily, Aitken, Karen S., Voss-Fels, Kai P. and Hayes, Ben J. (2023). Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategies. Frontiers in Plant Science, 14 1260517, 1260517. doi: 10.3389/fpls.2023.1260517

Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategies

2023

Conference Publication

Using Digital Twin Simulations to Optimize Genetic Selection in an Admixed Beef Herd

Engle, Bailey N., Moser, Gerhard, Villiers, Kira, Suarez, Mathias, Grey, Eliza, Hayes, Ben J. and Kelly, Matthew (2023). Using Digital Twin Simulations to Optimize Genetic Selection in an Admixed Beef Herd. 2023 ASAS-CSAS Annual Meeting, Albuquerque, NM United States, 16-20 July 2023. Champaign, IL United States: American Society of Animal Science. doi: 10.1093/jas/skad281.042

Using Digital Twin Simulations to Optimize Genetic Selection in an Admixed Beef Herd

2023

Journal Article

Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available

Hayes, Ben J., Copley, James, Dodd, Elsie, Ross, Elizabeth M., Speight, Shannon and Fordyce, Geoffry (2023). Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available. Genetics Selection Evolution, 55 (1) 71, 1-13. doi: 10.1186/s12711-023-00847-6

Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available

2023

Journal Article

Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations

Warburton, Christie L., Costilla, Roy, Engle, Bailey N., Moore, Stephen S., Corbet, Nicholas J., Fordyce, Geoffry, McGowan, Michael R., Burns, Brian M. and Hayes, Ben J. (2023). Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations. Heredity, 131 (5-6), 350-360. doi: 10.1038/s41437-023-00651-4

Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations

2023

Journal Article

Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits

Chen, Chensong, Powell, Owen, Dinglasan, Eric, Ross, Elizabeth M., Yadav, Seema, Wei, Xianming, Atkin, Felicity, Deomano, Emily and Hayes, Ben J. (2023). Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits. The Plant Genome, 16 (4) e20390, 1-13. doi: 10.1002/tpg2.20390

Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits

2023

Conference Publication

New diagnostic tools for bovine vibriosis

Tabor, Ala, Siddle, Hannah, Juli, Sogra Banu, Raza, Ali, Ong, Chian Teng, McCosker, Kieren, Hayes, Ben and Boe-Hansen, Gry (2023). New diagnostic tools for bovine vibriosis. Northern Beef Research Update Conference, Darwin, NT Australia, 22-25 August 2023.

New diagnostic tools for bovine vibriosis

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

    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

    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

    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