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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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.
Funding
Current funding
Supervision
Availability
- Professor Ben Hayes is:
- Available for supervision
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Supervision history
Current supervision
-
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
Reducing methane emissions and improving profitability in Northern Australian beef
Principal Advisor
Other advisors: Dr Kieren McCosker
-
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
-
2024
Doctor Philosophy
Genotype by environment interaction for beef cattle fertility traits in northern Australia
Principal Advisor
Other advisors: Dr Ben Wood, Dr Elizabeth Ross
-
2024
Doctor Philosophy
Genomic selection in multi-breed and multi-subspecies populations
Principal Advisor
-
2023
Doctor Philosophy
Optimising Genomic Selection for Sugarcane
Principal Advisor
Other advisors: Professor Lee Hickey, Dr Kai Voss-Fels, Dr Elizabeth Ross, Dr Owen Powell
-
2023
Doctor Philosophy
On-farm genotyping to accelerate genetic gain in Australia's northern beef industry
Associate Advisor
Other advisors: Dr Elizabeth Ross
-
2023
Doctor Philosophy
A transcriptomic-based comparison of host leukocyte and skin responses to cattle tick infestation in Brangus steers
Associate Advisor
Other advisors: Dr Elizabeth Ross, Professor Ala Tabor
-
2023
Doctor Philosophy
Correlation Scan: developing and applying a new method to uncover the genomic locations that affect the genetic correlations between traits
Associate Advisor
Other advisors: Associate Professor Marina Fortes
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2022
Doctor Philosophy
Pathogenomics of bovine infertility in northern Australia
Associate Advisor
Other advisors: Dr Conny Turni, Dr Gry Boe-Hansen, Professor Ala Tabor
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2022
Doctor Philosophy
Investigating envirotyping methodology to evaluate contributions of stay-green traits to wheat yield in Australian environments
Associate Advisor
Other advisors: Professor Mark Cooper, Associate Professor Karine Chenu, Dr Kai Voss-Fels, Professor Lee Hickey
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2021
Doctor Philosophy
Strategies to improve dairy cow productivity and welfare in Vietnam
Associate Advisor
Other advisors: Professor John Gaughan
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2019
Doctor Philosophy
Integrating genomic selection and speed breeding to increase genetic gain in spring wheat (Triticum aestivum) breeding
Associate Advisor
Other advisors: Professor Lee Hickey
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2019
Doctor Philosophy
Selection strategies to improve yield in macadamia using component traits and genomics
Associate Advisor
Other advisors: Professor Robert Henry, Associate Professor Craig Hardner, Dr Mobashwer Alam, Professor Bruce Topp
Media
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