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
- Certificate of Quantum Information, Computation and Communication, Massachusetts Institute of Technology
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
2022
Conference Publication
Simultaneous mapping of quantitative trait loci in multiple subspecies using hybrid populations
Warburton, C.L., Costilla, R.C., Engle, B.N. and Hayes, B.J. (2022). Simultaneous mapping of quantitative trait loci in multiple subspecies using hybrid populations. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, The Netherlands, 3-8 July 2022. Wageningen, The Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_179
2022
Conference Publication
The long and short of Nanopore genomic prediction: the effect of read length on prediction accuracy
Lamb, H.J., Nguyen, L.T., Randhawa, I.A.S., Hayes, B.J. and Ross, E.M. (2022). The long and short of Nanopore genomic prediction: the effect of read length on prediction accuracy. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_279
2022
Journal Article
Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane
Yadav, Seema, Ross, Elizabeth, Wei, Xianming, Powell, Owen, Hivert, Valentin, Hickey, Lee T., Atkin, Felicity, Deomano, Emily, Aitken, Karen S., Voss-Fels, Kai P. and Hayes, Ben J. (2022). Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane.
2022
Journal Article
CELPI: trial protocol for a randomised controlled trial of a Carer End of Life Planning Intervention in people dying with dementia
Arendts, G., Chenoweth, L., Hayes, B. J., Campbell, E., Agar, M., Etherton-Beer, C., Spilsbury, K., Howard, K., Braitberg, G., Cubitt, M., Sheehan, C., Magann, L., Sudharshan, T., Schnitker, L. M., Pearce, J., Gilmore,, Cerra, N., DuPreez, J., Jaworski, R., Soh, S-C and Celenza, A. (2022). CELPI: trial protocol for a randomised controlled trial of a Carer End of Life Planning Intervention in people dying with dementia. BMC Geriatrics, 22 (1) 869. doi: 10.1186/s12877-022-03534-1
2022
Journal Article
Identification of genomic variants causing variation in quantitative traits: a review
Meuwissen, Theo, Hayes, Ben, MacLeod, Iona and Goddard, Michael (2022). Identification of genomic variants causing variation in quantitative traits: a review. Agriculture, 12 (10) 1713, 1-11. doi: 10.3390/agriculture12101713
2022
Conference Publication
A conditional multi‑trait sequence GWAS of heifer fertility in tropically adapted beef cattle
Forutan, M., Engle, B., Goddard, M. E. and Hayes, B. J. (2022). A conditional multi‑trait sequence GWAS of heifer fertility in tropically adapted beef cattle. World Congress on Genetics Applied to Livestock Production, Rotterdam, The Netherlands, 3 July-8 July 2022.
2022
Journal Article
Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits
Olasege, Babatunde S., Porto-Neto, Laercio R., Tahir, Muhammad S., Gouveia, Gabriela C., Cánovas, Angela, Hayes, Ben J. and Fortes, Marina R. S. (2022). Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits. BMC Genomics, 23 (1) 684, 1-20. doi: 10.1186/s12864-022-08898-7
2022
Journal Article
Application of infrared thermal technology to assess the level of heat stress and milk yield reduction of cows in tropical smallholder dairy farms
Bang, Nguyen N., Gaughan, John B., Hayes, Ben J., Lyons, Russell E. and McNeill, David M. (2022). Application of infrared thermal technology to assess the level of heat stress and milk yield reduction of cows in tropical smallholder dairy farms. Journal of Dairy Science, 105 (10), 8454-8469. doi: 10.3168/jds.2021-21343
2022
Journal Article
Multivariate analysis identifying the main factors associated with cow productivity and welfare in tropical smallholder dairy farms in Vietnam
Bang, Nguyen N., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N., Hayes, Ben J., Gaughan, John B., Lyons, Russell E. and McNeill, David M. (2022). Multivariate analysis identifying the main factors associated with cow productivity and welfare in tropical smallholder dairy farms in Vietnam. Tropical Animal Health and Production, 54 (5) 313, 313. doi: 10.1007/s11250-022-03303-7
2022
Journal Article
Promoting sustainable utilization and genetic improvement of Indonesian local beef cattle breeds: a review
Widyas, Nuzul, Widi, Tri Satya Mastuti, Prastowo, Sigit, Sumantri, Ika, Hayes, Ben J. and Burrow, Heather M. (2022). Promoting sustainable utilization and genetic improvement of Indonesian local beef cattle breeds: a review. Agriculture, 12 (10) 1566, 1566. doi: 10.3390/agriculture12101566
2022
Journal Article
genomicSimulation: fast R functions for stochastic simulation of breeding programs
Villiers, Kira, Dinglasan, Eric, Hayes, Ben J and Voss-Fels, Kai P (2022). genomicSimulation: fast R functions for stochastic simulation of breeding programs. G3 Genes|Genomes|Genetics, 12 (10) jkac216, 1-6. doi: 10.1093/g3journal/jkac216
2022
Journal Article
Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes
Ong, Chian Teng, Ross, Elizabeth M., Boe-Hansen, Gry, Turni, Conny, Hayes, Ben J., Fordyce, Geoffry and Tabor, Ala E. (2022). Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes. Scientific reports, 12 (1) 15075, 1-12. doi: 10.1038/s41598-022-19022-w
2022
Journal Article
The CattleGTEx atlas reveals regulatory mechanisms underlying complex traits
Fang, Lingzhao and Hayes, Ben (2022). The CattleGTEx atlas reveals regulatory mechanisms underlying complex traits. Nature Genetics, 54 (9), 1273-1274. doi: 10.1038/s41588-022-01155-3
2022
Journal Article
Metagenomic predictions: a review 10 years on
Ross, Elizabeth M. and Hayes, Ben J. (2022). Metagenomic predictions: a review 10 years on. Frontiers in Genetics, 13 865765, 1-9. doi: 10.3389/fgene.2022.865765
2022
Journal Article
Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis
Mantilla Valdivieso, Emily F., Ross, Elizabeth M., Raza, Ali, Naseem, Muhammad Noman, Kamran, Muhammad, Hayes, Ben J., Jonsson, Nicholas N., James, Peter and Tabor, Ala E. (2022). Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis. BMC Genomics, 23 (1) 454, 1-20. doi: 10.1186/s12864-022-08686-3
2022
Journal Article
Genomics applied to livestock and aquaculture breeding
Yáñez, José M., Xu, Peng, Carvalheiro, Roberto and Hayes, Ben (2022). Genomics applied to livestock and aquaculture breeding. Evolutionary Applications, 15 (4), 517-522. doi: 10.1111/eva.13378
2022
Journal Article
Evaluation of host depletion and extraction methods for shotgun metagenomic analysis of bovine vaginal samples
Ong, Chian Teng, Boe-Hansen, Gry, Ross, Elizabeth M., Blackall, Patrick J., Turni, Conny, Hayes, Ben J. and Tabor, Ala E. (2022). Evaluation of host depletion and extraction methods for shotgun metagenomic analysis of bovine vaginal samples. Microbiology Spectrum, 10 (2), e0041221. doi: 10.1128/spectrum.00412-21
2022
Journal Article
Environmental variation effects fertility in tropical beef cattle
Copley, James P., Engle, Bailey N., Ross, Elizabeth M., Speight, Shannon, Fordyce, Geoffry, Wood, Benjamin J., Voss-Fels, Kai P. and Hayes, Benjamin J. (2022). Environmental variation effects fertility in tropical beef cattle. Translational Animal Science, 6 (2) txac035, 1-10. doi: 10.1093/tas/txac035
2022
Journal Article
Author correction: a chickpea genetic variation map based on the sequencing of 3,366 genomes
Varshney, Rajeev K., Roorkiwal, Manish, Sun, Shuai, Bajaj, Prasad, Chitikineni, Annapurna, Thudi, Mahendar, Singh, Narendra P., Du, Xiao, Upadhyaya, Hari D., Khan, Aamir W., Wang, Yue, Garg, Vanika, Fan, Guangyi, Cowling, Wallace A., Crossa, José, Gentzbittel, Laurent, Voss-Fels, Kai Peter, Valluri, Vinod Kumar, Sinha, Pallavi, Singh, Vikas K., Ben, Cécile, Rathore, Abhishek, Punna, Ramu, Singh, Muneendra K., Tar’an, Bunyamin, Bharadwaj, Chellapilla, Yasin, Mohammad, Pithia, Motisagar S., Singh, Servejeet ... Liu, Xin (2022). Author correction: a chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 604 (7905), E12-E12. doi: 10.1038/s41586-022-04660-x
2022
Journal Article
Extensive variation in gene expression is revealed in 13 fertility-related genes using RNA-Seq, ISO-Seq, and CAGE-Seq from Brahman cattle
Ross, Elizabeth M., Sanjana, Hari, Nguyen, Loan T., Cheng, YuanYuan, Moore, Stephen S. and Hayes, Ben J. (2022). Extensive variation in gene expression is revealed in 13 fertility-related genes using RNA-Seq, ISO-Seq, and CAGE-Seq from Brahman cattle. Frontiers in Genetics, 13 784663, 784663. doi: 10.3389/fgene.2022.784663
Funding
Current funding
Supervision
Availability
- Professor Ben Hayes is:
- Available for supervision
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Supervision history
Current supervision
-
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
New approaches to maximise gain and genetic diversity in plant breeding programs
Principal Advisor
Other advisors: Dr Owen Powell
-
Doctor Philosophy
Genomic selection for finfish Breeding Programs
Principal Advisor
Other advisors: 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
AI-accelerated breeding of high-protein mungbean
Principal Advisor
Other advisors: Professor Lee Hickey, Dr Eric Dinglasan, Dr Millicent Smith
-
Doctor Philosophy
Genomic prediction for faster genetic gains in sugarcane improvement
Principal Advisor
Other advisors: Dr Eric Dinglasan, Dr Seema Yadav
-
Doctor Philosophy
Reducing methane emissions and improving profitability in Northern Australian beef
Principal Advisor
Other advisors: Dr Kieren McCosker
-
Doctor Philosophy
Machine learning strategies to accelerate genetic gain in agricultural species
Principal Advisor
Other advisors: Dr Eric Dinglasan, Dr Elizabeth Ross, Dr Owen Powell
-
Doctor Philosophy
Genomic Prediction of Specific Combining Ability in Sugarcane
Associate Advisor
Other advisors: Professor Lee Hickey, Dr Seema Yadav
-
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
-
Master Philosophy
Applying genomics tools for novel nematode resistance in sugarcane
Associate Advisor
Other advisors: Professor Lee Hickey, Dr Eric Dinglasan
-
Doctor Philosophy
Predicting better parents to accelerate genetic gain in wheat breeding
Associate Advisor
Other advisors: Dr Alison Kelly, Associate Professor Karine Chenu, Dr Eric Dinglasan, Professor Lee Hickey
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
-
2022
Doctor Philosophy
Pathogenomics of bovine infertility in northern Australia
Associate Advisor
Other advisors: Dr Conny Turni, Associate Professor Gry Boe-Hansen, Professor Ala Tabor
-
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
-
2021
Doctor Philosophy
Strategies to improve dairy cow productivity and welfare in Vietnam
Associate Advisor
Other advisors: Professor John Gaughan
-
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
-
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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