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
2021
Conference Publication
Investigating host biomarkers associated with cattle tick resistance
Mantilla Valdivieso, E., Ross, E., Hayes, B., Jonsson, N., James, P. and Tabor, A. (2021). Investigating host biomarkers associated with cattle tick resistance. 33rd Biennial Conference of the Australian Association of Animal Sciences, Fremantle, WA, Australia and online, 1-3 February 2020. Toowong, QLD, Australia: Australian Association of Animal Sciences.
2021
Journal Article
Breed-adjusted genomic relationship matrices as a method to account for population stratification in multibreed populations of tropically adapted beef heifers
Warburton, Christie L., Costilla, Roy, Engle, Bailey N., Corbet, Nicholas J., Allen, Jack M., Fordyce, Geoffry, McGowan, Michael R., Burns, Brian M. and Hayes, Ben J. (2021). Breed-adjusted genomic relationship matrices as a method to account for population stratification in multibreed populations of tropically adapted beef heifers. Animal Production Science, 61 (18), 1788-1795. doi: 10.1071/an21057
2021
Conference Publication
Factors affecting fertility in northern Australian beef herds
Copley, J., Engle, B., Ross, E., Landmark, S., Fordyce, G., Burns, B. and Hayes, B. (2021). Factors affecting fertility in northern Australian beef herds. 33rd Biennial Conference of the Australian Association of Animal Sciences, Fremantle, WA, Australia and online, 1-3 February 2020. Toowong, QLD, Australia: Australian Association of Animal Sciences.
2020
Journal Article
Feed preference response of weaner bull calves to Bacillus amyloliquefaciens H57 probiotic and associated volatile organic compounds in high concentrate feed pellets
Ngo, Thi Thuy, Bang, Nguyen N., Dart, Peter, Callaghan, Matthew, Klieve, Athol, Hayes, Ben and McNeill, David (2020). Feed preference response of weaner bull calves to Bacillus amyloliquefaciens H57 probiotic and associated volatile organic compounds in high concentrate feed pellets. Animals, 11 (1) 51, 51-15. doi: 10.3390/ani11010051
2020
Journal Article
Gene expression of the heat stress response in bovine peripheral white blood cells and milk somatic cells in vivo
Garner, J. B., Chamberlain, A. J., Vander Jagt, C., Nguyen, T. T.T., Mason, B. A., Marett, L. C., Leury, B. J., Wales, W. J. and Hayes, B. J. (2020). Gene expression of the heat stress response in bovine peripheral white blood cells and milk somatic cells in vivo. Scientific Reports, 10 (1) 19181, 19181. doi: 10.1038/s41598-020-75438-2
2020
Journal Article
The future of livestock management: a review of real-time portable sequencing applied to livestock
Lamb, Harrison J., Hayes, Ben J., Nguyen, Loan T. and Ross, Elizabeth M. (2020). The future of livestock management: a review of real-time portable sequencing applied to livestock. Genes, 11 (12) 1478, 1-27. doi: 10.3390/genes11121478
2020
Conference Publication
The impact of physiological non-additivity on variance components for complex traits
Voss-Fels, Kai, Powell, Owen, Jordan, David, Hammer, Graeme, Barbier, Francois, Werner, Christian, Hayes, Ben, Beveridge, Christine and Cooper, Mark (2020). The impact of physiological non-additivity on variance components for complex traits. The 6th International Conference on Quantitative Genetics, Brisbane, QLD Australia, 3-13 November 2020.
2020
Journal Article
Genomic predictions for enteric methane production are improved by metabolome and microbiome data in sheep (Ovis aries)
Ross, Elizabeth M., Hayes, Ben J., Tucker, David, Bond, Jude, Denman, Stuart E. and Oddy, Victor Hutton (2020). Genomic predictions for enteric methane production are improved by metabolome and microbiome data in sheep (Ovis aries). Journal of Animal Science, 98 (10) skaa262. doi: 10.1093/jas/skaa262
2020
Journal Article
Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock
Raymond, Biaty, Yengo, Loic, Costilla, Roy, Schrooten, Chris, Bouwman, Aniek C., Hayes, Ben J., Veerkamp, Roel F. and Visscher, Peter M. (2020). Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock. PLoS Genetics , 16 (9) e1008780, 1-20. doi: 10.1371/journal.pgen.1008780
2020
Journal Article
Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament
Costilla, Roy, Kemper, Kathryn E., Byrne, Enda M., Porto-Neto, Laercio R., Carvalheiro, Roberto, Purfield, Deirdre C., Doyle, Jennifer L., Berry, Donagh P., Moore, Stephen S., Wray, Naomi R. and Hayes, Ben J. (2020). Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament. Genetics Selection Evolution, 52 (1) 51, 51. doi: 10.1186/s12711-020-00569-z
2020
Journal Article
X chromosome variants are associated with male fertility traits in two bovine populations
Fortes, Marina R. S., Porto-Neto, Laercio R., Satake, Nana, Nguyen, Loan T., Freitas, Ana Claudia, Melo, Thaise P., Scalez, Daiane Cristina Becker, Hayes, Ben, Raidan, Fernanda S. S., Reverter, Antonio and Boe-Hansen, Gry B. (2020). X chromosome variants are associated with male fertility traits in two bovine populations. Genetics Selection Evolution, 52 (1) 46, 46. doi: 10.1186/s12711-020-00563-5
2020
Journal Article
Use of whole-genome sequence data and novel genomic selection strategies to improve selection for age at puberty in tropically-adapted beef heifers
Warburton, Christie L., Engle, Bailey N., Ross, Elizabeth M., Costilla, Roy, Moore, Stephen S., Corbet, Nicholas J., Allen, Jack M., Laing, Alan R., Fordyce, Geoffry, Lyons, Russell E., McGowan, Michael R., Burns, Brian M. and Hayes, Ben J. (2020). Use of whole-genome sequence data and novel genomic selection strategies to improve selection for age at puberty in tropically-adapted beef heifers. Genetics Selection Evolution, 52 (1) 28, 28. doi: 10.1186/s12711-020-00547-5
2020
Journal Article
Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB
Naval-Sánchez, Marina, Porto-Neto, Laercio R., Cardoso, Diercles F., Hayes, Ben J., Daetwyler, Hans D., Kijas, James and Reverter, Antonio (2020). Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB. Genetics Selection Evolution, 52 (1) 27, 27. doi: 10.1186/s12711-020-00546-6
2020
Journal Article
Characterization of the poll allele in Brahman cattle using long-read Oxford Nanopore sequencing
Lamb, Harrison J., Ross, Elizabeth M., Nguyen, Loan T., Lyons, Russell E., Moore, Stephen S. and Hayes, Ben J. (2020). Characterization of the poll allele in Brahman cattle using long-read Oxford Nanopore sequencing. Journal of Animal Science, 98 (5) skaa127, skaa127. doi: 10.1093/jas/skaa127
2020
Journal Article
Accelerating genetic gain in sugarcane breeding using genomic selection
Yadav, Seema, Jackson, Phillip, Wei, Xianming, Ross, Elizabeth M., Aitken, Karen, Deomano, Emily, Atkin, Felicity, Hayes, Ben J. and Voss-Fels, Kai P. (2020). Accelerating genetic gain in sugarcane breeding using genomic selection. Agronomy, 10 (4) 585, 1-21. doi: 10.3390/agronomy10040585
2020
Journal Article
Genome-wide association studies for yield component traits in a macadamia breeding population
O’Connor, Katie, Hayes, Ben, Hardner, Craig, Nock, Catherine, Baten, Abdul, Alam, Mobashwer, Henry, Robert and Topp, Bruce (2020). Genome-wide association studies for yield component traits in a macadamia breeding population. BMC Genomics, 21 (1) 199, 199. doi: 10.1186/s12864-020-6575-3
2020
Journal Article
Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships
Hunt, Colleen H., Hayes, Ben J., van Eeuwijk, Fred A., Mace, Emma S. and Jordan, David R. (2020). Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships. Theoretical and Applied Genetics, 133 (3), 1009-1018. doi: 10.1007/s00122-019-03526-7
2019
Journal Article
Optimized genetic testing for polledness in multiple breeds of cattle
Randhawa, Imtiaz A. S., Burns, Brian M., McGowan, Michael R., Porto-Neto, Laercio R., Hayes, Ben J., Ferretti, Ryan, Schutt, Karen M. and Lyons, Russell E. (2019). Optimized genetic testing for polledness in multiple breeds of cattle. G3: Genes, Genomes, Genetics, 10 (2), g3.400866.2019-544. doi: 10.1534/g3.119.400866
2019
Journal Article
Boosting genetic gain in allogamous crops via speed breeding and genomic selection
Jighly, Abdulqader, Lin, Zibei, Pembleton, Luke W., Cogan, Noel O. I., Spangenberg, German C., Hayes, Ben J. and Daetwyler, Hans D. (2019). Boosting genetic gain in allogamous crops via speed breeding and genomic selection. Frontiers in Plant Science, 10 1364, 1364. doi: 10.3389/fpls.2019.01364
2019
Journal Article
The impact of genomic and traditional selection on the contribution of mutational variance to long-term selection response and genetic variance
Mulder, Herman A., Lee, Sang Hong, Clark, Sam, Hayes, Ben J. and van der Werf, Julius H. J. (2019). The impact of genomic and traditional selection on the contribution of mutational variance to long-term selection response and genetic variance. Genetics, 213 (2), 361-378. doi: 10.1534/genetics.119.302336
Funding
Current funding
Supervision
Availability
- Professor Ben Hayes is:
- Available for supervision
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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
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
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
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
Genomic Prediction of Specific Combining Ability in Sugarcane
Associate Advisor
Other advisors: Professor Lee Hickey, Dr Seema Yadav
-
Master Philosophy
Applying genomics tools for novel nematode resistance in sugarcane
Associate 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
-
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
Genomic selection in multi-breed and multi-subspecies populations
Principal Advisor
-
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
-
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
-
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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