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
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.
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.
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
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
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
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
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
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
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
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
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
2021
Journal Article
Issues of feeding strategy for lactating cows in Vietnamese smallholder dairy farms
Bang, Nguyen N., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N., Hayes, Ben J., Gaughan, John B., Lyons, Russell E., Hai, Nguyen T. and McNeill, David M. (2021). Issues of feeding strategy for lactating cows in Vietnamese smallholder dairy farms. Animals, 11 (3) 729, 1-25. doi: 10.3390/ani11030729
2021
Journal Article
Assessment of performance and some welfare indicators of cows in Vietnamese smallholder dairy farms
Bang, Nguyen N., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N., Hayes, Ben J., Gaughan, John B., Lyons, Russell E., Hai, Nguyen T. and McNeill, David M. (2021). Assessment of performance and some welfare indicators of cows in Vietnamese smallholder dairy farms. Animals, 11 (3) 674, 1-22. doi: 10.3390/ani11030674
2021
Journal Article
Investigating the effect of imputed structural variants from whole‐genome sequence on genome‐wide association and genomic prediction in dairy cattle
Chen, Long, Pryce, Jennie E., Hayes, Ben J. and Daetwyler, Hans D. (2021). Investigating the effect of imputed structural variants from whole‐genome sequence on genome‐wide association and genomic prediction in dairy cattle. Animals, 11 (2) 541, 1-16. doi: 10.3390/ani11020541
2021
Journal Article
Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding
Voss-Fels, Kai P., Wei, Xianming, Ross, Elizabeth M., Frisch, Matthias, Aitken, Karen S., Cooper, Mark and Hayes, Ben J. (2021). Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding. Theoretical and Applied Genetics, 134 (5), 1493-1511. doi: 10.1007/s00122-021-03785-3
2021
Journal Article
Accuracy of genomic prediction of complex traits in sugarcane
Hayes, Ben J., Wei, Xianming, Joyce, Priya, Atkin, Felicity, Deomano, Emily, Yue, Jenny, Nguyen, Loan, Ross, Elizabeth M., Cavallaro, Tony, Aitken, Karen S. and Voss-Fels, Kai P. (2021). Accuracy of genomic prediction of complex traits in sugarcane. Theoretical and Applied Genetics, 134 (5), 1455-1462. doi: 10.1007/s00122-021-03782-6
2021
Journal Article
Characteristics of cowsheds in Vietnamese smallholder dairy farms and their associations with microclimate—a preliminary study
Bang, Nguyen N., Gaughan, John B., Hayes, Ben J., Lyons, Russell E., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N. and McNeill, David M. (2021). Characteristics of cowsheds in Vietnamese smallholder dairy farms and their associations with microclimate—a preliminary study. Animals, 11 (2) 351, 1-21. doi: 10.3390/ani11020351
2021
Conference Publication
Effect of bovine reference genome choice in RNA-SEQ alignment and differential gene expression analysis in Brangus cattle
Mantilla Valdivieso, E., Ross, E., Raza, A., Hayes, B., Jonsson, N., James, P. and Tabor, A. (2021). Effect of bovine reference genome choice in RNA-SEQ alignment and differential gene expression analysis in Brangus cattle. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.
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
Funding
Current funding
Supervision
Availability
- Professor Ben Hayes is:
- Available for supervision
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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
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
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
-
Doctor Philosophy
Genomic Prediction of Specific Combining Ability in Sugarcane
Associate Advisor
Other advisors: Professor Lee Hickey
-
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
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
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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
Enquiries
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