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
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
2022
Journal Article
Genetic variation in PLAG1 is associated with early fertility in Australian Brahman cattle
Engle, Bailey N and Hayes, Ben J (2022). Genetic variation in PLAG1 is associated with early fertility in Australian Brahman cattle. Journal of Animal Science, 100 (4) skac084. doi: 10.1093/jas/skac084
2022
Journal Article
Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing
Ong, Chian Teng, Ross, Elizabeth M., Boe-Hansen, Gry B., Turni, Conny, Hayes, Ben J. and Tabor, Ala E. (2022). Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing. Journal of Animal Science, 100 (1) skab344. doi: 10.1093/jas/skab344
2021
Journal Article
Genomic prediction using low-coverage portable Nanopore sequencing
Lamb, Harrison J., Hayes, Ben J., Randhawa, Imtiaz A. S., Nguyen, Loan T. and Ross, Elizabeth M. (2021). Genomic prediction using low-coverage portable Nanopore sequencing. PLoS One, 16 (12) e0261274, e0261274. doi: 10.1371/journal.pone.0261274
2021
Conference Publication
Genomic prediction of lifetime productivity in Brahman cows
Engle, B.N., Collins Snr, A. and Hayes, B.J. (2021). Genomic prediction of lifetime productivity in Brahman cows. 24th Association for the Advancement of Animal Breeding and Genetics Conference, Online, 2-4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.
2021
Conference Publication
Assessing the relationship between beef cattle fertility traits and novel environmental descriptors in northern Australia
Copley, J.P., Engle, B.N., Speight, S., Fordyce, G., Ross, E.M., Voss-Fels, K.P. and Hayes, B.J. (2021). Assessing the relationship between beef cattle fertility traits and novel environmental descriptors in northern Australia. 24th Association for the Advancement of Animal Breeding and Genetics Conference, Online, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.
2021
Journal Article
An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology
Hayes, Ben J., Nguyen, Loan T., Forutan, Mehrnush, Engle, Bailey N., Lamb, Harrison J., Copley, James P., Randhawa, Imtiaz A. S. and Ross, Elizabeth M. (2021). An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology. Frontiers in Genetics, 12 760450, 760450. doi: 10.3389/fgene.2021.760450
2021
Journal Article
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 (2021). A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 599 (7886), 622-627. doi: 10.1038/s41586-021-04066-1
2021
Journal Article
Maximal rigid subalgebras of deformations and L2-cohomology
de Santiago, Rolando, Hayes, Ben, Hoff, Daniel J. and Sinclair, Thomas (2021). Maximal rigid subalgebras of deformations and L2-cohomology. Analysis and PDE, 14 (7), 2269-2306. doi: 10.2140/apde.2021.14.2269
2021
Conference Publication
Accuracy of genomic prediction in Brahman cattle using simulated genotypes from low-coverage nanopore sequencing
Lamb, H. J. , Nguyen, L. T., Engle, B. N., Hayes, B. J. and Ross, E. M. (2021). Accuracy of genomic prediction in Brahman cattle using simulated genotypes from low-coverage nanopore sequencing. 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
Multibreed genomic prediction for male fertility in tropical beef cattle
Porto-Neto, L. R., Bertram, J., McWilliam, S., Fortes, M. R. S., Alexandre, P., McGowan, M. R., Hayes, B. J. and Reverter, A. (2021). Multibreed genomic prediction for male fertility in tropical beef cattle. Association for the Advancement of Animal Breeding and Genetics, Adelaide, SA, Australia, 2-4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.
2021
Conference Publication
Assessing the potential of parentage testing using portable long read sequencing technologies
Ross, E. M., Lamb, H. J., Engle, B. N. , Nguyen, L. T. and Hayes, B. J. (2021). Assessing the potential of parentage testing using portable long read sequencing technologies. 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
PHENOBANK: A platform to facilitate collaboration and genomic selection for female fertility in beef cattle
Wockner, K. B., Tahir, M. S., Kour, J., Tan, W. L. A., Olasege, B. S., Porto-Neto, L. R., Little, B. A., Wilson, C. R., Dollemore, W., Reverter, A., Hayes, B. and Fortes, M. R. S. (2021). PHENOBANK: A platform to facilitate collaboration and genomic selection for female fertility in beef cattle. Association for the Advancement of Animal Breeding and Genetics, Adelaide, SA, Australia, 2 - 4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.
2021
Conference Publication
Genome wide analysis of bovine enhancers and promoters across developmental stages in liver
Forutan, M., Vander Jagt, C.J., Ross, E., Chamberlain, A. J., Mason, B., Nguyen, L., Moore, S., Garner, J. B., Xiang, R. and Hayes, B. J. (2021). Genome wide analysis of bovine enhancers and promoters across developmental stages in liver. 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
Journal Article
Challenges and opportunities in applying genomic selection to ruminants owned by smallholder farmers
Burrow, Heather M., Mrode, Raphael, Mwai, Ally Okeyo, Coffey, Mike P. and Hayes, Ben J. (2021). Challenges and opportunities in applying genomic selection to ruminants owned by smallholder farmers. Agriculture, 11 (11) 1172, 1172. doi: 10.3390/AGRICULTURE11111172
2021
Journal Article
A linkage disequilibrium-based approach to position unmapped SNPs in crop species
Yadav, Seema, Ross, Elizabeth M., Aitken, Karen S., Hickey, Lee T., Powell, Owen, Wei, Xianming, Voss-Fels, Kai P. and Hayes, Ben J. (2021). A linkage disequilibrium-based approach to position unmapped SNPs in crop species. BMC Genomics, 22 (1) 773, 1-9. doi: 10.1186/s12864-021-08116-w
2021
Book Chapter
Cattle genomics
Hayes, B. J. and Cocks, B. (2021). Cattle genomics. Encyclopedia of dairy sciences. (pp. 620-625) edited by John W. Fuquay. Amsterdam, Netherlands: Elsevier. doi: 10.1016/B978-0-12-818766-1.00338-X
2021
Journal Article
Genomic diversity and breed composition of Vietnamese smallholder dairy cows
Bang, Nguyen N., Hayes, Ben J., Lyons, Russell E., Randhawa, Imtiaz A. S., Gaughan, John B. and McNeill, David M. (2021). Genomic diversity and breed composition of Vietnamese smallholder dairy cows. Journal of Animal Breeding and Genetics, 139 (2), 1-16. doi: 10.1111/jbg.12651
2021
Journal Article
Prowler: a novel trimming algorithm for Oxford Nanopore sequence data
Lee, Simon, Nguyen, Loan T., Hayes, Ben J. and Ross, Elizabeth (2021). Prowler: a novel trimming algorithm for Oxford Nanopore sequence data. Bioinformatics, 37 (21), 3936-3937. doi: 10.1093/bioinformatics/btab630
2021
Journal Article
Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle
Olasege, Babatunde S., Tahir, Muhammad S., Gouveia, Gabriela C., Kour, Jagish, Porto-Neto, Laercio R., Hayes, Ben J. and Fortes, Marina R. S. (2021). Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle. Animal Production Science, 61 (18), 1863-1872. doi: 10.1071/an21097
Funding
Current funding
Supervision
Availability
- Professor Ben Hayes is:
- Available for supervision
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Supervision history
Current supervision
-
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, Dr Seema Yadav
-
Doctor Philosophy
Reducing methane emissions and improving profitability in Northern Australian beef
Principal Advisor
Other advisors: Dr Kieren McCosker
-
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
-
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
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
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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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