Overview
Background
Professor Mark Cooper is Chair of Prediction Based Crop Improvement at The University of Queensland, and a global leader in quantitative genetics and plant breeding. His work involves integrating genomic prediction and crop growth models into an ‘end to end’ framework for crop improvement.
Professor Cooper has pioneered the development of novel genetic modelling methodologies, based on gene networks, to study important properties of quantitative traits in biology, and demonstrated how this new genetic modelling framework can be successfully used in plant breeding to improve prediction of important traits under the influences of selection. Professor Cooper’s work at DuPont Pioneer on drought adaptation in one of the largest maize breeding programs in the world led to the AQUAmax hybrids that presently cover millions of hectares worldwide.
A quantitative geneticist by training, Professor Cooper spent 20 years working with industry in the United States and as CEO of his own consultancy firm Zenrun42, before returning to UQ to build upon the critical mass of predictive agricultural expertise in QAAFI and the wider university.
Availability
- Professor Mark Cooper is:
- Available for supervision
Qualifications
- Bachelor of Agricultural Science, The University of Queensland
- Doctor of Philosophy of Agriculture, The University of Queensland
- Graduate Certificate in Education, The University of Queensland
Works
Search Professor Mark Cooper’s works on UQ eSpace
2022
Journal Article
Investigations into the emergent properties of gene-to-phenotype networks across cycles of selection: a case study of shoot branching in plants
Powell, Owen M., Barbier, Francois, Voss-Fels, Kai P., Beveridge, Christine and Cooper, Mark (2022). Investigations into the emergent properties of gene-to-phenotype networks across cycles of selection: a case study of shoot branching in plants. in silico Plants, 4 (1) diac006, 1-9. doi: 10.1093/insilicoplants/diac006
2022
Journal Article
Physiological trait networks enhance understanding of crop growth and water use in contrasting environments
Gleason, Sean M., Barnard, Dave M., Green, Timothy R., Mackay, D. Scott, Wang, Diane R., Ainsworth, Elizabeth A., Altenhofen, Jon, Brodribb, Timothy J., Cochard, Hervé, Comas, Louise H., Cooper, Mark, Creek, Danielle, DeJonge, Kendall C., Delzon, Sylvain, Fritschi, Felix B., Hammer, Graeme, Hunter, Cameron, Lombardozzi, Danica, Messina, Carlos D., Ocheltree, Troy, Maxwell Stevens, Bo, Stewart, Jared J., Vadez, Vincent, Wenz, Joshua, Wright, Ian J., Yemoto, Kevin and Zhang, Huihui (2022). Physiological trait networks enhance understanding of crop growth and water use in contrasting environments. Plant, Cell & Environment, 45 (9), 2554-2572. doi: 10.1111/pce.14382
2022
Other Outputs
Investigations into the emergent properties of gene-to-phenotype networks across cycles of selection: a case study of shoot branching in plants
Powell, Owen M., Barbier, Francois, Voss-Fels, Kai P., Beveridge, Christine A. and Cooper, Mark (2022). Investigations into the emergent properties of gene-to-phenotype networks across cycles of selection: a case study of shoot branching in plants.
2022
Journal Article
Can we harness digital technologies and physiology to hasten genetic gain in United States maize breeding?
Diepenbrock, Christine, Tang, Tom, Jines, Michael, Technow, Frank, Lira, Sara, Podlich, Dean, Cooper, Mark and Messina, Carlos (2022). Can we harness digital technologies and physiology to hasten genetic gain in United States maize breeding?. Plant Physiology, 188 (2), 1141-1157. doi: 10.1093/plphys/kiab527
2022
Journal Article
Crop improvement for circular bioeconomy systems
Messina, Carlos D., van Eeuwijk, Fred, Tang, Tom, Truong, Sandra K., McCormick, Ryan F., Technow, Frank, Powell, Owen, Mayor, Laura, Gutterson, Neal, Jones, James W., Hammer, Graeme and Cooper, Mark (2022). Crop improvement for circular bioeconomy systems. Journal of the ASABE, 65 (3), 491-504. doi: 10.13031/ja.14912
2022
Conference Publication
The pursuit of excellence; some reflections after 50+ years of plant breeding at The University of Queensland (9771)
Lambrides, Christopher , Basford, Kaye , DeLacy, Ian , Cooper, Mark , Hardner, Craig , Godwin, Ian , Dieters, Mark and Arief, Vivi (2022). The pursuit of excellence; some reflections after 50+ years of plant breeding at The University of Queensland (9771). Australasian Plant Breeding Conference, Gold Coast, QLD, Australia, 9-11 May 2022.
2021
Journal Article
Can we harness “enviromics” to accelerate crop improvement by integrating breeding and agronomy?
Cooper, Mark and Messina, Carlos D. (2021). Can we harness “enviromics” to accelerate crop improvement by integrating breeding and agronomy?. Frontiers in Plant Science, 12 735143, 735143. doi: 10.3389/fpls.2021.735143
2021
Journal Article
Predicting phenotypes from genetic, environment, management, and historical data using CNNs
Washburn, Jacob D., Cimen, Emre, Ramstein, Guillaume, Reeves, Timothy, O'Briant, Patrick, McLean, Greg, Cooper, Mark, Hammer, Graeme and Buckler, Edward S. (2021). Predicting phenotypes from genetic, environment, management, and historical data using CNNs. Theoretical and Applied Genetics, 134 (12), 3997-4011. doi: 10.1007/s00122-021-03943-7
2021
Journal Article
Plant production in water-limited environments
Hammer, Graeme L., Cooper, Mark and Reynolds, Matthew P. (2021). Plant production in water-limited environments. Journal of Experimental Botany, 72 (14), 5097-5101. doi: 10.1093/jxb/erab273
2021
Journal Article
Perspectives on applications of hierarchical gene-to-phenotype (G2P) maps to capture non-stationary effects of alleles in genomic prediction
Powell, Owen M., Voss-Fels, Kai P., Jordan, David R., Hammer, Graeme and Cooper, Mark (2021). Perspectives on applications of hierarchical gene-to-phenotype (G2P) maps to capture non-stationary effects of alleles in genomic prediction. Frontiers in Plant Science, 12 663565, 663565. doi: 10.3389/fpls.2021.663565/full
2021
Journal Article
Addressing research bottlenecks to crop productivity
Reynolds, Matthew, Atkin, Owen K., Bennett, Malcolm, Cooper, Mark, Dodd, Ian C., Foulkes, M. John, Frohberg, Claus, Hammer, Graeme, Henderson, Ian R., Huang, Bingru, Korzun, Viktor, McCouch, Susan R., Messina, Carlos D., Pogson, Barry J., Slafer, Gustavo A., Taylor, Nicolas L. and Wittich, Peter E. (2021). Addressing research bottlenecks to crop productivity. Trends in Plant Science, 26 (6), 607-630. doi: 10.1016/j.tplants.2021.03.011
2021
Other Outputs
Predicting phenotypes from genetic, environment, management, and historical data using CNNs
Washburn, Jacob D., Cimen, Emre, Ramstein, Guillaume, Reeves, Timothy, O’Briant, Patrick, McLean, Greg, Cooper, Mark, Hammer, Graeme and Buckler, Edward S. (2021). Predicting phenotypes from genetic, environment, management, and historical data using CNNs. doi: 10.1101/2021.05.27.446033
2021
Journal Article
Reproductive resilience but not root architecture underpins yield improvement under drought in maize (Zea mays L.)
Messina, Carlos, McDonald, Dan, Poffenbarger, Hanna, Clark, Randy, Salinas, Andrea, Fang, Yinan, Gho, Carla, Tang, Tom, Graham, Geoff, Hammer, Graeme and Cooper, Mark (2021). Reproductive resilience but not root architecture underpins yield improvement under drought in maize (Zea mays L.). Journal of Experimental Botany, 72 (14), 5235-5245. doi: 10.1093/jxb/erab231
2021
Journal Article
In pursuit of a better world: crop improvement and the CGIAR
Kholova, J, Urban, M O, Cock, J, Arcos, J, Arnaud, E, Aytekin, D, Azevedo, V, Barnes, A P, Ceccarelli, S, Chavarriaga, P, Cobb, J, Connor, D, Cooper, M, Craufurd, P, Debouck, D, Fungo, R, Grando, S, Hammer, G L, Jara, C, Messina, C, Mosquera, G, Nchanji, E, Ng, E, Prager, S, Sankaran, S, Selvaraj, M, Tardieu, F, Thornton, P, Valdes, S ... Xu, Yunbi (2021). In pursuit of a better world: crop improvement and the CGIAR. Journal of Experimental Botany, 72 (14), 5158-5179. doi: 10.1093/jxb/erab226
2021
Journal Article
Back to the future: implications of genetic complexity for the structure of hybrid breeding programs
Technow, Frank, Podlich, Dean and Cooper, Mark (2021). Back to the future: implications of genetic complexity for the structure of hybrid breeding programs. G3: Genes, Genomes, Genetics, 11 (7) jkab153. doi: 10.1093/g3journal/jkab153
2021
Other Outputs
Limited transpiration traits and breeding methods in maize
Cooper, Mark, Messina, Carlos, Sinclair, Thomas and Hammer, Graeme (2021). Limited transpiration traits and breeding methods in maize. 10954527.
2021
Journal Article
Tackling G × E × M interactions to close on-farm yield-gaps: creating novel pathways for crop improvement by predicting contributions of genetics and management to crop productivity
Cooper, Mark, Voss-Fels, Kai P., Messina, Carlos D., Tang, Tom and Hammer, Graeme L. (2021). Tackling G × E × M interactions to close on-farm yield-gaps: creating novel pathways for crop improvement by predicting contributions of genetics and management to crop productivity. Theoretical and Applied Genetics, 134 (6), 1625-1644. doi: 10.1007/s00122-021-03812-3
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
Modelling selection response in plant breeding programs using crop models as mechanistic gene-to-phenotype (CGM-G2P) multi-trait link functions
Cooper, M., Powell, O., Voss-Fels, K. P., Messina, C. D., Gho, C., Podlich, D. W., Technow, F., Chapman, S. C., Beveridge, C. A., Ortiz-Barrientos, D. and Hammer, G. L. (2021). Modelling selection response in plant breeding programs using crop models as mechanistic gene-to-phenotype (CGM-G2P) multi-trait link functions. in silico Plants, 3 (1) diaa016, 1-21. doi: 10.1093/insilicoplants/diaa016
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.
Funding
Current funding
Supervision
Availability
- Professor Mark Cooper is:
- Available for supervision
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Supervision history
Current supervision
-
Doctor Philosophy
Phylogenomic and ecophysiological investigations of transferability of adaptation solutions within the Andropogoneae tribe
Principal Advisor
-
Doctor Philosophy
Experimental investigation in Arabidopsis thaliana of realised selection trajectories for complex branching and flowering traits under the control of gene networks following application of genomic prediction methods.
Principal Advisor
Other advisors: Professor Christine Beveridge, Dr Owen Powell
-
Doctor Philosophy
Phylogenomic and ecophysiological investigations of transferability of adaptation solutions within the Andropogoneae tribe
Principal Advisor
-
Doctor Philosophy
Assessment of machine learning methods to discover novel models of gene networks to improve genomic prediction for plant breeding
Principal Advisor
Other advisors: Dr James Lefevre, Dr Owen Powell
-
Doctor Philosophy
Unification of selection and inheritance informs adaptive potential for generations to come
Associate Advisor
Other advisors: Associate Professor Katrina McGuigan, Dr Yang Liu
-
Doctor Philosophy
Genomic prediction of lodging in sorghum
Associate Advisor
Other advisors: Professor Emma Mace, Dr Esinam Nancy Amuzu-Aweh, Professor David Jordan, Dr Colleen Hunt
-
Doctor Philosophy
Testing the branching model predictions using mutant perturbations of populations
Associate Advisor
Other advisors: Dr Yang Liu, Professor Christine Beveridge
-
Doctor Philosophy
Predicting Plant Success For Future Generations
Associate Advisor
Other advisors: Dr Owen Powell
-
Doctor Philosophy
Network biology of quantitative traits in sorghum
Associate Advisor
Other advisors: Professor Graeme Hammer, Professor Emma Mace, Dr Colleen Hunt, Dr Sofie Pearson, Professor David Jordan
Completed supervision
-
2004
Doctor Philosophy
Investigating quantitative genetic issues for a pedigree plant breeding program using computer simulation
Principal Advisor
Other advisors: Emeritus Professor Kaye Basford
-
2003
Master Agricultural Science
The inheritance of grain yield among Veery wheat lines under Qld environ.conditions.
Principal Advisor
-
2003
Doctor Philosophy
THE CONTRIBUTION OF OSMOTIC ADJUSTMENT TO GRAIN YIELD IN SORGHUM PRODUCTION ENVIRONMENTS
Principal Advisor
Other advisors: Professor Graeme Hammer
-
2022
Doctor Philosophy
Investigating envirotyping methodology to evaluate contributions of stay-green traits to wheat yield in Australian environments
Associate Advisor
Other advisors: Associate Professor Karine Chenu, Professor Ben Hayes, Dr Kai Voss-Fels, Professor Lee Hickey
-
2005
Doctor Philosophy
SIMULATING THE IMPACT OF MARKER-ASSISTED SELECTION IN A WHEAT BREEDING PROGRAM
Associate Advisor
Other advisors: Emeritus Professor Kaye Basford
-
2004
Doctor Philosophy
GENOTYPIC VARIATION IN SOYBEAN FOR STRATEGIES OF DROUGHT STRESS RESPONSE
Associate Advisor
Other advisors: Emeritus Professor Kaye Basford
-
2004
Doctor Philosophy
AN EVALUATION OF MARKER ASSISTED SELECTION (MAS) STRATEGIES FOR GENETIC IMPROVEMENT OF WHEAT
Associate Advisor
Other advisors: Professor Ian Godwin
-
2003
Doctor Philosophy
GENOTYPIC DIFFERENCES IN ADAPTATION TO DROUGHT AND INFERTILE SOILS IN RAINFED LOWLAND RICE IN CAMBODIA
Associate Advisor
Other advisors: Emeritus Professor Shu Fukai
Media
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