Professor Mark Cooper

Cooper, Mark, Hickey, Lee, Jiang, Xianxian, La Fata, Giorgio, Lomas, Harold, Miller, Tim, O’Brien, Susan, Patel, Parth and Tomarchio, Samuel (2024). Transforming food production with AI. Food AI: A game changer for Australia’s food and beverage sector. (pp. 5-13) edited by Janet R. McColl-Kennedy and Damian Hine. Brisbane, QLD, Australia: The University of Queensland, Australia's Food and Beverage Accelerator (FaBA).

Messina, Carlos D. and Cooper, Mark (2023). Incorporating genetics into crop models to identify new phenotypes adapted to climate change. Modelling climate change impacts on agricultural systems. (pp. 75-104) Cambridge, United Kingdom: Burleigh Dodds Science Publishing. doi: 10.19103/AS.2022.0115.04

Cooper, Mark, Messina, Carlos D., Tang, Tom, Gho, Carla, Powell, Owen M., Podlich, Dean W., Technow, Frank and Hammer, Graeme L. (2023). Predicting Genotype × Environment × Management (G × E × M) interactions for the design of crop improvement strategies: Integrating breeder, agronomist, and farmer perspectives. Plant breeding reviews. (pp. 467-585) edited by Irwin Goldman. Hoboken, NJ, United States: Wiley Blackwell. doi: 10.1002/9781119874157.ch8

Hammer, Graeme, Messina, Charlie, van Oosterom, Erik, Chapman, Scott, Singh, Vijaya, Borrell, Andrew, Jordan, David and Cooper, Mark (2016). Molecular breeding for complex adaptive traits: how integrating crop ecophysiology and modelling can enhance efficiency. Crop systems biology: narrowing the gaps between crop modelling and genetics. (pp. 147-162) edited by Xinyou Yin and Paul C. Struik. Cham, Switzerland: Springer International Publishing. doi: 10.1007/978-3-319-20562-5_7

Guo, Mei and Cooper, Mark (2014). Future maize hybrid development: Breeding with assistance of molecular and genomics technologies and transgenics. Genetics, Genomics and Breeding of Maize. (pp. 256-269) Boca Raton, FL United States: CRC Press. doi: 10.1201/b17274

Smith, Stephen, Cooper, Mark, Gogerty, Joseph, Loffler, Carlos, Borcherding, Delos and Wright, Kevin (2014). Maize. Yield gains in major U.S. field crops. (pp. 125-171) edited by Stephen Smith, Brian Diers, James Specht and Brett Carver. Madison: Crop Science Society of America. doi: 10.2135/cssaspecpub33.c6

Duvick, D. N., Smith, J. S. C. and Cooper, M. (2010). Long-term selection in a commercial hybrid maize breeding program. Plant breeding reviews. (pp. 109-151) edited by Jules Janick. Oxford, United Kingdom: John Wiley & Sons. doi: 10.1002/9780470650288.ch4

Messina, C., Hammer, G., Dong, Z., Podlich, D. and Cooper, M. (2009). Modelling crop improvement in a GXEXM framework via gene-trail-phenotype relationships. Crop physiology: Applications for Genetic Improvement and Agronomy. (pp. 235-265) edited by Sadras, V.O. and Calderini, D.. Netherlands: Elsevier. doi: 10.1016/B978-0-12-374431-9.00010-4

Cooper, M., Smith, O. S., Merrill, R. E., Arthur, L., Podlich, D. W. and Löffler, C. M. (2008). Integrating Breeding Tools to Generate Information for Efficient Breeding: Past, Present, and Future. Plant Breeding: The Arnel R. Hallauer International Symposium. (pp. 141-154) Blackwell Publishing. doi: 10.1002/9780470752708.ch10

Cooper, Mark, Podlich, Dean W. and Luo, Lang (2007). Modeling QTL effects and MAS in plant breeding. Genomics-Assisted Crop Improvement. (pp. 57-95) Dordrecht: Springer Netherlands. doi: 10.1007/978-1-4020-6295-7_4

Cooper, M., Smith, O.S., Merrill, R.E., Arthur, L., Podlich, D.W. and Loffler, C.M. (2006). Integrating breeding tools to generate information for efficient breeding: past, present, and future. Plant breeding: the Arnel R. Hallauer International Symposium. (pp. 141-154) edited by Kendall R. Lamkey and Michael Lee. Ames, IA, United States: Blackwell Publishing. doi: 10.1002/9780470752708.ch10

Cooper, Mark, van Eeuwijk, Fred, Chapman, Scott C., Podlich, Dean W. and Loffler, Carlos (2006). Genotype-by-environment interactions under water-limited conditions. Drought Adaptation in Cereals. (pp. 51-96) edited by Jean-Marcel Ribaut. New York, NY, United States: Food Products Press. doi: 10.1201/9781003578338-5

Barker, T., Campos, H., Cooper, M., Dolan, D., Edmeades, G., Habben, J., Schussler, J., Wright, D. and Zinselmeier, C. (2005). Improving drought tolerance in maize. Plant breeding reviews. (pp. 173-253) edited by Jules Janick. Hoboken, NJ, United States: John Wiley & Sons. doi: 10.1002/9780470650301.ch7

Duvick, Donald N., Smith, J.S.C. and Cooper, M. (2004). Changes in performance, parentage, and genetic diversity of successful corn hybrids, 1930-2000. Corn origin, history, technology, and production. (pp. 65-97) edited by C. Wayne Smith, Javier Betran and E.C.A. Runge. Hoboken, NJ, United States: John Wiley & Sons.

Ouk, M., Fukai, S., Fischer, K. S., Basnayake, J., Cooper, M. and Nesbitt, H. (2004). Drought response index for identifying drought resistant genotypes for rainfed lowland rice in Cambodia. Water in agriculture. (pp. 203-214) edited by V. Seng, E. Craswell, S. Fukai and K. Fischer. Canberra, ACT Australia: Australian Centre for International Agricultural Research.

Cooper, M., Podlich, D., Micallef, K. P., Smith, O. S., Jensen, N. M., Chapman, S. C. and Kruger, N. L. (2002). Complexity, quantitative traits and plant breeding: a role for simulation modelling in the genetic improvement of crops. Quantitative Genetics, Genomics and Plant Breeding. (pp. 143-166) edited by M. S. Kang. Wallingford, UK: CAB International.

Chapman, S.C., Hammer, G. L., Podlich, D. and Cooper, M. (2002). Linking biophysical and genetic models to integrate physiology, molecular biology and plant breeding. Quantitative Genetics, Genomics and Plant Breeding. (pp. 167-187) edited by M.S. Kang. Wallingford, UK: CAB International.

Eagles, H. A., Cooper, M., Shorter, R. and Fox, P. N. (2001). Using molecular information for decision support in wheat breedings. Plant Genotyping: The DNA Fingerprinting of Plants. (pp. 285-298) edited by R. J. Henry. Wallingford, UK: CABI Publishing.

Sibounheuang, V., Basnayake, J., Fukai, S. and Cooper, M. (2001). Leaf-water potential as a drought resistance character in rice. Increased lowland rice production in the Mekong region. (pp. 86-95) edited by Shu Fukai and Jaya Basnayake. Canberra, ACT Australia: Australian Centre for International Agricultural Research.

Pantuwan, G., Fukai, S., Cooper, M., Rajatasereekul, S. and O'Toole, J. C. (2001). Field screening for drought resistance. Increased lowland rice production in the Mekong region. (pp. 69-77) edited by Shu Fukai and Jaya Basnayake. Canberra, ACT Australia: Australian Centre for International Agricultural Research.

Makara, Ouk, Fukai, S., Cooper, M. and Nesbitt, H. J. (2001). Influence of seeding time and seedling age at time of transplanting on the productivity of rainfed lowland rice with different levels of photoperiod sensitivity. Increased lowland rice production in the Mekong region. (pp. 259-270) edited by Shu Fukai and Jaya Basnayake. Canberra, ACT Australia: Australian Centre for International Agricultural Research.

Cooper, M. and Podlich, D. (1999). Genotype x environment interactions, selection response and heterosis. The Genetics and Exploitation of Heterosis in Crops. (pp. 81-92) edited by J. G. Coors and S. Pandey. Madison, Wisconsin, USA: American Society of Agronomy, Crop Science Society of America, Soil Science Society....

Cooper, M., Podlich, D. and Fukai, S. (1999). Combining information from multi-environment trials and molecular markers to select adaptive traits for yield improvement of rice in water-limited environments. Genetic Improvement of Rice for Water-Limited Environments. (pp. 13-33) edited by O. Ito, J. O'Toole and B. Hardy. Los Banos, Philippines: International Rice Research Institute.

Cooper, M. and Podlich, D. W. (1999). Genotype x environment interactions, selection response and heterosis. The genetics and exploitation of heterosis in crops. (pp. 89-92) Madison, WI USA: American Society of Agronomy. doi: 10.2134/1999.geneticsandexploitation.c8

Cooper, M. and Boriboon Somrith (1997). Implications of genotype-by-environment interactions for yield adaptation of rainfed lowland rice: influence of flowering date on yield variation. Breeding strategies for rainfed lowland rice in drought-prone environments. (pp. 104-114) edited by S. Fukai, M. Cooper and J. Salisbury. Canberra, ACT, Australia: Australian Centre for International Agricultural Research.

Fukai, Shu, Piggin, C. and Cooper, M. (1997). Introduction. Breeding strategies for rainfed lowland rice in drought-prone environments. (pp. vi-xi) edited by S. Fukai, M. Cooper and J. Salisbury. Canberra, ACT Australia: Australian Centre for International Agricultural Research. doi: 10.1007/978-981-10-5221-7_1

Jongdee, Boonrat, Fukai, Shu and Cooper, M. (1997). Genotypic variation for water relations and growth during the vegetative stage among six rice lines contrasting in maintenance of high leaf water potential. Breeding strategies for rainfed lowland rice in drought-prone environments. (pp. 180-191) edited by S. Fukai, M. Cooper and J. Salisbury. Canberra, ACT Australia: Australian Centre for International Agricultural Research.

Pantuwan, Greinggrai, Fukai, Shu, Cooper, M., O'Toole, J. C. and Sarkarung, Surapong (1997). Root traits to increase drought resistance in rainfed lowland rice. Breeding strategies for rainfed lowland rice in drought-prone environments. (pp. 170-179) edited by S. Fukai, M. Cooper and J. Salisbury. Canberra, ACT Australia: Australian Centre for International Agricultural Research.

Fukai, Shu, Cooper, M., Fischer, K. S. and Wade, L. J. (1997). Breeding strategies for rainfed lowland rice: suggestions for future research. Breeding strategies for rainfed lowland rice in drought-prone environments. (pp. 245-248) edited by S. Fukai, M. Cooper and J. Salisbury. Canberra, ACT Australia: Australian Centre for International Agricultural Research.

Cooper, M. and Byth, D. E. (1996). Understanding plant adaptation to achieve systematic applied crop improvement - a fundamental challenge. Plant adaptation and crop improvement. (pp. 5-23) edited by M. Cooper and G. L. Hammer. Wallingford, United Kingdom: CAB International.

Cooper, Mark and Hammer, Graeme L. (1996). Preface. Plant adaptation and crop improvement. (pp. xiii-xv) edited by M. Cooper and G. L. Hammer. Wallingford, United Kingdom: CAB International.

Cooper, M., DeLacy, I. H. and Basford, K. E. (1996). Relationships among analytical methods used to analyse genotypic adaptation in multi-environment trials. Plant adaptation and crop improvement. (pp. 193-224) edited by M. Cooper and G. L. Hammer. Wallingford, United Kingdom: CAB International.

DeLacy, I. H., Basford, K. E., Cooper, M. and Fox, P. N. (1996). Retrospective analysis of historical data sets from multi-environment trials - theoretical development. Plant adaptation and crop improvement. (pp. 243-267) edited by M. Cooper and G. L. Hammer. Wallingford, United Kingdom: CAB International.

Basford, K. E., Kroonenberg, P. M. and Cooper, M. (1996). Three-mode analytical methods for crop improvement programs. Plant adaptation and crop improvement. (pp. 291-305) edited by M. Cooper and G. L. Hammer. Wallingford, United Kingdom: CAB International.

Muchow, R. C., Cooper, M. and Hammer, G. L. (1996). Characterizing environmental challenges using models. Plant adaptation and crop improvement. (pp. 349-364) edited by M. Cooper and G. L. Hammer. Wallingford, United Kingdom: CAB International.

Cooper, M., Brennan, P. S. and Sheppard, J. A. (1996). A strategy for yield improvement of wheat which accommodates large genotype by environment interactions. Plant adaptation and crop improvement. (pp. 487-511) edited by M. Cooper and G.L. Hammer. Oxon, United Kingdom: CAB International.

Cooper, M. and Fox, P. N. (1996). Environmental characterization based on probe and reference genotypes. Plant adaptation and crop improvement. (pp. 529-547) edited by M. Cooper and G.L. Hammer. Oxon, United Kingdom: CAB International.

Cooper, M. and Hammer, G. L. (1996). Synthesis of strategies for crop improvement. Plant adaptation and crop improvement. (pp. 591-623) edited by M. Cooper and G. L. Hammer. Wallingford, United Kingdom: CAB International.

Henderson, S. A., Fukai, S., Jongdee, B. and Cooper, M. (1996). Comparing simulation and experimental approaches to analysing genotype by environment interactions for yield in rainfed lowland rice. Plant adaptation and crop improvement. (pp. 443-464) edited by M. Cooper and G. L. Hammer. Abingdon, Oxon United Kingdom: CAB International.

DeLacy, I. H., Basford, K. E., Cooper, M., Bull, J. K. and McLaren, C. G. (1996). Analysis of multi-environment trials - an historical perspective. Plant adaptation and crop improvement. (pp. 39-124) edited by M. Cooper and G. L. Hammer. Wallingford, United Kingdom: CAB International.

Linares, Julien F., Coles, Nathan D., Mo, Hua, Habben, Jeffrey E., Humbert, Sabrina, Messina, Carlos, Tang, Tom, Cooper, Mark, Gho, Carla, Carrasco, Ricardo, Carter, Javier, Flounders, Jillian Wicher and Brummer, E. Charles (2024). Transgene effects vary among maize populations with implications for improving quantitative traits. Crop Science. doi: 10.1002/csc2.21408

Linares, Julien F., Coles, Nathan D., Mo, Hua, Habben, Jeffrey E., Humbert, Sabrina, Messina, Carlos, Tang, Tom, Cooper, Mark, Gho, Carla, Carrasco, Ricardo, Carter, Javier, Flounders, Jillian Wicher and Brummer, E. Charles (2024). Methods for evaluating effects of transgenes for quantitative traits. Crop Science, 64 (1), 141-148. doi: 10.1002/csc2.21141

Wu, Alex, Truong, Sandra Huynh, McCormick, Ryan, van Oosterom, Erik J., Messina, Carlos D., Cooper, Mark and Hammer, Graeme L. (2024). Contrasting leaf‐scale photosynthetic low‐light response and its temperature dependency are key to differences in crop‐scale radiation use efficiency. New Phytologist, 241 (6), 2435-2447. doi: 10.1111/nph.19537

Khaipho-Burch, Merritt, Cooper, Mark, Crossa, Jose, de Leon, Natalia, Holland, James, Lewis, Ramsey, McCouch, Susan, Murray, Seth C., Rabbi, Ismail, Ronald, Pamela, Ross-Ibarra, Jeffrey, Weigel, Detlef and Buckler, Edward S. (2023). Genetic modification can improve crop yields — but stop overselling it. Nature, 621 (7979), 470-473. doi: 10.1038/d41586-023-02895-w

Messina, Carlos D., Gho, Carla, Hammer, Graeme L., Tang, Tom and Cooper, Mark (2023). Two decades of harnessing standing genetic variation for physiological traits to improve drought tolerance in maize. Journal of Experimental Botany, 74 (16), 4847-4861. doi: 10.1093/jxb/erad231

Interdisciplinary Plant Science Consortium and Cooper, Mark (2023). Inclusive collaboration across plant physiology and genomics: Now is the time!. Plant Direct, 7 (5) e493. doi: 10.1002/pld3.493

Cooper, Mark, Powell, Owen, Gho Brito, Carla, Tang, Tom and Messina, Carlos (2023). Extending the breeder’s equation to take aim at the target population of environments. Frontiers in Plant Science, 14 1129591, 1-10. doi: 10.3389/fpls.2023.1129591

Linares, Julien F., Coles, Nathan D., Mo, Hua, Habben, Jeff E., Humbert, Sabrina, Messina, Carlos, Tang, Tom, Cooper, Mark, Gho, Carla, Carrasco, Ricardo, Carter, Javier, Flounders, Jillian Wicher and Brummer, E Charles (2023). Transgene by germplasm interactions can impact transgene evaluation. Crop Science, 63 (4), 1988-1997. doi: 10.1002/csc2.20939

Mayor, L., Demarco, P., Lira, S., Fang, Y., Abadie, T., Gambin, B., Hammer, G., Ciampitti, I., Cooper, M. and Messina, C. (2023). Retrospective study in US commercial sorghum breeding: I. Genetic gain in relation to relative maturity. Crop Science, 63 (2), 501-510. doi: 10.1002/csc2.20897

Cooper, Mark and Messina, Carlos D. (2023). Breeding crops for drought-affected environments and improved climate resilience. The Plant Cell, 35 (1), 162-186. doi: 10.1093/plcell/koac321

Senapati, Nimai, Semenov, Mikhail A., Halford, Nigel G., Hawkesford, Malcolm J., Asseng, Senthold, Cooper, Mark, Ewert, Frank, van Ittersum, Martin K., Martre, Pierre, Olesen, Jørgen E., Reynolds, Matthew, Rötter, Reimund P. and Webber, Heidi (2022). Global wheat production could benefit from closing the genetic yield gap. Nature Food, 3 (7), 532-541. doi: 10.1038/s43016-022-00540-9

Messina, Carlos D., Rotundo, Jose, Hammer, Graeme L., Gho, Carla, Reyes, Andres, Fang, Yinan, van Oosterom, Erik, Borras, Lucas and Cooper, Mark (2022). Radiation use efficiency increased over a century of maize (Zea mays L.) breeding in the US corn belt. Journal of Experimental Botany, 73 (16), 5503-5513. doi: 10.1093/jxb/erac212

Messina, Carlos, Ciampitti, Ignacio Antonio, Berning, Dan, Bubeck, Dave, Hammer, Graeme and Cooper, Mark (2022). Sustained improvement in tolerance to water deficit accompanies maize yield increase in temperate environments. Crop Science, 62 (6), 1-13. doi: 10.1002/csc2.20781

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Choudhary, Sunita , Guha, Anirban , Kholova, Jana , Pandravada, Anand , Messina, Charlie D. , Cooper, Mark and Vadez, Vincent (2020). Maize, sorghum, and pearl millet have highly contrasting species strategies to adapt to water stress and climate change-like conditions. Plant Science, 295 110297, 110297. doi: 10.1016/j.plantsci.2019.110297

Peng, Bin, Guan, Kaiyu, Tang, Jinyun, Ainsworth, Elizabeth A., Asseng, Senthold, Bernacchi, Carl J., Cooper, Mark, Delucia, Evan H., Elliott, Joshua W., Ewert, Frank, Grant, Robert F., Gustafson, David I, Hammer, Graeme L., Jin, Zhenong, Jones, James W., Kimm, Hyungsuk, Lawrence, David M., Li, Yan, Lombardozzi, Danica L., Marshall-Colon, Amy, Messina, Carlos D., Ort, Donald R., Schnable, James C., Vallejos, C. Eduardo, Wu, Alex, Yin, Xinyou and Zhou, Wang (2020). Towards a multiscale crop modelling framework for climate change adaptation assessment. Nature Plants, 6 (4), 338-348. doi: 10.1038/s41477-020-0625-3

Cooper, Mark, Tang, Tom, Gho, Carla, Hart, Tim, Hammer, Graeme and Messina, Carlos (2020). Integrating genetic gain and gap analysis to predict improvements in crop productivity. Crop Science, 60 (2) csc2.20109, 582-604. doi: 10.1002/csc2.20109

Messina, Carlos D., Cooper, Mark, Reynolds, Matthew and Hammer, Graeme L. (2020). Crop science: a foundation for advancing predictive agriculture. Crop Science, 60 (2) csc2.20116, 544-546. doi: 10.1002/csc2.20116

Wurtzel, Eleanore T., Vickers, Claudia E., Hanson, Andrew D., Millar, A. Harvey, Cooper, Mark, Voss-Fels, Kai P., Nikel, Pablo I. and Erb, Tobias J. (2019). Revolutionizing agriculture with synthetic biology. Nature Plants, 5 (12), 1207-1210. doi: 10.1038/s41477-019-0539-0

Hammer, Graeme, Messina, Charlie, Wu, Alex and Cooper, Mark (2019). Biological reality and parsimony in crop models—why we need both in crop improvement!. In Silico Plants, 1 (1), 1-21. doi: 10.1093/insilicoplants/diz010

Messina, Carlos D., Hammer, Graeme L., McLean, Greg, Cooper, Mark, Oosterom, Erik J. van, Tardieu, Francois, Chapman, Scott C., Doherty, Alastair and Gho, Carla (2019). On the dynamic determinants of reproductive failure under drought in maize. In Silico Plants, 1 (1), 1-14. doi: 10.1093/insilicoplants/diz003

Voss-Fels, Kai Peter, Cooper, Mark and Hayes, Ben John (2018). Accelerating crop genetic gains with genomic selection. Theoretical and Applied Genetics, 132 (3), 669-686. doi: 10.1007/s00122-018-3270-8

Soufizadeh, S., Munaro, E., McLean, G., Massignam, A., van Oosterom, E. J., Chapman, S. C., Messina, C., Cooper, M. and Hammer, G. L. (2018). Modelling the nitrogen dynamics of maize crops - enhancing the APSIM maize model. European Journal of Agronomy, 100, 118-131. doi: 10.1016/j.eja.2017.12.007

DeBruin, Jason L., Schussler, Jeffrey R., Mo, Hua and Cooper, Mark (2017). Grain yield and nitrogen accumulation in maize hybrids released during 1934 to 2013 in the US Midwest. Crop Science, 57 (3), 1431-1446. doi: 10.2135/cropsci2016.08.0704

Cooper, Mark, Technow, Frank, Messina, Carlos, Gho, Carla and Totir, L. Radu (2016). Use of crop growth models with whole-genome prediction: application to a maize multienvironment trial. Crop Science, 56 (5), 2141-2156. doi: 10.2135/cropsci2015.08.0512

van Oosterom, Erik J., Yang, Zongjian, Zhang, Fenglu, Deifel, Kurt S., Cooper, Mark, Carlos D. Messina and Hammer, Graeme L. (2016). Hybrid variation for root system efficiency in maize: potential links to drought adaptation. Functional Plant Biology, 43 (6), 502-511. doi: 10.1071/FP15308

Shekoofa, Avat, Sinclair, Thomas R., Messina, Carlos D. and Cooper, Mark (2016). Variation among maize hybrids in response to high vapor pressure deficit at high temperatures. Crop Science, 56 (1), 392-396. doi: 10.2135/cropsci2015.02.0134

Reyes, Andres, Messina, Carlos D., Hammer, Graeme L., Liu, Lu, van Oosterom, Erik, Lafitte, Renee and Cooper, Mark (2015). Soil water capture trends over 50 years of single-cross maize (Zea mays L.) breeding in the US corn-belt. Journal of Experimental Botany, 66 (22), 7339-7346. doi: 10.1093/jxb/erv430

Messina, Carlos D., Sinclair, Thomas R., Hammer, Graeme L., Curan, Dian, Thompson, Jason, Oler, Zac, Gho, Carla and Cooper, Mark (2015). Limited-transpiration trait may increase maize drought tolerance in the US corn belt. Agronomy Journal, 107 (6), 1978-1986. doi: 10.2134/agronj15.0016

Gaffney, Jim, Schussler, Jeff, Loeffler, Carlos, Cai, Weiguo, Paszkiewicz, Steve, Messina, Carlos, Groeteke, Jeremy, Keaschall, Joe and Cooper, Mark (2015). Industry-scale evaluation of maize hybrids selected for increased yield in drought-stress conditions of the US corn belt. Crop Science, 55 (4), 1608-1618. doi: 10.2135/cropsci2014.09.0654

Technow, Frank, Messina, Carlos D., Totir, L. Radu and Cooper, Mark (2015). Integrating crop growth models with whole genome prediction through approximate Bayesian computation. PLoS One, 10 (6) e0130855, e0130855. doi: 10.1371/journal.pone.0130855

Choudhary, Sunita, Sinclair, Thomas R., Messina, Carlos D., Cai, Weiguo, Warner, Dave and Cooper, Mark (2015). Inhibitor screen for limited-transpiration trait among maize hybrids. Environmental and Experimental Botany, 109, 161-167. doi: 10.1016/j.envexpbot.2014.07.015

Sunita, Choudhary, Sinclair, Thomas R., Messina, Carlos D. and Cooper, Mark (2014). Hydraulic conductance of maize hybrids differing in transpiration response to vapor pressure deficit. Crop Science, 54 (3), 1147-1152. doi: 10.2135/cropsci2013.05.0303

Guo, Mei, Rupe, Mary A., Wei, Jun, Winkler, Chris, Goncalves-Butruille, Marymar, Weers, Ben P., Cerwick, Sharon F., Dieter, Jo Ann, Duncan, Keith E., Howard, Richard J., Hou, Zhenglin, Loeffler, Carlos M., Cooper, Mark and Simmons, Carl R. (2014). Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield. Journal of Experimental Botany, 65 (1), 249-260. doi: 10.1093/jxb/ert370

Cooper, Mark, Messina, Carlos D., Podlich, Dean, Totir, L. Radu, Baumgarten, Andrew, Hausmann, Neil J., Wright, Deanne and Graham, Geoffrey (2014). Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction. Crop and Pasture Science, 65 (4), 311-336. doi: 10.1071/cp14007

Boyer, J. S., Byrne, P., Cassman, K. G., Cooper, M., Delmer, D., Greene, T., Gruis, F., Habben, J., Hausmann, N., Kenny, N., Lafitte, R., Paszkiewicz, S., Porter, D., Schlegel, A., Schussler, J., Setter, T., Shanahan, J., Sharp, R. E., Vyn, T. J., Warner, D. and Gaffney, J. (2013). The US drought of 2012 in perspective: A call to action. Global Food Security-Agriculture Policy Economics and Environment, 2 (3), 139-143. doi: 10.1016/j.gfs.2013.08.002

Meade, Kendra A., Cooper, Mark and Beavis, William D. (2013). Modeling biomass accumulation in maize kernels. Field Crops Research, 151, 92-100. doi: 10.1016/j.fcr.2013.07.014

Gholipoor, M., Choudhary, S., Sinclair, T. R., Messina, C. D. and Cooper, M. (2013). Transpiration response of maize hybrids to atmospheric vapour pressure deficit. Journal of Agronomy and Crop Science, 199 (3), 155-160. doi: 10.1111/jac.12010

Gholipoor, M., Sinclair, T. R., Raza, M. A. S., Loeffler, C., Cooper, M. and Messina, C. D. (2013). Maize hybrid variability for transpiration decrease with progressive soil drying. Journal of Agronomy and Crop Science, 199 (1), 23-29. doi: 10.1111/j.1439-037X.2012.00530.x

Dong, Zhanshan, Danilevskaya, Olga, Abadie, Tabare, Messina, Carlos, Coles, Nathan and Cooper, Mark (2012). A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modeling. PLoS One, 7 (8) e43450, e43450. doi: 10.1371/journal.pone.0043450

Yang, Zongjian, Sinclair, Thomas R., Zhu, Maggie, Messina, Carlos D., Cooper, Mark and Hammer, Graeme L. (2012). Temperature effect on transpiration response of maize plants to vapour pressure deficit. Environmental and Experimental Botany, 78, 157-162. doi: 10.1016/j.envexpbot.2011.12.034

Chenu, K., Cooper, M., Hammer, G. L., Mathews, K. L., Dreccer, M. F. and Chapman, S. C. (2011). Environment characterization as an aid to wheat improvement: Interpreting genotype-environment interactions by modelling water-deficit patterns in north-eastern Australia. Journal of Experimental Botany, 62 (6), 1743-1755. doi: 10.1093/jxb/erq459

Peake, Allan S., Gilmour, Arthur and Cooper, Mark (2011). The 1BL/1RS translocation decreases grain yield of spring wheat germplasm in low yield environments of north-eastern Australia. Crop and Pasture Science, 62 (4), 276-288. doi: 10.1071/CP10219

Mathews, Ky L., Trethowan, Richard, Milgate, Andrew W., Payne, Thomas, van Ginkel, Maarten, Crossa, Jose, DeLacy, Ian, Cooper, Mark and Chapman, Scott C. (2011). Indirect selection using reference and probe genotype performance in multi-environment trials. Crop and Pasture Science, 62 (4), 313-327. doi: 10.1071/CP10318

Messina, Carlos D., Podlich, Dean, Dong, Zhanshan, Samples, Mitch and Cooper, Mark (2011). Yield-trait performance landscapes: from theory to application in breeding maize for drought tolerance. Journal of Experimental Botany, 62 (3), 855-868. doi: 10.1093/jxb/erq329

DeLacy, I. H., Kaul, S., Rana, B. S. and Cooper, M. (2010). Genotypic variation for grain and stover yield of dryland (rabi) sorghum in India: 1. Magnitude of genotype x environment interactions. Field Crops Research, 118 (3), 228-235. doi: 10.1016/j.fcr.2010.05.013

DeLacy, I. H., Kaul, S., Rana, B. S. and Cooper, M. (2010). Genotypic variation for grain and stover yield of dryland (rabi) sorghum in India 2. A characterisation of genotype x environment interactions. Field Crops Research, 118 (3), 236-242. doi: 10.1016/j.fcr.2010.05.014

Singh, V, van Oosterom, EJ, Jordan, DR, Messina, CD, Cooper, M and Hammer, GL (2010). Morphological and architectural development of root systems in sorghum and maize. Plant and Soil, 333 (1-2), 287-299. doi: 10.1007/s11104-010-0343-0

van Eeuwijk, Fred A., Boer, Martin, Totir, L. Radu, Bink, Marco, Wright, Deanne, Winkler, Christopher R., Podlich, Dean, Boldman, Keith, Baumgarten, Andy, Smalley, Matt, Arbelbide, Martin, ter Braak, Cajo J. F. and Cooper, Mark (2010). Mixed model approaches for the identification of QTLs within a maize hybrid breeding program. Theoretical and Applied Genetics, 120 (2), 429-440. doi: 10.1007/s00122-009-1205-0

Cooper, Mark, van Eeuwijk, Fred A., Hammer, Graeme L., Podlich, Dean W. and Messina, Carlos (2009). Modeling QTL for complex traits: detection and context for plant breeding. Current Opinion In Plant Biology, 12 (2), 231-240. doi: 10.1016/j.pbi.2009.01.006

Hammer, G.L., Dong, Z.S., McLean, G., Doherty, A., Messina, C., Schusler, J., Zinselmeier, C., Paszkiewicz, S. and Cooper, M. (2009). Can changes in canopy and/or root system architecture explain historical maize yield trends in the US corn belt?. Crop Science, 49 (1), 299-312. doi: 10.2135/cropsci2008.03.0152

James, A. T., Lawn, R. J. and Cooper, M. (2008). Genotypic variation for drought stress response traits in soybean. I. Variation in soybean and wild Glycine spp. for epidermal conductance, osmotic potential, and relative water content. Australian Journal of Agricultural Research, 59 (7), 656-669. doi: 10.1071/AR07159

James, A. T., Lawn, R. J. and Cooper, M. (2008). Genotypic variation for drought stress response traits in soybean. III. Broad-sense heritability of epidermal conductance, osmotic potential, and relative water content. Australian Journal of Agricultural Research, 59 (7), 679-689. doi: 10.1071/AR07161

James, A. T., Lawn, R. J. and Cooper, M. (2008). Genotypic variation for drought stress response traits in soybean. II. Inter-relations between epidermal conductance, osmotic potential, relative water content, and plant survival. Australian Journal of Agricultural Research, 59 (7), 670-678. doi: 10.1071/AR07160

Boer, Martin P., Wright, Deanne, Feng, Lizhi, Podlich, Dean W., Luo, Lang, Cooper, Mark and van Eeuwijk, Fred A. (2007). A mixed-model quantitative trait loci (QTL) analysis for multiple-environment trial data using environmental covariables for QTL-by-environment interactions, with an example in maize. Genetics, 177 (3), 1801-1813. doi: 10.1534/genetics.107.071068

Mathews, K. L., Chapman, S. C., Trethowan, R., Pfeiffer, W., van Ginkel, M., Crossa, J., Payne, T., DeLacy, I., Fox, P. N. and Cooper, M. (2007). Global adaptation patterns of Australian and CIMMYT spring bread wheat. Theoretical And Applied Genetics, 115 (6), 819-835. doi: 10.1007/s00122-007-0611-4

Ouk, M., Basnayake, J., Tsubo, M., Fukai, S., Fischer, K. S., Kang, S., Men, S., Thun, V. and Cooper, M. (2007). Genotype-by-environment interactions for grain yield associated with water availability at flowering in rainfed lowland rice. Field Crops Research, 101 (2), 145-154. doi: 10.1016/j.fcr.2006.10.003

Hammer, G. L., Cooper, M., Tardieu, F., Welch, S., Walsh, B., van Eeuwijk, A., Chapman, S. C. and Podlich, D. (2006). Models for navigating biological complexity in breeding improved crop plants. Trends in Plant Science, 11 (12), 587-593. doi: 10.1016/j.tplants.2006.10.006

Ouk, Makara, Basnayake, J., Tsubo, M., Fukai, S., Fischer, K.S., Cooper, M. and Nesbitt, H. (2006). Use of drought response index for identification of drought tolerant genotypes in rainfed lowland rice. Field Crops Research, 99 (1), 48-58. doi: 10.1016/j.fcr.2006.03.003

Ouk, M, Basnayake, J, Tsubo, M, Fukai, S, Fischer, KS, Cooper, M and Nesbitt, H (2006). Use of drought response index for identification of drought tolerant genotypes in rainfed lowland rice. Field Crops Research, 99 (1), 48-58. doi: 10.1016/j.fcr.2006.03.003

Feng, L., Sebastian, S., Smith, S. and Cooper, M. (2006). Temporal trends in SSR allele frequencies associated with long-term selection for yield of maize. Maydica, 51 (2), 293-300.

Campos, H., Cooper, M., Edmeades, G. O., Loffler, C., Schussler, J. R. and Ibanez, M. (2006). Changes in drought tolerance in maize associated with fifty years of breeding for yield in the US corn belt. Maydica, 51 (2), 369-381.

Smith, S., Loffler, C. and Cooper, M. (2006). Genetic diversity among maize hybrids widely grown in contrasting regional environments in the United States during the 1990s. Maydica, 51 (2), 233-242.

Cooper, Mark, Podlich, Dean W. and Smith, Oscar S. (2005). Gene-to-phenotype models and complex trait genetics. Australian Journal of Agricultural Research, 56 (9), 895-918. doi: 10.1071/AR05154

Loffler, C.M., Wei, J., Fast, T., Gogerty, J., Langton, S., Bergman, M., Merrill, B. and Cooper, M. (2005). Classification of maize environments using crop simulation and geographic information systems. Crop Science, 45 (5), 1708-1716. doi: 10.2135/cropsci2004.0370

Cooper, M. and Hammer, G. L. (2005). Preface to Special Issue: Complex traits and plant breeding - can we understand the complexities of gene-to-phenotype relationships and use such knowledge to enhance plant breeding outcomes?. Australian Journal Of Agricultural Research, 56 (9), 869-872. doi: 10.1071/AR05151

Jordan, D., Tao, Y. Z., Henzell, R. G., Godwin, I. D., Cooper, M. and McIntyre, C. L. (2005). Comparison of identity by descent and identity by state for detecting genetic regions under selection in a sorghum pedigree breeding program. Molecular Breeding, 14 (4), 441-454. doi: 10.1007/s11032-005-0901-y

Stephen, J., Smith, C., Duvick, Donald N., Smith, Oscar S., Cooper, Mark and Feng, Lizhi (2004). Changes in pedigree backgrounds of pioneer brand maize hybrids widely grown from 1930 to 1999. Crop Science, 44 (6), 1935-1946. doi: 10.2135/cropsci2004.1935

Pantuwan, G., Fukai, S., Cooper, M., Rajatasereekul, S., O'Toole, J. C. and Basnayake, J. (2004). Yield response of rice (Oryza sativa L.) genotypes to drought under rainfed lowlands 4. Vegetative stage screening in the dry season. Field Crops Research, 89 (2-3), 281-297. doi: 10.1016/j.fcr.2004.02.007

Podlich, Dean W., Winkler, Christopher R. and Cooper, Mark (2004). Mapping as you go: an effective approach for marker-assisted selection of complex traits. Crop Science, 44 (5), 1560-1571. doi: 10.2135/cropsci2004.1560

Peccoud, J., Vander Velden, K., Podlich, D., Winkler, C., Arthur, L. and Cooper, M. (2004). The selective values of alleles in a molecular network model are context dependent. Genetics, 166 (4), 1715-1725. doi: 10.1534/genetics.166.4.1715

Ellis, R. N., Basford, K. E., Leslie, J. K., Hogarth, D. M. and Cooper, M. (2004). A methodology for analysis of sugarcane productivity trends - 2. Comparing variety trials with commercial productivity. Australian Journal of Agricultural Research, 55 (2), 109-116. doi: 10.1071/AR03074

Qiao, C. G., Basford, K. E., DeLacy, I. H. and Cooper, M. (2004). Advantage of single-trial models for response to selection in wheat breeding multi-environment trials. Theoretical And Applied Genetics, 108 (7), 1256-1264. doi: 10.1007/s00122-003-1541-4

Winkler, Christopher R., Jensen, Nicole M., Cooper, Mark, Podlich, Dean W. and Smith, Oscar S. (2003). On the determination of recombination rates in intermated recombinant inbred populations. Genetics, 164 (2), 741-745.

Jearakongman, Suwat, Immark, Somdej, Noenplub, Apichart, Fukai, Shu and Cooper, Mark (2003). Effect of plot size on accuracy of yield estimation of rainfed lowland rice genotypes with different plant heights and grown under different soil fertility conditions. Plant Production Science, 6 (1), 95-102. doi: 10.1626/pps.6.95

Jordan, DR, Tao, Y, Godwin, ID, Henzell, RG, Cooper, M and McIntyre, CL (2003). Prediction of hybrid performance in grain sorghum using RFLP markers. Theoretical And Applied Genetics, 106 (3), 559-567. doi: 10.1007/s00122-002-1144-5

Wang, Jiankang, van Ginkel, Maarten, Podlich, Dean, Ye, Guoyou, Trethowan, Richard, Pfeiffer, Wolfgang, Delacy, Ian, Cooper, Mark and Rajaram, Sanjaya (2003). Comparison of two breeding strategies by computer simulation. Crop Science, 43 (5), 1764-1773. doi: 10.2135/cropsci2003.1764

Cooper, Mark and Podlich, Dean W. (2002). The E(NK) model: extending the NK model to incorporate gene-by-environment interactions and epistasis for diploid genomes. Complexity, 7 (6), 31-47. doi: 10.1002/cplx.10044

Jongdee, B., Fukai, S. and Cooper, M. (2002). Leaf water potential and osmotic adjustment as physiological traits to improve drought tolerance in rice. Field Crops Research, 76 (2-3), 153-163. doi: 10.1016/S0378-4290(02)00036-9

Nadella, K. D., Peake, A. S., Bariana, H. S., Cooper, M., Godwin, I. D. and Carroll, B. J. (2002). A rapid PCR protocol for marker assisted detection of heterozygotes in segregating generations involving 1BL/1RS translocation and normal wheat lines. Australian Journal of Agricultural Research, 53 (8), 931-938. doi: 10.1071/AR00088

Cooper, Mark, Chapman, Scott C., Podlich, Dean W. and Hammer, Graeme L. (2002). The GP problem: quantifying gene-to-phenotype relationships. Silico Biology, 2, 151-164.

Jahufer, M. Z. Z., Cooper, M., Ayres, J. F. and Bray, R. A. (2002). Identification of research to improve the efficiency of breeding strategies for white clover in Australia - a review. Australian Journal of Agricultural Research, 53 (3), 239-257. doi: 10.1071/AR01110

Cruickshank, A. W., Cooper, M. and Ryley, M. J. (2002). Peanut resistance to Sclerotinia minor and S-sclerotiorum. Australian Journal of Agricultural Research, 53 (10), 1105-1110. doi: 10.1071/AR02013

Pantuwan, G., Fukai, S., Cooper, M., Rajatasereekul, S. and O'Toole, J. C. (2002). Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands - Part 3. Plant factors contributing to drought resistance. Field Crops Research, 73 (2-3), 181-200. doi: 10.1016/S0378-4290(01)00194-0

Pantuwan, G., Fukai, S., Cooper, M., Rajatasereekul, S. and O'Toole, JC (2002). Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands - Part 2. Selection of drought resistant genotypes. Field Crops Research, 73 (2-3), 169-180. doi: 10.1016/S0378-4290(01)00195-2

Pantuwan, G., Fukai, S., Cooper, M., Rajatasereekul, S. and O'Toole, J. C. (2002). Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands - Part 1. Grain yield and yield components. Field Crops Research, 73 (2-3), 153-168. doi: 10.1016/S0378-4290(01)00187-3

Chapman, S. C., Cooper, M. and Hammer, G. L. (2002). Using crop simulation to generate genotype by environment interaction effects for sorghum in water-limited environments. Australian Journal of Agricultural Research, 53 (4), 379-389. doi: 10.1071/AR01070

Atlin, G. N., Cooper, M. and Bjornstad, A. (2001). A comparison of formal and participatory breeding approaches using selection theory. Euphytica, 122 (3), 463-475. doi: 10.1023/A:1017557307800

Cooper, M., Woodruff, D. R., Philips, I. G., Basford, K. E. and Gilmour, A. R. (2001). Erratum: "Genotype-by-management interactions for grain yield and grain protein concentration of wheat" (Field Crops Research (2001) 69 (47-67) PII: S0378429000001313). Field Crops Research, 70 (1), 87-88. doi: 10.1016/S0378-4290(01)00134-4

Micallef, Kevin P., Cooper, Mark and Podlich, Dean W. (2001). Using clusters of computers for large QU-GENE simulation experiments. Bioinformatics, 17 (2), 194-195. doi: 10.1093/bioinformatics/17.2.194

van Eeuwijk, F. A., Cooper, M., DeLacy, I. H., Ceccarelli, S. and Grando, S. (2001). Some vocabulary and grammar for the analysis of multi-environment trials, as applied to the analysis of FPB and PPB trials. Euphytica, 122 (3), 477-490. doi: 10.1023/A:1017591407285

Wang, J., Podlich, D. W., Cooper, M. and DeLacy, I. H. (2001). Power of the joint segregation analysis method for testing mixed major-gene and polygene inheritance models of quantitative traits. Theoretical And Applied Genetics, 103 (5), 804-816. doi: 10.1007/s001220100628

Ellis, R. N., Basford, K. E., Cooper, M., Leslie, J. K. and Byth, D. E. (2001). A methodology for analysis of sugarcane productivity trends - I. Analysis across districts. Australian Journal of Agricultural Research, 52 (10), 1001-1009. doi: 10.1071/AR00130

Cooper, M., Woodruff, D. R., Phillips, I. G., Basford, K. E. and Gilmour, A. R. (2001). Genotype-by-management interactions for grain yield and grain protein concentration of wheat. Field Crops Research, 69 (1), 47-67. doi: 10.1016/S0378-4290(00)00131-3

Chapman, S. C., Cooper, M., Butler, D. G. and Henzell, R. G. (2000). Genotype by environment interactions affecting grain sorghum. I. Characteristics that confound interpretation of hybrid yield. Australian Journal of Agricultural Research, 51 (2), 197-207. doi: 10.1071/AR99020

Chapman, SC, Hammer, GL, Butler, DG and Cooper, M (2000). Genotype by environment interactions affecting grain sorghum. III. Temporal sequences and spatial patterns in the target population of environments. Australian Journal of Agricultural Research, 51 (2), 223-233. doi: 10.1071/AR99022

Chapman, S. C., Cooper, M., Hammer, G. L. and Butler, D. G. (2000). Genotype by environment interactions affecting grain sorghum. II. Frequencies of different seasonal patterns of drought stress are related to location effects on hybrid yields. Australian Journal of Agricultural Research, 51 (2), 209-221. doi: 10.1071/AR99021

DeLacy, I. H., Rajaram, S., Cooper, M., Fox, P. N. and Basford, K. E. (2000). The effect of the accumulation of disease resistance genes on the long-term association of a global sample of environments for testing spring bread wheat. Theoretical and Applied Genetics, 101 (7), 1164-1172. doi: 10.1007/s001220051593

Qiao, C. G., Basford, K. E., DeLacy, I. H. and Cooper, M. (2000). Evaluation of experimental designs and spatial analyses in wheat breeding trials. Theoretical and Applied Genetics, 100 (1), 9-16. doi: 10.1007/s001220050002

Cooper, M., Fukai, S. and Wade, L. J. (1999). How can breeding contribute to more productive and sustainable rainfed lowland rice systems?. Field Crops Research, 64 (1-2), 199-209. doi: 10.1016/S0378-4290(99)00060-X

Cooper, M., Rajatasereekul, S., Immark, S., Fukai, S., Basnayake, J. W. M. and Podlich, D. (1999). Rainfed lowland rice breeding strategies for northeast Thailand. II. Comparison of interstation and intrastation selection. Field Crops Research, 64 (1-2), 153-176. doi: 10.1016/S0378-4290(99)00047-7

Cooper, M. (1999). Concepts and strategies for plant adaptation research in rainfed lowland rice. Field Crops Research, 64 (1-2), 13-34. doi: 10.1016/S0378-4290(99)00048-9

Fukai, S., Cooper, M. and Wade, L. J. (1999). Adaptation of rainfed lowland rice. Field Crops Research, 64 (1-2), 1-2. doi: 10.1016/S0378-4290(99)00062-3

Cooper, M., Rajatasereekul, S., Somrith, B., Sriwisut, S., Immark, S., Boonwite, C., Suwanwongse, A., Ruangsook, S., Hanviriyapant, P., Romyen, P., Porn-Uraisanit, P., Skulkhu, E., Fukai, S., Basnayake, J. and Podlich, D. W. (1999). Rainfed lowland rice breeding strategies for Northeast Thailand. II. Comparison of intrastation and interstation selection. Field Crops Research, 64 (1-2), 153-176. doi: 10.1016/S0378-4290(99)00057-X

Fukai, S., Pantuwan, G., Jongdee, B. and Cooper, M. (1999). Screening for drought resistance in rainfed lowland rice. Field Crops Research, 64 (1-2), 61-74. doi: 10.1016/S0378-4290(99)00051-9

Cooper, M., Rajatasereekul, S., Immark, S., Fukai, S. and Basnayake, J. W. M. (1999). Rainfed lowland rice breeding strategies for northeast Thailand. I. Genotypic variation and genotype x environment interactions for grain yield. Field Crops Research, 64 (1-2), 131-151. doi: 10.1016/S0378-4290(99)00056-8

Jahufer, M. Z. Z., Cooper, M., Bray, R. A. and Ayres, J. F. (1999). Evaluation of white clover (Trifolium repens L.) populations for summer moisture stress adaptation in Australia. Australian Journal of Agricultural Research, 50 (4), 561-574. doi: 10.1071/A98141

Kamoshita, A., Fukai, S., Muchow, R. C. and Cooper, M. (1999). Grain nitrogen concentration differences among three sorghum hybrids with similar grain yield. Australian Journal of Agricultural Research, 50 (2), 137-145. doi: 10.1071/A98029

Podlich, D. and Cooper, M. (1999). Modelling plant breeding programs as search strategies on a complex response surface. Lecture Notes in Computer Science, 1585, 171-178. doi: 10.1007/3-540-48873-1

Podlich, D. W., Cooper, M. and Basford, K. E. (1999). Computer simulation of a selection strategy to accommodate genotype-environment interactions in a wheat recurrent selection programme. Plant Breeding, 118 (1), 17-28. doi: 10.1046/j.1439-0523.1999.118001017.x

Kamoshita, A., Fukai, S., Muchow, R. C. and Cooper, M. (1998). Sorghum hybrid differences in grain yield and nitrogen concentration under low soil nitrogen availability II. Hybrids with contrasting phenology. Australian Journal of Agricultural Research, 49 (8), 1277-1286. doi: 10.1071/A98019

Kamoshita, A., Fukai, S., Muchow, R. C. and Cooper, M. (1998). Sorghum hybrid differences in grain yield and nitrogen concentration under low soil nitrogen availability. I. Hybrids with similar phenology. Australian Journal of Agricultural Research, 49 (8), 1267-1276. doi: 10.1071/A98018

Basford, K. E. and Cooper, M. (1998). Genotypexenvironment interactions and some considerations of their implications for wheat breeding in Australia. Australian Journal of Agricultural Research, 49 (2), 153-174. doi: 10.1071/A97035

Jordan, D. R., Tao, Y. Z., Godwin, I. D., Henzell, R. G., Cooper, M. and McIntyre, C. L. (1998). Loss of genetic diversity associated with selection for resistance to sorghum midge in Australian sorghum. Euphytica, 102 (1), 1-7. doi: 10.1023/A:1018311908636

Kamoshita, A., Fukai, S., Muchow, R. C. and Cooper, M. (1998). Genotypic variation for grain yield and grain nitrogen concentration among sorghum hybrids under different levels of nitrogen fertiliser and water supply. Australian Journal of Agricultural Research, 49 (4), 737-747. doi: 10.1071/A97130

Podlich D.W. and Cooper M. (1998). QU-GENE: A simulation platform for quantitative analysis of genetic models. Bioinformatics, 14 (7), 632-653. doi: 10.1093/bioinformatics/14.7.632

Cooper, M, Stucker, RE, DeLacy, IH and Harch, BD (1997). Wheat breeding nurseries, target environments, and indirect selection for grain yield. Crop Science, 37 (4), 1168-1176. doi: 10.2135/cropsci1997.0011183X003700040024x

Fabrizius, MA, Cooper, M and Basford, KE (1997). Genetic analysis of variation for grain yield and protein concentration in two wheat crosses. Australian Journal of Agricultural Research, 48 (5), 605-614. doi: 10.1071/A96152

Jahufer, MZZ, Cooper, M and Harch, BD (1997). Pattern analysis of the diversity of morphological plant attributes and herbage yield in a world collection of white clover (Trifolium repens L.) germplasm characterised in a summer moisture stress environment of Australia. Genetic Resources and Crop Evolution, 44 (4), 289-300. doi: 10.1023/A:1008692629734

Lawson, W. R., Godwin, I. D., Cooper, M. and Brennan, P. S. (1997). Genetic analysis of preharvest sprouting tolerance in three wheat crosses. Australian Journal of Agricultural Research, 48 (2), 215-221. doi: 10.1071/A96071

Basnayake, J., Cooper, M., Henzell, R. G. and Ludlow, M. M. (1996). Influence of rate of development of water deficit on the expression of maximum osmotic adjustment and desiccation tolerance in three grain sorghum lines. Field Crops Research, 49 (1), 65-76. doi: 10.1016/S0378-4290(96)01032-5

Jackson, P, Robertson, M, Cooper, M and Hammer, G (1996). The role of physiological understanding in plant breeding; From a breeding perspective. Field Crops Research, 49 (1), 11-37. doi: 10.1016/S0378-4290(96)01012-X

Mitchell J.H., Fukai S. and Cooper M. (1996). Influence of phenology on grain yield variation among barley cultivars grown under terminal drought. Australian Journal of Agricultural Research, 47 (5), 757-774. doi: 10.1071/AR9960757

Basnayake, J., Cooper, M., Ludlow, M. M., Henzell, R. G. and Snell, P. J. (1995). Inheritance of osmotic adjustment to water stress in three grain sorghum crosses. Theoretical and Applied Genetics, 90 (5), 675-682. doi: 10.1007/BF00222133

Cooper, M., Woodruff, D. R., Eisemann, R. L., Brennan, P. S. and DeLacy, I. H. (1995). A selection strategy to accommodate genotype-by-environment interaction for grain yield of wheat: managed-environments for selection among genotypes. Theoretical and Applied Genetics, 90 (3-4), 492-502. doi: 10.1007/BF00221995

Fukai, S. and Cooper, M. (1995). Development of drought-resistant cultivars using physiomorphological traits in rice. Field Crops Research, 40 (2), 67-86. doi: 10.1016/0378-4290(94)00096-U

Jahufer, M. Z.Z., Cooper, M. and Lane, L. A. (1995). Variation among low rainfall white clover (Trifolium repens l.) accessions for morphological attributes and herbage yield. Australian Journal of Experimental Agriculture, 35 (8), 1109-1116. doi: 10.1071/EA9951109

Fukai S. and Cooper M. (1995). Development of drought-resistant cultivars using physiomorphological traits in rice. Field Crops Research, 40 (2), 67-86. doi: 10.1016/0378-4290(94)00096-U

Iamsupasit, N., Cameron, D. F., Cooper, M., Chakraborty, S. and Edye, L. A. (1995). Inheritance of anthracnose resistance in the tropical pasture legume Stylosanthes hamata. Australian Journal of Agricultural Research, 46 (7), 1353-1364. doi: 10.1071/AR9951353

Basnayake, J., Cooper, M., Ludlow, M. M. and Henzell, R. G. (1994). Combining ability variation for osmotic adjustment among a selected range of grain sorghum (Sorghum bicolor L. Moench) lines. Field Crops Research, 38 (3), 147-155. doi: 10.1016/0378-4290(94)90086-8

Mirzawan, P. D.N., Cooper, M., DeLacy, I. H. and Hogarth, D. M. (1994). Retrospective analysis of the relationships among the test environments of the Southern Queensland sugarcane breeding programme. Theoretical and Applied Genetics, 88 (6-7), 707-716. doi: 10.1007/BF01253974

Bull, JK, Cooper, M and Basford, KE (1994). A Procedure for Investigating the Number of Genotypes Required to Provide a Stable Classification of Environments. Field Crops Research, 38 (1), 47-56. doi: 10.1016/0378-4290(94)90031-0

Cooper M. and DeLacy I.H. (1994). Relationships among analytical methods used to study genotypic variation and genotype-by-environment interaction in plant breeding multi-environment experiments. Theoretical and Applied Genetics, 88 (5), 561-572. doi: 10.1007/BF01240919

Connolly, A. G., Godwin, I. D., Cooper, M. and DeLacy, I. H. (1994). Interpretation of randomly amplified polymorphic DNA marker data for fingerprinting sweet potato (Ipomoea batatas L.) genotypes. Theoretical and Applied Genetics, 88 (3-4), 332-336. doi: 10.1007/BF00223641

Bull, JK, Basford, KE, Cooper, M and Delacy, IH (1994). Enhanced Interpretation of Pattern Analyses of Environments - the Use of Blocks. Field Crops Research, 37 (1), 25-32. doi: 10.1016/0378-4290(94)90078-7

Jahufer, M. Z. Z., Cooper, M. and Brien, L. A. (1994). Genotypic variation for stolon and other morphological attributes of white clover (Trifolium repens L.). Populations and their influence on herbage yield in the summer rainfall region of New South Wales. Australian Journal of Agricultural Research, 45 (3), 703-720. doi: 10.1071/AR9940703

Cooper, M., Byth, D. E. and Woodruff, D. R. (1994). An investigation of the grain yield adaptation of advanced CIMMYT wheat lines to water stress environments in Queensland. II. Classification analysis. Australian Journal of Agricultural Research, 45 (5), 985-1002. doi: 10.1071/AR9940985

Cooper, M., Byth, D. E. and Woodruff, D. R. (1994). An investigation of the grain yield adaptation of advanced CIMMYT wheat lines to water stress environments in Queensland. I. Crop physiological analysis. Australian Journal of Agricultural Research, 45 (5), 965-984. doi: 10.1071/AR9940965

Srivastava, B. L., Cooper, M. and Mullins, R. T. (1994). Quantitative analysis of the effect of selection history on sugar yield adaptation of sugarcane clones. Theoretical and Applied Genetics, 87 (6), 627-640. doi: 10.1007/BF00222887

Cooper, M. and Woodruff, D. R. (1993). Predicting grain yield in Australian environments using data from CIMMYT international wheat performance trials 3. Testing predicted correlated response to selection. Field Crops Research, 35 (3), 191-204. doi: 10.1016/0378-4290(93)90153-E

Basnayake, J., Ludlow, M. M., Cooper, M. and Henzell, R. G. (1993). Genotypic variation of osmotic adjustment and desiccation tolerance in contrasting sorghum inbred lines. Field Crops Research, 35 (1), 51-62. doi: 10.1016/0378-4290(93)90136-B

Cooper, M., Byth, D. E. and DeLacy, I. H. (1993). A procedure to assess the relative merit of classification strategies for grouping environments to assist selection in plant breeding regional evaluation trials. Field Crops Research, 35 (1), 63-74. doi: 10.1016/0378-4290(93)90137-C

Cooper, M., DeLacy, I. H., Byth, D. E. and Woodruff, D. R. (1993). Predicting grain yield in Australian environments using data from CIMMYT international wheat performance trials. 2. The application of classification to identify environmental relationships which exploit correlated response to selection. Field Crops Research, 32 (3-4), 323-342. doi: 10.1016/0378-4290(93)90040-T

Bull, JK, Basford, KE, Delacy, IH and Cooper, M (1993). Determining Appropriate Group Number and Composition for Data Sets Containing Repeated Check Cultivars. Field Crops Research, 31 (3-4), 369-383. doi: 10.1016/0378-4290(93)90074-W

Cooper, M., Byth, D. E., DeLacy, I. H. and Woodruff, D. R. (1993). Predicting grain yield in Australian environments using data from CIMMYT international wheat performance trials. 1. Potential for exploiting correlated response to selection. Field Crops Research, 32 (3-4), 305-322. doi: 10.1016/0378-4290(93)90039-P

Mirzawan, P. D. N., Cooper, M. and Hogarth, D. M. (1993). The impact of genotype x environment interactions for sugar yield on the use of indirect selection in southern queensland. Australian Journal of Experimental Agriculture, 33 (5), 629-638. doi: 10.1071/EA9930629

Bull, JK, Basford, KE, Delacy, IH and Cooper, M (1992). Classifying Genotypic Data From Plant-Breeding Trials - a Preliminary Investigation Using Repeated Checks. Theoretical and Applied Genetics, 85 (4), 461-469. doi: 10.1007/BF00222328

Bull, JK, Cooper, M, Delacy, IH, Basford, KE and Woodruff, DR (1992). Utility of Repeated Checks for Hierarchical-Classification of Data From Plant-Breeding Trials. Field Crops Research, 30 (1-2), 79-95. doi: 10.1016/0378-4290(92)90058-H

Powell, Owen, McLean, Greg, Brider, Jason, Saddigh, Joe, Technow, Frank, Tang, Tom, Totir, Radu, Messina, Carlos D., Hammer, Graeme and Cooper, Mark (2024). Prediction of non-additive genetic effects with hierarchical genomic prediction models. International Conference of Quantitative Genetics (ICQG) 7, Vienna, Austria, 22-26 July 2024. doi: 10.6084/m9.figshare.26425735.v1

Powell, Owen, McLean, Greg, Brider, Jason, Hammer, Graeme and Cooper, Mark (2023). APSIM-WGP: a software platform to predict crop GxExM interactions. GxExM Symposium II, Gainesville, FL USA, 6-7 November 2023.

Tomura, Shunichiro, Powell, Owen and Cooper, Mark (2023). Random Forest Importance Diagnostics can Capture Quantitative Genetic Properties of Markers for Genomic Prediction. International Congress of Genetics, Melbourne, VIC Australia, 16-21 July 2023. figShare. doi: 10.6084/m9.figshare.24211230.v1

Tomura, Shunichiro, Powell, Owen and Cooper, Mark (2023). GPU can Accelerate the Prediction of Complex Phenotypes. Australasian Leadership Computing Symposium, Canberra, ACT Australia, 14-16 June 2023. doi: 10.6084/m9.figshare.24484831.v1

Powell, Owen, McLean, Greg, Brider, Jason, Technow, Frank, Tang, Tom, Messina, Carlos D., Hammer, Graeme and Cooper, Mark (2023). Hierarchical Gene-Phenotype Maps as a Framework to Predict GxExM Interactions. Quantitative Genetics and Genomics Gordon Research Conference, Ventura, CA, United States, 12-17 February 2023.

Powell, Owen, McLean, Greg, Brider, Jason, Technow, Frank, Tang, Tom, Messina, Carlos D., Hammer, Graeme and Cooper, Mark (2022). Integrating Hierarchical G2P Maps with Genomic Prediction. Interdrought VII - The 7th Congress on plant production in water-limited environments, Dakar, Senegal, 1 December 2022.

Powell, Owen, Barbier, Francois, Voss-Fels, Kai, Beveridge, Christine and Cooper, Mark (2022). Utilising prior knowledge to improve breeding. GxExM Symposium, Brisbane, QLD Australia, 3-4 November 2022.

Powell, Owen, Barbier, Francois, Fichtner, Franziska, Sukumaran, Sivakumar, McLean, Greg, Brider, Jason, Technow, Frank, Tang, Tom, Messina, Carlos D., Jordan, David, Hammer, Graeme, Beveridge, Christine and Cooper, Mark (2022). Transferring prediction models: from model organisms to crops. TropAg International Agriculture Conference, Brisbane, QLD, Australia, 31 October - 2 November 2022.

Wijerathna-Yapa, A., Fortuna, N., Cooper, M. and Beveridge, C. A. (2022). Prior knowledge-driven branching phenotype prediction for shoot architecture improvement. ComBio 2022, Melbourne Convention and Exhibition Centre (MCE), 27-30 September 2022.

Powell, Owen, McLean, Greg, Brider, Jason, Technow, Frank, Sukumaran, Sivakumar, Jordan, David, Hammer, Graeme and Cooper, Mark (2022). Increasing Predictive Ability for Crop Improvement: Linking Crop Growth Models with Whole Genome Prediction. AuSoRGM, Toowoomba, QLD Australia, 18-19 August 2022.

Wijerathna-Yapa, Akila, Fortuna, Nicole, Dun, Elizabeth, Lawson, Brodie, Cooper, Mark and Beveridge, Christine A. (2022). Prior Knowledge-driven Branching Phenotype Prediction for Shoot Architecture Improvement. ARC Centre of Excellence for Plant Success in Nature and Agriculture Research Retreat, Hobart, TAS Australia, 30 May - 1 June 2022.

Powell, Owen, Technow, Frank, Messina, Carlos D., McLean, Greg, Brider, Jason, Van Oosterom, Erik, Wu, Alex, Jordan, David, Hammer, Graeme and Cooper, Mark (2022). An Ecophysiology-Inspired Gene-Phenotype Map for Breeding. Australasian Plant Breeding Conference, Gold Coast, QLD, Australia, 9-11 May 2022.

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.

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.

Amin, Asad, Christopher, Jack, Ababaei, Behnam, Cooper, Mark, Hayes, Ben, Voss-Fels, Kai, Hickey, Lee and Chenu, Karine (2019). Environmental characterization facilitate G × E interaction to highlight the role of stay-green traits for genetic gain. Translational Photosynthesis Conference: Innovations in Agriculture for Food Security (ASPS 2019), Brisbane, QLD, Australia, 30 June - 3 July 2019.

Messina, C. D., Technow, F., Tang, T., Totir, R., Gho, C. and Cooper, M. (2018). Leveraging biological insight and environmental variation to improve phenotypic prediction: integrating crop growth models (CGM) with whole genome prediction (WGP). International Crop Modelling Symposium on Crop Modelling for Agriculture and Food Security under Global Change (iCropM), Berlin, Germany, 15-17 March 2016. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.eja.2018.01.007

Cooper, Mark, Gho, Carla, Leafgren, Roger, Tang, Tom and Messina, Carlos (2014). Breeding drought-tolerant maize hybrids for the US corn-belt: discovery to product. 4th InterDrought Conference, Perth, Australia, 2-6 September 2013. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/jxb/eru064

Mathews, Ky L., Trethowan, Richard, Milgate, Andrew, Payne, Thomas, van Ginkel, Maarten, Crossa, Jose, DeLacy, Ian H., Cooper, Mark and Chapman, Scott C. (2010). Indirect selection using reference genotype performance in a global spring wheat multi-environment trial. 8th International Wheat Conference, St Petersburg, Russia, 1-4 June 2010. St. Petersburg, Russia: N.I. Vavilov Research Institute of Plant Industry (VIR).

Smith, J. Stephen C., Duvick, Donald N., Smith, Oscar S., Cooper, Mark and Feng, Lizhi (2004). Changes in pedigree backgrounds of pioneer brand maize hybrids widely grown from 1930 to 1999.

Ouk, M., Fukai, S., Fischer, K. S., Basnayake, J. W. M., Cooper, M. and Nesbitt, H. J. (2004). Drought response index for identifying drought resistant genotypes for rainfed lowland rice in Cambodia. Water in Agriculture, Phnom Penh, Cambodia, 25-28 November 2003. Canberra: Australian Centre for International Agricultural Research.

Campos, H., Cooper, M., Habben, J.E., Edmeades, G.O. and Schussler, J.R. (2004). Improving drought tolerance in maize: a view from industry. Annual Meeting of the Crop Science Society of America, Denver, Colorado, 2-6 November 2003 . Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.fcr.2004.07.003

Cooper, Mark, Smith, Oscar S., Graham, Geoff, Arthur, Lane, Feng, Lizhi Z. and Podlich, Dean W. (2004). Genomics, genetics, and plant breeding: a private sector perspective. Symposium on Genomics and Plant Breeding, Indianapolis, United States, 13 November 2002. Madison, WI, United States: Crop Science Society of America. doi: 10.2135/cropsci2004.1907

Wang, JK, van Ginkel, M, Trethowan, R, Ye, GY, DeLacy, I, Podlich, D and Cooper, M (2004). Simulating the effects of dominance and epistasis on selection response in the CIMMYT wheat breeding program using QuCim. -, -, -. Madison, United States: Crop Science Society of America. doi: 10.2135/cropsci2004.2006

Chapman, S, Cooper, M, Podlich, D and Hammer, G (2003). Evaluating plant breeding strategies by simulating gene action and dryland environment effects. Madison, Wis., USA: American Society of Agronomy.

Pantuwan, G., Fukai, S., Cooper, M., Rajatasereekul, S. and O'Toole, J.C. (2002). Yield responses of rice (Oryza Sativa L.) genotypes to water deficit in rainfed lowlands. Internl Wksh on Field Screening for Drought Tolerance in Rice, Patencheru, India, 11-14 December, 2000. Patencheru, India: International Crops Research Inst for the Semi-Arid Tropics.

Fukai, S. and Cooper, M. (2002). Field screening for adaptability in drought-prone rainfed lowland rice: ACAIR experience in Thailand and Laos. Internl Wksp on Field Screening for Drought Tolerance in Rice, Patencheru, India, 11-14 December, 2000. Patancheru, India: International Crops Research Inst for the Semi-Arid Tropics.

Kruger, N., Cooper, M. and Podlich, D. (2002). Comparison of phenotypic, marker and marker-assisted selection strategies in an S1 family recurrent selection strategy. 12th Australasian Plant Breeding Conference, Perth, Western Australia, 15-20 September, 2002. Perth, W.A.: The Australasian Plant Breeding Assocation.

Susanto, D., Cooper, M., Carroll, B. J. and Godwin, I. D. (2002). Genetic diversity among the 13 wheat lines used to create base populations for yield improvement by recurrent selection in the Germplasm Enhancement Program. 12th Australasian Plant Breeding Conference, Perth, Western Australia, 15-20 September, 2002. Perth, W.A.: The Australasian Plant Breeding Association.

Mathews, K. L., Chapman, S.C., Butler, D., Cooper, M., Delacy, I. H., Sheppard, J. A., Kelly, A. and Sahama, T. R. (2002). Inter-annual changes in genotypic and genotype by environment variance components for different stages of the Northern Wheat Improvement Program. 12th Australasian Plant Breeding Conference, Perth, Western Australia, 15-20 December, 2002. Perth, W.A.: The Australasian Plant Breeding Association.

Chapman, S. C., Hammer, G. L., Podlich, D. and Cooper, M. (2002). Simulated influence of drought incidence on conventional and marker-assisted selection in sorghum breeding. 12th Australasian Plant Breeding Conference, Perth, Western Australia, 15-20 September, 2002. Perth, W.A.: The Australasian Plant Breeding Association.

Cooper, Mark, Chapman, Scott C., Podlich, Dean W. and Hammer, Graeme L. (2002). The GP problem: Quantifying gene-to-phenotype relationships.

Basford, Kaye, DeLacy, I. H. and Cooper, M. (2002). Correlated Genetic Advance from Multi-Environment Trials to the Target Population of Environments. Australasian Genstat Conference 2002, Busselton, Western Australia, 4-6 December 2002.

Sibounheuang, V., Basnayake, J. W. M., Fukai, S. and Cooper, M. (2001). Genotypic variation in water protential at different positions and water conductance in rice. 10th Australian Agronomy Conference, Hobart, Tas, 28 January - 1 February, 2001. Hobart, Tas: The Regional Institute Ltd..

Chapman, S. C., Mathews, K. L., Cooper, M., Jensen, N. M., Wang, E., Butler, D. G., Sheppard, J. A. and Sahama, T. R. (2001). Using environment characterization to interpret wheat yield in water-limited environments. Wheat Breeding Society fo Australian Inc. 10th Assembly, Mildura, Victoria, Australia, 16-21 September, 2001. Australia: Wheat Breeding Society of Australia Inc..

Chapman, S.C., Hammer, G. L., Cooper, M., Podlich, D. and Borrell, A. (2001). The role of modelling in linking physiology, molecular biology and plant breeding. Fourth Australian Sorghum Conference, Kooralbyn, Queensland, 5-8 February, 2001. Brisbane: Range Media Pty Ltd.

Cooper, M., Podlich, D. and Micallef, K. P. (2001). Modelling plant breeding programs: applications to forage crops. 2nd International Symposium, Molecular Breeding of Forage Crops, Lorne and Hamilton, Victoria, Australia, 19-24 November 2000. Dordrecht, The Netherlands: Kluwer Academic Publishers.

Ouk, M., Fukai, S., Cooper, M. and Nesbitt, H.J. (2001). Influence of seedling time and seedling age at time of transplanting on the productivity of rainfed lowland rice with different level so fphotoperiod sensitivity. Increased Lowland Rice Production in the Mekong Region, Vientiane, Laos, 30 October - 2 November, 2000. Canberra, Australia: Australian Centre for International Agricultural Research.

Sibounheuang, V., Basnayake, J. W. M., Fukai, S. and Cooper, M. (2001). Leaf-water potential as a drought resistance character in rice. Increased Lowland Rice Production in the Mekong Region, Vientiane, Laos, 30 October - 2 November, 2000. Canberra, ACT: Australian Centre for International Agricultural Research.

Pantuwan, G., Fukai, S., Cooper, M., Rajatasereekul, S. and O'Toole, J.C. (2001). Field screening for drought resistance. Increased Lowland Rice Production in the Mekong Region, Vientiane, Laos, 30 October - 2 November, 2000. Canberra, ACT: Australian Centre for International Agricultural Research.

Fukai, S. and Cooper, M. (2001). Development of drought resistant cultivars for rainfed lowland rice-experience from northeast Thailand and surrounding area. The Impact of Agricultural Research for Development in SE Asia, Phnom Penh, Cambodia, 24-26 October 2000. Phnom Penh, Cambodia: Cambodian Agricultural Research & Development Institute.

Banziger, M and Cooper, M (2001). Breeding for low input conditions and consequences for participatory plant breeding: Examples from tropical maize and wheat. Dordrecht, The Netherlands: Kluwer Academic Publishers. doi: 10.1023/A:1017510928038

Kruger, N. L., Cooper, M., Podlich, D., Jensen, N. and Basford, K. E. (2001). The effect of population size on QTL detection in recombinant inbred lines. Wheat Breeding Society of Australia Inc. 10th Assembly, Mildura, Victoria, Australia, 16-21 September, 2001. Australia: Wheat Breeding Society of Australia Inc..

Fukai, S., Basnayake, J. W. M. and Cooper, M. (2000). Modeling water availability, crop growth, and yield of rainfed lowland rice genotypes in northeast Thailand. Characterizing and Understanding Rainfed Environments, Bali, Indonesia, 5-9 December, 1999. Manilla, Philippines: International Rice Research Institute.

Poppi, D. P., Jensen, N., Sheppard, J. A. and Cooper, M. (2000). The digestibility and some associated nutritional parameters of a new wheat cultivar (Seri 82-Aus) and barley (Gilbert) for sheep. 9th Congress of Asian-Australasian Association of Animal Production Societies and 23rd Biennial conference of Australian Society of Animal Production, UNSW, Sydney, 3-7 July, 2000. Seoul, South Korea: Asian-Australasian Assoc of Animal Production Societies.

Ellis, R., Basford, K. E., Cooper, M., Leslie, J. K. and Byth, D. E. (2000). Analysis of sugarcane yield productivity trends in the wet tropics at a district level. 2000 Conf of the Aust Soc of Sugar Cane Technologists, Bundaberg, Queensland, 2-5 May, 2000. Brisbane: Australian Society of Sugar Cane Technologists.

Wegener, M. K., Sheppard, J. A., DeLacy, I. H., Butler, D. G., Ratnasiri, W. G., Ellison, F. W., Brennan, P. S. and Cooper, M. (1999). Wheat multi-environment testing in the GRDC Northern Region. V. Optimum number of regional trials for cultivar selection. Vision 2020, The Univ. of Southern Qld., Toowoomba, Qld., 27 Sept - 1 Oct 1999. Toowoomba, Qld.: Organising Committee Aust. Wheat Breeding Society.

Wegener, M. K., Sheppard, J. A., DeLacy, I. H., Butler, D. G., Ratnasiri, W. G., Ellison, F. W., Brennan, P. S. and Cooper, M. (1999). Wheat multi-environment testing in the GRDC Northern Region. III. An analysis of trial costs in Central and Southern Queensland. Vision 2020, The Univ. of Southern Qld., Toowoomba, Qld., 27 Sept - 1 Oct, 1999. Toowoomba, Qld.: Organising Committee Aust. Wheat Breeding Society.

Sheppard, J. A., DeLacy, I. H., Butler, D. G., Ratnasiri, W. G., Ellison, F. W., Brennan, P. S. and Cooper, M. (1999). Wheat multi-environment testing in the GRDC Northern Region. IV. Geographical zoning. Vision 2020, The Univ. of Southern Qld, Toowoomba, Qld, 27 September - 1 October 1999. Toowoomba, Qld: Organising Committee Aust. Wheat Breeding Society.

Sheppard, J. A., DeLacy, I. H., Butler, D. G., Ratnasiri, W. G., Ellison, F. W., Brennan, P. S. and Cooper, M. (1999). Wheat multi-environment testing in the GRDC Northern Region. II. Genotype-by-environment interactions. Vision 2020, The Univ. of Southern Qld, Toowoomba, Qld, 27 September - 1 October 1999. Toowoomba, Qld: Organising Committee Aust. Wheat Breeding Society.

Sheppard, J. A., DeLacy, I. H., Butler, D. G., Ratnasiri, W. G., Ellison, F. W., Brennan, P. S. and Cooper, M. (1999). Wheat multi-environment testing in the GRDC Northern Region. I. Grain yield database. Vision 2020, The Univ. of Southern Qld, Toowoomba, Qld, 27 September - 1 October 1999. Toowoomba, Qld: Organising Committee Aust. Wheat Breeding Society.

Qiao, C., Basford, K. E., Cooper, M., DeLacy, I. H., Phillips, I. G. and Matassa, V. J. (1999). Quantifying the effect of analytical methods on estimates of heritability from wheat multi-environment trials. Biometrics 99, Univ. of Tas., Hobart, Tas, Aust., 12-16 December 1999. Hobart, Aust.: Int. Biometric Society, Australasian Region.

Cooper, M., Podlich, D. and Jensen, N. (1999). Modelling breeding programs: Genes, phenotypes and breeding strategies. Vision 2020, The Univ. of Southern Qld, Toowoomba, 27 September - 1 October 1999. Toowoomba, Qld: Organising Committee Aust. Wheat Breeding Society.

Qiao, C., DeLacy, I. H., Cooper, M. and Basford, K. E. (1999). Effect of check genotypes on the combined analysis of wheat breeding multi-environment trials. Vision 2020, The Univ. of Southern Qld, Toowoomba, 27 September - 1 October 1999. Toowoomba, Qld: Organising Committee Aust. Wheat Breeding Society.

Gororo, N. N., Eagles, H. A., Ogbonnaya, F. C., Eastwood, R. F., Podlich, D., Cooper, M. and Howes, N. (1999). Strategies for the efficient utilisation of molecular markers. Vision 2020, The Univ. of Southern Qld, Toowoomba, 27 September - 1 October 1999. Toowoomba, Qld: Organising Committee Aust. Wheat Breeding Society.

Jensen, N., DeLacy, I. H., Cooper, M., McLaren, C. G. and Fox, P. N. (1999). The ICIS solution to pedigree and data management in the germplasm enhancement program. Vision 2020, The Univ. of Southern Qld, Toowoomba, 27 September - 1 October 1999. Toowoomba, Qld: Organising Committee Aust. Wheat Breeding Society.

Jensen, N., Podlich, D. and Cooper, M. (1999). The influence of crossing strategy on genetic progress from pedigree breeding. 11th Australian Plant Breeding Conference, Stamford Grand Hotel, Glenelg, SA, 19-23 April 1999. Adelaide: Univ. of Adelaide (Waite Campus), SA.

Cooper, M., Godwin, I. D., Henzell, R. G., Jordan, D., McIntyre, C. L. and Tao, Y. Z. (1999). Pedigree analysis provides a useful adjunct to QTL analysis in sorghum. 11th Australian Plant Breeding Conference, Stamford Grand Hotel, Glenelg, SA, 19-23 April 1999. Adelaide: Univ. of Adelaide (Waite Campus), SA.

Chapman, S. C., Hammer, G. L. and Cooper, M. (1999). Using crop simulation models to examine genotype by environment interaction in variable water-limited environments. 11th Australian Plant Breeding Conference, Stamford Grand Hotel, Glenelg, SA, 19-23 April 1999. Adelaide: Univ. of Adelaide (Waite Campus), SA.

Cooper, M. and Podlich, D. (1999). Breeding field crops for farming systems: a case for modelling breeding programs. 11th Australian Plant Breeding Conference, Stamford Grand Hotel, Glenelg, SA, 19-23 April 1999. Adelaide: Univ. of Adelaide (Waite Campus), SA.

Kruger, N. L., Podlich, D. and Cooper, M. (1999). Comparison of S1 and doubled haploid recurrent selection strategies by computer simulation with applications for the Germplasm Enhancement Program of the Northern Wheat Improvement Program. Vision 2020, The Univ. of Southern Qld, Toowoomba, 27 September - 1 October 1999. Toowoomba, Qld: Organising Committee Aust. Wheat Breeding Society.

Cooper, M., Podlich, D. and Fukai, S. (1999). Combining information from multi-environment trials and molecular markers to select adaptive traits for yield improvement of rice in water-limited environments. Workshop on Genetic Improvement of Rice for Water-Limited Ens, Los Banos, Philippines, 1-3 December 1998. Los Banos, philippines: Int. Rice Res. Institute.

Qiao, C., Basford, K. E., DeLacy, I. H. and Cooper, M. (1999). Application of different experimental designs and analytical methods in the analysis of variety trials. 11th Australian Plant Breeding Conference, Stamford Grand Hotel, Glenelg, SA, 19-23 April 1999. Adelaide: Univ. of Adelaide (Waite Campus), SA.

Fukai, S. and Cooper, M. (1999). Plant breeding strategies for rainfed lowland rice in Northeast Thailand. World Food Security and Crop Production Technologies for Tomorrow, Kyoto, Japan, 8-9 October 1998. Kyoto, Japan: Kyoto University.

Fukai, S., Cooper, M., Fischer, K.S. and Wade, L.J. (1997). Breeding strategies for rainfed lowland rice: suggestions for future research. International Workshop on Breeding Strategies for Rainfed Lowland Rice in Drought-Prone Environments, Ubon Ratchathani, Thailand, 5-8 November 1996. Canberra, ACT, Australia: Australian Centre for International Agricultural Research.

Mortlock, M. Y., Cooper, M. and Fukai, S. (1996). The effect of nitrogen on the expression of osmotic adjustment in grain sorghum. 3rd Australian Sorghum Conference, Tamworth, Australia, 20-22 September , 1996. Melbourne VIC Australia: Australian Institute of agricultural science.

Powell, Owen and Cooper, Mark (2020, 10 02). Breeding with an eye on genes for paddocks Groundcover

Tomura, Shunichiro, Cooper, Mark and Powell, Owen (2024). Improvements in prediction performance of ensemble approaches for genomic prediction in crop breeding. doi: 10.1101/2024.09.06.611589

Messina, Carlos D., Borras, Lucas, Tang, Tom and Cooper, Mark (2023). Crop improvement can accelerate agriculture adaptation to societal demands and climate change.

Clark, Randy, Chamberlain, Dan, Diepenbrock, Christine, Cooper, Mark and Messina, Carlos D. (2023). Root system growth and function response to soil temperature in maize (Zea mays L.).

Cooper, Mark, Owen Powell, Gho, Carla, Tang, Tom and Messina, Carlos (2022). Extending the breeder’s equation to take aim at the Target Population of Environments.

Linares, Julien F., Coles, Nathan D., Mo, Hua, Habben, Jeffrey E., Humbert, Sabrina, Messina, Carlos, Tang, Tom, Cooper, Mark, Gho, Carla, Carrasco, Ricardo, Carter, Javier, Wicher Flounders, Jillian and Brummer, E. Charles (2022). Methods for evaluating effects of transgenes for quantitative traits.

Linares, Julien F., Coles, Nathan D., Mo, Hua, Habben, Jeff E., Humbert, Sabrina, Messina, Carlos, Tang, Tom, Cooper, Mark, Gho, Carla, Carrasco, Ricardo, Carter, Javier, Wicher Flounders, Jillian and Brummer, E. Charles (2022). Transgene by Germplasm Interactions Can Impact Transgene Evaluation.

Messina, Carlos D. and Cooper, Mark (2022). Plant Breeding in the face of climate change.

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.

Cooper, Mark, Messina, Carlos, Technow, Frank and Totir, Radu (2024). Molecular Breeding Methods. 11985930.

Cooper, Mark, Messina, Carlos, Sinclair, Thomas and Hammer, Graeme (2021). Limited transpiration traits and breeding methods in maize. 10954527.

Brenner, Everton Alen, Coles, Nathan David, Cooper, Mark, Curran, Bill S., Lee, Travis J and Mengistu, Neway Challa (2018). Maize hybrid X03H001. 9968049.

Cooper, Mark (2018). Maize Hybrid X00H315. 9888643.

Cooper, Mark (2017). Maize Inbred PH25AG. 9788517.

Cooper, M., Lee, T. J., Curran, B. S., Coles, N. D., Mengistu, N. C., Wardyn, B. M., Kilgore-Norquest, L. L. and Barker, T. C. (2016). Maize hybrid X08F124. 9474228.

Cooper, M., Lee, T. J., Curran, B. S., Coles, N. D., Mengistu, N. C., Wardyn, B. M. and Barker, T. C. (2016). Maize hybrid X08F091. 9445571.

Ross, Andrew Jon , Cooper, Mark and Fischer, David B (2016). Maize hybrid X08F109. 9433176.

Cooper, Mark (2016). Maize inbred PH25AK. 9426962.

Messina, Carlos, Wei, Jun, Dong, Zhanshan, Qing, Zhisheng, Laffont, Jean-Louis, Samples, Mitchell, Schussler, Jeffrey R., Graham, Geoffrey I., Loeffler, Carlos and Cooper, Mark (2015). Real-time process for targeting trait phenotyping of plant breeding experiments. 9107355.

Cooper, Mark and Verde Chifflet, Luis A. (2015). Maize hybrid X13D099. 9084408.

Hausmann, Neil Jonathan , Abadie, Tabare E., Cooper, Mark, Lafitte, Honor Renee and Schussler, Jeffrey R. (2015). Method and system for digital image analysis of ear traits. 9008409.

Barker, T. C., Carlone Jr., M. R. and Cooper, M. (2015). Maize hybrid X08B746. 8975491.

Cooper, Mark and Barker, Thomas Charles (2015). Maize hybrid X08C961. 8957289.

Smalley, Matthew David, Carlone Jr, Mario Rosario, Fox, Russell L. and Cooper, Mark (2014). Maize hybrid X08C980. 8872005.

Cooper, Mark, Kilgore-Norquest, Lora Lynn, Barker, Thomas Charles and Wardyn, Brandon Michael (2014). Maize hybrid X13C726. 8809646.

Barker, T. C., Smalley, M. D. and Cooper, M. (2014). Maize hybrid X03C201. 8809644.

Cooper, Mark, Wilson, William Andrew and Lee, Travis J. (2014). Maize hybrid X08C962. 8754306.

Cooper, Mark (2014). Maize inbred PH1M3D. 8742231.

Lee, Travis J., Kilgore-Norquest, Lora Lynn, Barker, Thomas Charles and Cooper, Mark (2014). Maize hybrid X08C908. 8742232.

Cooper, Mark and Ross, Andrew Jon (2014). Maize inbred PH1M3M. 8735692.

Grote, E. M., Wilson, W. A. and Cooper, M. (2014). Maize hybrid X05B912. 8686248.

Hausmann, Neil J., Abadie, Tabare E., Cooper, Mark, Lafitte, Honor R. and Schussler, Jeffrey R. (2013). Method and system for digital image analysis of ear traits. 8488865.

Hausmann, Neil Jonathan , Abadie, Tabare E., Cooper, Mark, Lafitte, Honor Renee and Schussler, Jeffrey R. (2011). Method and system for digital image analysis of ear traits. 8073235.

Podlich, Dean, Cooper, Mark and Winkler, Chris (2011). QTL "mapping as-you-go". 8039686.

Owen Powell, Greg McLean, Jason Brider, Mark Cooper and Graeme Hammer (2023). In Silico Sorghum GxExM Dataset For Prediction Algorithm Comparisons. figShare. (Dataset) doi: 10.6084/m9.figshare.23789685.v2

Powell, Owen and Cooper, Mark (2023). Stochastic Simulation of Divergent Selection Experiment on a Gene-Phenotype Network: A Case Study of Shoot Branching in Plants. figShare. (Dataset) doi: 10.6084/m9.figshare.23590083

Professor Mark Cooper

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