The University of Queensland

Breeding strategies for rainfed lowland rice in drought-prone environments

S. Fukai, M. Cooper and J. Salisbury eds. (1997). Breeding strategies for rainfed lowland rice in drought-prone environments. Canberra, ACT Australia: Australian Centre for International Agricultural Research.

Plant adaptation and crop improvement

M. Cooper and G.L. Hammer eds. (1996). Plant adaptation and crop improvement. Wallingford: CAB International.

Incorporating genetics into crop models to identify new phenotypes adapted to climate change

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

Predicting Genotype × Environment × Management (G × E × M) interactions for the design of crop improvement strategies: Integrating breeder, agronomist, and farmer perspectives

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

Molecular breeding for complex adaptive traits: how integrating crop ecophysiology and modelling can enhance efficiency

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

Future maize hybrid development: Breeding with assistance of molecular and genomics technologies and transgenics

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

Maize

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

Long-term selection in a commercial hybrid maize breeding program

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

Modelling crop improvement in a GXEXM framework via gene-trail-phenotype relationships

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

Integrating Breeding Tools to Generate Information for Efficient Breeding: Past, Present, and Future

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

Modeling QTL effects and MAS in plant breeding

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

Genotype-by-environment interactions under water-limited conditions

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.

Integrating breeding tools to generate information for efficient breeding: past, present, and future

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

Improving drought tolerance in maize

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

Changes in performance, parentage, and genetic diversity of successful corn hybrids, 1930-2000

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.

Drought response index for identifying drought resistant genotypes for rainfed lowland rice in Cambodia

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.

Complexity, quantitative traits and plant breeding: a role for simulation modelling in the genetic improvement of crops

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.

Linking biophysical and genetic models to integrate physiology, molecular biology and plant breeding

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.

Field screening for drought resistance

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.

Influence of seeding time and seedling age at time of transplanting on the productivity of rainfed lowland rice with different levels of photoperiod sensitivity

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.

Leaf-water potential as a drought resistance character in rice

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.

Using molecular information for decision support in wheat breedings

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.

Combining information from multi-environment trials and molecular markers to select adaptive traits for yield improvement of rice in water-limited environments

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.

Genotype x environment interactions, selection response and heterosis

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....

Genotype x environment interactions, selection response and heterosis

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

Breeding strategies for rainfed lowland rice: suggestions for future 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.

Genotypic variation for water relations and growth during the vegetative stage among six rice lines contrasting in maintenance of high leaf water potential

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.

Implications of genotype-by-environment interactions for yield adaptation of rainfed lowland rice: influence of flowering date on yield variation

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.

Introduction

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

Root traits to increase drought resistance in rainfed lowland rice

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.

A strategy for yield improvement of wheat which accommodates large genotype by environment interactions

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.

Analysis of multi-environment trials - an historical perspective

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.

Characterizing environmental challenges using models

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.

Comparing simulation and experimental approaches to analysing genotype by environment interactions for yield in rainfed lowland rice

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.

Environmental characterization based on probe and reference genotypes

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.

Preface

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.

Relationships among analytical methods used to analyse genotypic adaptation in multi-environment trials

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.

Retrospective analysis of historical data sets from multi-environment trials - theoretical development

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.

Synthesis of strategies for crop improvement

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.

Three-mode analytical methods for crop improvement programs

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.

Understanding plant adaptation to achieve systematic applied crop improvement - a fundamental challenge

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.

Genetic modification can improve crop yields — but stop overselling it

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, 470-473. doi: 10.1038/d41586-023-02895-w

Two decades of harnessing standing genetic variation for physiological traits to improve drought tolerance in maize

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

Inclusive collaboration across plant physiology and genomics: Now is the time!

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

Extending the breeder’s equation to take aim at the target population of environments

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

Transgene by germplasm interactions can impact transgene evaluation

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

Retrospective study in US commercial sorghum breeding: I. Genetic gain in relation to relative maturity

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

Breeding crops for drought-affected environments and improved climate resilience

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

Global wheat production could benefit from closing the genetic yield gap

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

Radiation use efficiency increased over a century of maize (Zea mays L.) breeding in the US corn belt

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

Sustained improvement in tolerance to water deficit accompanies maize yield increase in temperate environments

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

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

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: 10.1101/2022.03.11.482897

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

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

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

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

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

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

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

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

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

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

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

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

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

Maize, sorghum, and pearl millet have highly contrasting species strategies to adapt to water stress and climate change-like conditions

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

Towards a multiscale crop modelling framework for climate change adaptation assessment

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

Crop science: a foundation for advancing predictive agriculture

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

Integrating genetic gain and gap analysis to predict improvements in crop productivity

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

Revolutionizing agriculture with synthetic biology

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

Biological reality and parsimony in crop models—why we need both in crop improvement!

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

On the dynamic determinants of reproductive failure under drought in maize

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

Accelerating crop genetic gains with genomic selection

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

Modelling the nitrogen dynamics of maize crops - enhancing the APSIM maize model

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

Grain yield and nitrogen accumulation in maize hybrids released during 1934 to 2013 in the US Midwest

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

Use of crop growth models with whole-genome prediction: application to a maize multienvironment trial

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

Hybrid variation for root system efficiency in maize: potential links to drought adaptation

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

Variation among maize hybrids in response to high vapor pressure deficit at high temperatures

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

Soil water capture trends over 50 years of single-cross maize (Zea mays L.) breeding in the US corn-belt

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

Limited-transpiration trait may increase maize drought tolerance in the US corn belt

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

Industry-scale evaluation of maize hybrids selected for increased yield in drought-stress conditions of the US corn belt

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

Integrating crop growth models with whole genome prediction through approximate Bayesian computation

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

Inhibitor screen for limited-transpiration trait among maize hybrids

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

Hydraulic conductance of maize hybrids differing in transpiration response to vapor pressure deficit

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

Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield

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

Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction

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

Modeling biomass accumulation in maize kernels

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

The US drought of 2012 in perspective: A call to action

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

Transpiration response of maize hybrids to atmospheric vapour pressure deficit

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

Maize hybrid variability for transpiration decrease with progressive soil drying

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

A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modeling

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

Temperature effect on transpiration response of maize plants to vapour pressure deficit

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

Environment characterization as an aid to wheat improvement: Interpreting genotype-environment interactions by modelling water-deficit patterns in north-eastern Australia

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

Indirect selection using reference and probe genotype performance in multi-environment trials

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

The 1BL/1RS translocation decreases grain yield of spring wheat germplasm in low yield environments of north-eastern Australia

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

Yield-trait performance landscapes: from theory to application in breeding maize for drought tolerance

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

Genotypic variation for grain and stover yield of dryland (rabi) sorghum in India 2. A characterisation of genotype x environment interactions

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

Genotypic variation for grain and stover yield of dryland (rabi) sorghum in India: 1. Magnitude of genotype x environment interactions

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

Morphological and architectural development of root systems in sorghum and maize

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

Mixed model approaches for the identification of QTLs within a maize hybrid breeding program

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

Modeling QTL for complex traits: detection and context for plant breeding

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

Can changes in canopy and/or root system architecture explain historical maize yield trends in the US corn belt?

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

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

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

Genotypic variation for drought stress response traits in soybean. II. Inter-relations between epidermal conductance, osmotic potential, relative water content, and plant survival

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

Genotypic variation for drought stress response traits in soybean. III. Broad-sense heritability of epidermal conductance, osmotic potential, and relative water content

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

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

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

Genotype-by-environment interactions for grain yield associated with water availability at flowering in rainfed lowland rice

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

Global adaptation patterns of Australian and CIMMYT spring bread wheat

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

Models for navigating biological complexity in breeding improved crop plants

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

Use of drought response index for identification of drought tolerant genotypes in rainfed lowland rice

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

Changes in drought tolerance in maize associated with fifty years of breeding for yield in the US corn belt

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.

Genetic diversity among maize hybrids widely grown in contrasting regional environments in the United States during the 1990s

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.

Temporal trends in SSR allele frequencies associated with long-term selection for yield of maize

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.

Use of drought response index for identification of drought tolerant genotypes in rainfed lowland rice

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

Gene-to-phenotype models and complex trait genetics

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

Classification of maize environments using crop simulation and geographic information systems

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

Comparison of identity by descent and identity by state for detecting genetic regions under selection in a sorghum pedigree breeding program

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

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?

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

Changes in pedigree backgrounds of pioneer brand maize hybrids widely grown from 1930 to 1999

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

Yield response of rice (Oryza sativa L.) genotypes to drought under rainfed lowlands 4. Vegetative stage screening in the dry season

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

Mapping as you go: an effective approach for marker-assisted selection of complex traits

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

The selective values of alleles in a molecular network model are context dependent

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

A methodology for analysis of sugarcane productivity trends - 2. Comparing variety trials with commercial productivity

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

Advantage of single-trial models for response to selection in wheat breeding multi-environment trials

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

On the determination of recombination rates in intermated recombinant inbred populations

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.

Comparison of two breeding strategies by computer simulation

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

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

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

Prediction of hybrid performance in grain sorghum using RFLP markers

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

Leaf water potential and osmotic adjustment as physiological traits to improve drought tolerance in rice

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

The E(NK) model: extending the NK model to incorporate gene-by-environment interactions and epistasis for diploid genomes

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

A rapid PCR protocol for marker assisted detection of heterozygotes in segregating generations involving 1BL/1RS translocation and normal wheat lines

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

Identification of research to improve the efficiency of breeding strategies for white clover in Australia - a review

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

Peanut resistance to Sclerotinia minor and S-sclerotiorum

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

The GP problem: quantifying gene-to-phenotype relationships

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.

Using crop simulation to generate genotype by environment interaction effects for sorghum in water-limited environments

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

Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands - Part 1. Grain yield and yield components

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

Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands - Part 2. Selection of drought resistant genotypes

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

Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands - Part 3. Plant factors contributing to drought resistance

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

A comparison of formal and participatory breeding approaches using selection theory

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

Erratum: "Genotype-by-management interactions for grain yield and grain protein concentration of wheat" (Field Crops Research (2001) 69 (47-67) PII: S0378429000001313)

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

Using clusters of computers for large QU-GENE simulation experiments

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

A methodology for analysis of sugarcane productivity trends - I. Analysis across districts

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

Genotype-by-management interactions for grain yield and grain protein concentration of wheat

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

Power of the joint segregation analysis method for testing mixed major-gene and polygene inheritance models of quantitative traits

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

Some vocabulary and grammar for the analysis of multi-environment trials, as applied to the analysis of FPB and PPB trials

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

Evaluation of experimental designs and spatial analyses in wheat breeding trials

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

Genotype by environment interactions affecting grain sorghum. I. Characteristics that confound interpretation of hybrid yield

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

Genotype by environment interactions affecting grain sorghum. II. Frequencies of different seasonal patterns of drought stress are related to location effects on hybrid yields

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

Genotype by environment interactions affecting grain sorghum. III. Temporal sequences and spatial patterns in the target population of environments

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

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

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

Adaptation of rainfed lowland rice

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

Concepts and strategies for plant adaptation research in rainfed lowland rice

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

How can breeding contribute to more productive and sustainable rainfed lowland rice systems?

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

Rainfed lowland rice breeding strategies for Northeast Thailand. II. Comparison of intrastation and interstation selection

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

Rainfed lowland rice breeding strategies for northeast Thailand. II. Comparison of interstation and intrastation selection

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

Computer simulation of a selection strategy to accommodate genotype-environment interactions in a wheat recurrent selection programme

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

Evaluation of white clover (Trifolium repens L.) populations for summer moisture stress adaptation in Australia

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

Grain nitrogen concentration differences among three sorghum hybrids with similar grain yield

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

Modelling plant breeding programs as search strategies on a complex response surface

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

Rainfed lowland rice breeding strategies for northeast Thailand. I. Genotypic variation and genotype x environment interactions for grain yield

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

Screening for drought resistance in rainfed lowland rice

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

Genotypexenvironment interactions and some considerations of their implications for wheat breeding in Australia

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

Genotypic variation for grain yield and grain nitrogen concentration among sorghum hybrids under different levels of nitrogen fertiliser and water supply

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

Loss of genetic diversity associated with selection for resistance to sorghum midge in Australian sorghum

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

QU-GENE: A simulation platform for quantitative analysis of genetic models

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

Sorghum hybrid differences in grain yield and nitrogen concentration under low soil nitrogen availability II. Hybrids with contrasting phenology

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

Sorghum hybrid differences in grain yield and nitrogen concentration under low soil nitrogen availability. I. Hybrids with similar phenology

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

Wheat breeding nurseries, target environments, and indirect selection for grain yield

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

Genetic analysis of preharvest sprouting tolerance in three wheat crosses

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

Genetic analysis of variation for grain yield and protein concentration in two wheat crosses

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

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

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

Influence of rate of development of water deficit on the expression of maximum osmotic adjustment and desiccation tolerance in three grain sorghum lines

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

Influence of phenology on grain yield variation among barley cultivars grown under terminal drought

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

The role of physiological understanding in plant breeding; From a breeding perspective

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

Inheritance of osmotic adjustment to water stress in three grain sorghum crosses

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

A selection strategy to accommodate genotype-by-environment interaction for grain yield of wheat: managed-environments for selection among genotypes

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

Development of drought-resistant cultivars using physiomorphological traits in rice

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

Development of drought-resistant cultivars using physiomorphological traits in rice

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

Inheritance of anthracnose resistance in the tropical pasture legume Stylosanthes hamata

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

Variation among low rainfall white clover (Trifolium repens l.) accessions for morphological attributes and herbage yield

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

Combining ability variation for osmotic adjustment among a selected range of grain sorghum (Sorghum bicolor L. Moench) lines

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

Retrospective analysis of the relationships among the test environments of the Southern Queensland sugarcane breeding programme

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

A Procedure for Investigating the Number of Genotypes Required to Provide a Stable Classification of Environments

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

Relationships among analytical methods used to study genotypic variation and genotype-by-environment interaction in plant breeding multi-environment experiments

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

Interpretation of randomly amplified polymorphic DNA marker data for fingerprinting sweet potato (Ipomoea batatas L.) genotypes

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

Enhanced Interpretation of Pattern Analyses of Environments - the Use of Blocks

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

An investigation of the grain yield adaptation of advanced CIMMYT wheat lines to water stress environments in Queensland. I. Crop physiological analysis

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

An investigation of the grain yield adaptation of advanced CIMMYT wheat lines to water stress environments in Queensland. II. Classification analysis

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

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

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

Quantitative analysis of the effect of selection history on sugar yield adaptation of sugarcane clones

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

Predicting grain yield in Australian environments using data from CIMMYT international wheat performance trials 3. Testing predicted correlated response to selection

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

A procedure to assess the relative merit of classification strategies for grouping environments to assist selection in plant breeding regional evaluation trials

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

Genotypic variation of osmotic adjustment and desiccation tolerance in contrasting sorghum inbred lines

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

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

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

Determining Appropriate Group Number and Composition for Data Sets Containing Repeated Check Cultivars

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

Predicting grain yield in Australian environments using data from CIMMYT international wheat performance trials. 1. Potential for exploiting correlated response to selection

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

The impact of genotype x environment interactions for sugar yield on the use of indirect selection in southern queensland

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

Classifying Genotypic Data From Plant-Breeding Trials - a Preliminary Investigation Using Repeated Checks

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

Utility of Repeated Checks for Hierarchical-Classification of Data From Plant-Breeding Trials

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

Hierarchical Gene-Phenotype Maps as a Framework to Predict GxExM Interactions

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.

Integrating Hierarchical G2P Maps with Genomic Prediction

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.

Transferring prediction models: from model organisms to crops

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

Prior knowledge-driven branching phenotype prediction for shoot architecture improvement

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.

Increasing Predictive Ability for Crop Improvement: Linking Crop Growth Models with Whole Genome Prediction

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.

Prior Knowledge-driven Branching Phenotype Prediction for Shoot Architecture Improvement

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.

An Ecophysiology-Inspired Gene-Phenotype Map for Breeding

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.

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.

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.

Environmental characterization facilitate G × E interaction to highlight the role of stay-green traits for genetic gain

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.

Leveraging biological insight and environmental variation to improve phenotypic prediction: integrating crop growth models (CGM) with whole genome prediction (WGP)

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

Breeding drought-tolerant maize hybrids for the US corn-belt: discovery to product

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

Indirect selection using reference genotype performance in a global spring wheat multi-environment trial

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).

Changes in pedigree backgrounds of pioneer brand maize hybrids widely grown from 1930 to 1999

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.

Drought response index for identifying drought resistant genotypes for rainfed lowland rice in Cambodia

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.

Genomics, genetics, and plant breeding: a private sector perspective

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

Improving drought tolerance in maize: a view from industry

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

Simulating the effects of dominance and epistasis on selection response in the CIMMYT wheat breeding program using QuCim

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

Evaluating plant breeding strategies by simulating gene action and dryland environment effects

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.

Comparison of phenotypic, marker and marker-assisted selection strategies in an S1 family recurrent selection strategy

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.

Correlated Genetic Advance from Multi-Environment Trials to the Target Population of Environments

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.

Field screening for adaptability in drought-prone rainfed lowland rice: ACAIR experience in Thailand and Laos

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.

Genetic diversity among the 13 wheat lines used to create base populations for yield improvement by recurrent selection in the Germplasm Enhancement Program

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.

Inter-annual changes in genotypic and genotype by environment variance components for different stages of the Northern Wheat Improvement Program

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.

Simulated influence of drought incidence on conventional and marker-assisted selection in sorghum breeding

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.

The GP problem: Quantifying gene-to-phenotype relationships

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

Yield responses of rice (Oryza Sativa L.) genotypes to water deficit in rainfed lowlands

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.

Breeding for low input conditions and consequences for participatory plant breeding: Examples from tropical maize and wheat

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

Development of drought resistant cultivars for rainfed lowland rice-experience from northeast Thailand and surrounding area

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.

Field screening for drought resistance

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.

Genotypic variation in water protential at different positions and water conductance in rice

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..

Influence of seedling time and seedling age at time of transplanting on the productivity of rainfed lowland rice with different level so fphotoperiod sensitivity

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.

Leaf-water potential as a drought resistance character in rice

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.

Modelling plant breeding programs: applications to forage crops

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.

The effect of population size on QTL detection in recombinant inbred lines

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..

The role of modelling in linking physiology, molecular biology and plant breeding

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.

Using environment characterization to interpret wheat yield in water-limited environments

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..

Analysis of sugarcane yield productivity trends in the wet tropics at a district level

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.

Modeling water availability, crop growth, and yield of rainfed lowland rice genotypes in northeast Thailand

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.

The digestibility and some associated nutritional parameters of a new wheat cultivar (Seri 82-Aus) and barley (Gilbert) for sheep

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.

Application of different experimental designs and analytical methods in the analysis of variety trials

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.

Breeding field crops for farming systems: a case for modelling breeding programs

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.

Combining information from multi-environment trials and molecular markers to select adaptive traits for yield improvement of rice in water-limited environments

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.

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

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.

Effect of check genotypes on the combined analysis of wheat breeding multi-environment trials

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.

Modelling breeding programs: Genes, phenotypes and breeding strategies

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.

Pedigree analysis provides a useful adjunct to QTL analysis in sorghum

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.

Plant breeding strategies for rainfed lowland rice in Northeast Thailand

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.

Quantifying the effect of analytical methods on estimates of heritability from wheat multi-environment trials

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.

Strategies for the efficient utilisation of molecular markers

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.

The ICIS solution to pedigree and data management in the germplasm enhancement program

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.

The influence of crossing strategy on genetic progress from pedigree breeding

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.

Using crop simulation models to examine genotype by environment interaction in variable water-limited environments

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.

Wheat multi-environment testing in the GRDC Northern Region. I. Grain yield database

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.

Wheat multi-environment testing in the GRDC Northern Region. II. Genotype-by-environment interactions

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.

Wheat multi-environment testing in the GRDC Northern Region. III. An analysis of trial costs in Central and Southern Queensland

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.

Wheat multi-environment testing in the GRDC Northern Region. IV. Geographical zoning

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.

Wheat multi-environment testing in the GRDC Northern Region. V. Optimum number of regional trials for cultivar selection

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.

Breeding strategies for rainfed lowland rice: suggestions for future research

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.

The effect of nitrogen on the expression of osmotic adjustment in grain sorghum

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.

Crop improvement can accelerate agriculture adaptation to societal demands and climate change

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

In Silico Sorghum GxExM Dataset For Prediction Algorithm Comparisons

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

Stochastic Simulation of Divergent Selection Experiment on a Gene-Phenotype Network: A Case Study of Shoot Branching in Plants

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

Root system growth and function response to soil temperature in maize (Zea mays L.)

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.).

Extending the breeder’s equation to take aim at the Target Population of Environments

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.

Methods for evaluating effects of transgenes for quantitative traits

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.

Transgene by Germplasm Interactions Can Impact Transgene Evaluation

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.

Plant Breeding in the face of climate change

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

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.

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.

Breeding with an eye on genes for paddocks

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

Maize hybrid X03H001

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

Maize Hybrid X00H315

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

Maize Inbred PH25AG

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

Maize hybrid X08F124

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.

Maize hybrid X08F091

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.

Maize hybrid X08F109

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

Maize inbred PH25AK

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

Real-time process for targeting trait phenotyping of plant breeding experiments

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.

Maize hybrid X13D099

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

Method and system for digital image analysis of ear traits

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.

Maize hybrid X08B746

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

Maize hybrid X08C961

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

Maize hybrid X08C980

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

Maize hybrid X03C201

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

Maize hybrid X13C726

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

Maize hybrid X08C962

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

Maize hybrid X08C908

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

Maize inbred PH1M3D

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

Maize inbred PH1M3M

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

Maize hybrid X05B912

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

Method and system for digital image analysis of ear traits

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.

Method and system for digital image analysis of ear traits

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.

QTL "mapping as-you-go"

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