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?
Mark Cooper A D and Graeme L. Hammer B CA Pioneer Hi-Bred International Inc., 7250 N. W. 62nd Avenue, PO Box 552, Johnston, IA 50131, USA.
B Agricultural Production Systems Research Unit, School of Land and Food Sciences, The University of Queensland, Brisbane, Qld 4072, Australia.
C Agricultural Production Systems Research Unit, Queensland Department of Primary Industries and Fisheries, Toowoomba, Qld 4350, Australia.
D Corresponding author. Email: Mark.Cooper@pioneer.com
Australian Journal of Agricultural Research 56(9) 869-872 https://doi.org/10.1071/AR05151
Submitted: 9 May 2005 Accepted: 20 June 2005 Published: 28 September 2005
Additional keywords: modelling, prediction, epistasis, pleiotropy, interaction.
Allard, RW (1999).
Axelrod, R ,
and
Cohen, MD (1999). ‘Harnessing complexity organizational implications of a scientific frontier’ (The Free Press: New York)
Cahill DJ, Schmidt DH
(2004) Use of marker assisted selection in a product development breeding program. In ‘Proceedings of the 4th International Crop Science Congress’. 26 Sept.–1 Oct. 2004, Brisbane, Australia. Invited Symposium Paper: ‘New Directions for a Diverse Planet’. (CD-ROM, Web site: http://www.w3.org/1999/xlink)
http://www.w3.org/1999/xlink
Comstock, RE (1996).
Comstock RE,
Robinson HF, Harvey PH
(1949) A procedure designed to make maximum use of both general and specific combining ability. Agronomy Journal 41, 360–367.
Cooper M,
Chapman SC,
Podlich DW, Hammer GL
(2002) The GP problem: quantifying gene-to-phenotype relationships. In Silico Biology 2, 151–164.
| PubMed |
Cooper M, Hammer GL
(1996) Synthesis of strategies for crop improvement. In ‘Plant adaptation and crop improvement’. (Eds M Cooper, GL Hammer)
pp. 591–623. (CAB International, ICRISAT & IRRI: Wallingford, UK)
Cooper M, Podlich DW, Smith OS
(2004) Complex traits and gene to phenotype models. In ‘Proceedings of the 4th International Crop Science Congress’. 26 Sept.–1 Oct. 2004, Brisbane, Australia. Invited Symposium Paper: ‘New Directions for a Diverse Planet’. (CD-ROM, Web site: http://www.w3.org/1999/xlink)
http://www.w3.org/1999/xlink
Cooper M,
Podlich DW, Smith OS
(2005) Gene-to-phenotype models and complex trait genetics. Australian Journal of Agricultural Research 56, 895–918.
Coors JG
(1999) Selection methodologies and heterosis. In ‘The genetics and exploitation of heterosis in crops’. (Eds JG Coors, S Pandey)
pp. 225–245. (ASA-CSSA-SSSA: Madison, WI)
Duvick DN,
Smith JSC, Cooper M
(2004) Long-term selection in a commercial hybrid maize breeding program. Plant Breeding Reviews 24, 109–151.
van Eeuwijk FA,
Malosetti M,
Yin X,
Struik PC, Stam P
(2005) Statistical models for genotype by environment data: from conventional ANOVA models to eco-physiological QTL models. Australian Journal of Agricultural Research 56, 883–894.
Falconer, DS (1960).
Falconer, DS ,
and
Mackay, TFC (1996).
Fehr, WR (Ed.) (1984).
Hallauer, AR ,
and
Miranda, JB (1988).
Hammer GL,
Chapman S,
van Oosterom E, Podlich DW
(2005) Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems. Australian Journal of Agricultural Research 56, 947–960.
Hammer GL,
Kropff MJ,
Sinclair TR, Porter JR
(2002) Future contributions of crop modelling—from heuristics and supporting decision-making to understanding genetic regulation and aiding crop improvement. European Journal of Agronomy 18, 15–31.
| Crossref | GoogleScholarGoogle Scholar |
Hanson, WD ,
and
Robinson, HF (1963).
Ideker T,
Thorsson V,
Ranish JA,
Christmas R,
Buhler J,
Eng JK,
Bum-garner R,
Goodlett DR,
Aebersold R, Hood L
(2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929–934.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Kearsey, MJ ,
and
Pooni, HS (1996).
Kuhn, TS (1996).
Lynch, M ,
and
Walsh, B (1998).
Mather, K ,
and
Jinks, JL (1971).
Niebur WS, Rafalski JA, Smith OS, Cooper M
(2004) Applications of genomics technologies to enhance rate of genetic progress for yield of maize within a commercial breeding program. Invited Symposium Paper: ‘New Directions for a Diverse Planet’. ‘New Directions for a Diverse Planet’. In ‘Proceedings of the 4th International Crop Science Congress’. 26 Sept.–1 Oct. 2004, Brisbane, Australia. (CD-ROM, Web site: http://www.w3.org/1999/xlink)
http://www.w3.org/1999/xlink
Reymond M,
Muller B,
Leonardi A,
Charcosset A, Tardieu F
(2003) Combining quantitative trait loci analysis and an ecophysiological model to analyse the genetic variability of the responses of leaf growth to temperature and water deficit. Plant Physiology 131, 664–675.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Sinclair TR, Seligman NG
(1996) Crop modelling: from infancy to maturity. Agronomy Journal 88, 698–704.
Sing CF,
Stengård JH, Kardia SLR
(2003) Genes, environment, and cardiovascular disease. Arteriosclerosis, Thrombosis, and Vascular Biology 23, 1190–1196.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Strohman RC
(1997) The coming Kuhnian revolution in biology. Nature Biotechnology 15, 194–200.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Tardieu F
(2003) Virtual plants: modelling as a tool for the genomics of tolerance to water deficit. Trends in Plant Science 8, 9–14.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Tardieu F,
Reymond M,
Muller B,
Granier C,
Simonneau T,
Sadok W, Welcker C
(2005) Linking physiological and genetic analyses of the control of leaf growth under changing environmental conditions. Australian Journal of Agricultural Research 56, 937–946.
Walsh B
(2005) The struggle to exploit non-additive variation. Australian Journal of Agricultural Research 56, 873–881.
Welch SM,
Dong Z,
Roe JL, Das S
(2005) Flowering time control: gene network modelling and the link to quantitative genetics. Australian Journal of Agricultural Research 56, 919–936.
Yin X,
Struik PC, Kropff MJ
(2004) Role of crop physiology in predicting gene-to-phenotype relationships. Trends in Plant Science 9, 426–432.
| Crossref | GoogleScholarGoogle Scholar | PubMed |