Applying modelling experiences from the past to shape crop systems biology: The need to converge crop physiology and functional genomics

New Phytologist

Volumn 179, Issue 3, 2008, Pages 629-642

  Yin, Xinyou ^a   Struik, Paul C ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Biological scales; Crop improvement; Crop phenotypes; Modelling; Systems biology

Indexed keywords

CROP IMPROVEMENT; GENETIC ENGINEERING; GENOMICS; HEURISTICS; MODELING; PHYSIOLOGY;

ALGORITHM; BIOLOGICAL MODEL; CROP; ENVIRONMENT; GENE; GENETICS; GENOMICS; GROWTH, DEVELOPMENT AND AGING; INBREEDING; PHENOTYPE; PHOTOSYNTHESIS; REVIEW; SYSTEMS BIOLOGY;

ALGORITHMS; CROPS, AGRICULTURAL; ENVIRONMENT; GENES, PLANT; GENOMICS; INBREEDING; MODELS, BIOLOGICAL; PHENOTYPE; PHOTOSYNTHESIS; SYSTEMS BIOLOGY;

EID: 48249136116     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2008.02424.x     Document Type: Review

References (87)

1. Aggarwal PK, Kropff MJ, Cassman KG, ten Berge HFM. 1997. Simulating genotypic strategies for increasing rice yield potential in irrigated, tropical environments. Field Crops Research 51 : 5 17.
2. 2 concentration on soybean gene expression. An analysis of growing and mature leaves. Plant Physiology 142 : 135 147.
3. Ashikari M, Sakakibara H, Lin S, Yamamoto K, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M. 2005. Cytokinin oxidase regulates rice grain production. Science 309 : 741 745.
4. Bernardo R. 2001. What if we knew all the genes for a quantitative trait in hybrid crops? Crop Science 41 : 1 4.
5. von Bertalanffy L. 1933. Modern theories of development: an introduction to theoretical biology. Oxford, UK : University Press.
6. von Bertalanffy L. 1969. General systems theory; foundation, development, applications. New York, NY, USA : George Braziller.
7. Bindraban PS. 1997. Bridging the gap between plant physiology and breeding: identifying traits to increase wheat yield potential using systems approaches. PhD thesis, Wageningen Agricultural University, the Netherlands.
8. Boote KJ, Kropff MJ, Bindraban PS. 2001. Physiology and modelling of traits in plants: implications for genetic improvement. Agricultural Systems 70 : 395 420.
9. von Caemmerer S, Farquhar GD. 1981. Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves. Planta 153 : 376 387.
10. 4 plant biology. Toronto, Canada : Academic Press, 173 211.
11. Cassman KG. 1999. Ecological intensification of cereal production systems: yield potential, soil quality, and precision agriculture. Proceedings of the National Academy of Sciences, USA 96 : 5952 5959.
12. Chapman S, Cooper M, Podlich D, Hammer GL. 2003. Evaluating plant breeding strategies by simulating gene action and dryland environment effects. Agronomy Journal 95 : 99 113.
13. Cooper M, Hammer GL. 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 : 869 872.
14. Corbesier L, Coupland G. 2006. The quest for florigen: a review of recent progress. Journal of Experimental Botany 57 : 3395 3403.
15. Corbesier L, Vincent C, Jang S, Fornara F, Fan Q, Searle I, Giakkountis A, Farrona S, Gissot L, Turnbull C et al. 2007. FT protein movement contributes to long-distance signalling in floral induction of Arabidopsis. Science 316 : 1030 1033.
16. Cremer F, Coupland G. 2003. Distinct photoperiodic responses are conferred by the same genetic pathway in Arabidopsis and in rice. Trends in Plant Science 8 : 405 407.
17. Dua AB, Penning de Vries FWT, Seshu DV. 1990. Simulation to support evaluation of the production potential of rice varieties in tropical climates. Transactions of American Society of Agricultural Engineers 33 : 1185 1194.
18. Dwivedi SL, Crouch JH, Mackill DJ, Xu Y, Blair MW, Ragot M, Upadhyaya HD, Ortiz R. 2007. The molecularization of public sector crop breeding: progress, problems and prospects. Advances in Agronomy 95 : 163 318.
19. Evans JR. 1983. Nitrogen and photosynthesis in the flag leaf of wheat (Triticum aestivum L.). Plant Physiology 72 : 297 302.
20. 3 species. Planta 149 : 78 90.
21. Field C. 1983. Allocating leaf nitrogen for the maximization of carbon gain: leaf age as a control on the allocation program. Oecologia 56 : 341 347.
22. Fischer RA. 2007. Understanding the physiological basis of yield potential in wheat. Journal of Agricultural Science Cambridge 145 : 99 113.
23. Forrester JW. 1961. Industrial dynamics. Cambridge, MA, USA : MIT Press.
24. Gutiérrez RA, Shasha DE, Coruzzi GM. 2005. System biology for the virtual plant. Plant Physiology 138 : 550 554.
25. Hammer G, Cooper M, Tardieu F, Welch S, Walch B, van Eeuwijk F, Chapman S, Podlich D. 2006. Models for navigating biological complexity in breeding improved crop plants. Trends in Plant Science 11 : 587 593.
26. Hammer GL, Sinclair TR, Chapman SC, van Oosterom E. 2004. On systems thinking, systems biology, and the in silico plants. Plant Physiology 134 : 909 911.
27. Hirel B, Bertin P, Quilleré I, Bourdoncle W, Attagnant C, Dellay C, Gouy A, Cadiou S, Retailliau C, Falque M et al. 2001. Towards a better understanding of the genetic and physiological basis for nitrogen use efficiency in maize. Plant Physiology 125 : 1258 1270.
28. Hood L. 1998. Systems biology: new opportunities arising from genomics, proteomics and beyond. Experimental Hematology 26 : 681.
29. Ideker T, Galitski T, Hood L. 2001. A new approach to decoding life: systems biology. Annual Review of Genomics and Human Genetics 2 : 343 372.
30. Imaizumi T, Kay SA. 2006. Photoperiodic control of flowering: not only by coincidence. Trends in Plant Science 11 : 550 558 (erratum in 11: 567).
31. Jarvis PG. 1976. The interpretation of the variations in leaf water potential and stomatal conductance found in canopies in the field. Philosophical Transactions of the Royal Society of London Series B - Biological Sciences 273 : 593 610.
32. 3 plants: facts or artefacts? Journal of Experimental Botany 56 : 407 416.
33. Karaba A, Dixit S, Greco R, Aharoni A, Trijatmiko KR, Marsch-Martinez N, Krishnan A, Nataraja KN, Udayakumar M, Pereira A. 2007. Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene. Proceedings of the National Academy of Sciences, USA 104 : 15270 15275.
34. Kitano H. 2002. Systems biology: a brief overview. Science 295 : 1662 1664.
35. Koornneef M, Alonso-Blanco C, Peeters AJM, Soppe W. 1998. Genetic control of flowering time in Arabidopsis. Annual Review of Plant Physiology and Plant Molecular Biology 49 : 345 370.
36. Kropff MJ, Bouma J, Jones JW. 2001. Systems approaches for the design of sustainable agro-ecosystems. Agricultural Systems 70 : 369 393.
37. Kropff MJ, Haverkort AJ, Aggarwal PK, Kooman PL. 1995. Using systems approaches to design and evaluate ideotypes for specific environments. In : Bouma J, Kuyvenhoven A, Bouman BAM, Luyten JC, Zandstra HG, eds. Eco-regional approaches for sustainable land use and food production. Dordrecht, the Netherlands : Kluwer Academic Publishers, 417 435.
38. 3 photosynthesis in silico. Photosynthesis Research 90 : 45 66.
39. Lawlor DW. 2003. Carbon and nitrogen assimilation in relation to yield: mechanisms are the key to understanding production systems. Journal of Experimental Botany 53 : 773 787.
40. 3 plants. Plant, Cell & Environment 18 : 339 355.
41. 2 concentrations. Science 312 : 1918 1921.
42. 2 enrichment. Journal of Experimental Botany 51 : 383 389.
43. Miflin B. 2000. Crop improvement in the 21st century. Journal of Experimental Botany 51 : 1 8.
44. Minorsky PV. 2003. Achieving the in silico plant. Systems biology and the future of plant biological research. Plant Physiology 132 : 404 409.
45. Mitchell PL, Sheehy JE. 2006. Supercharging rice photosynthesis to increase yield. New Phytologist 171 : 688 693.
46. Nakagawa H, Yamagishi J, Miyamoto N, Motoyamo M, Yano M, Nemoto K. 2005. Flowering response of rice to photoperiod and temperature: a QTL analysis using a phenological model. Theoretical and Applied Genetics 110 : 778 786.
47. Nemhauser JL, Maloof JN, Chory J. 2003. Building integrated models of plant growth and development. Plant Physiology 132 : 436 439.
48. 3 photosynthesis: a contribution from nitrate assimilation and its associated respiratory activity? Journal of Experimental Botany 49 : 1895 1908.
49. Normile D. 1999. Crossing rice strains to keep Asia's rice bowls brimming. Science 283 : 313.
50. Passioura JB. 1979. Accountability, philosophy and plant physiology. Search 10 : 347 350.
51. Penning de Vries FWT, Jansen DM, ten Berge HFM, Bakema A. 1989. Simulation of ecophysiological processes of growth in several annual crops. Wageningen, the Netherlands : Pudoc.
52. Quilot B, Kervella J, Génard M, Lescourret F. 2005. Analysing the genetic control of peach fruit quality through an ecophysiological model combined with a QTL approach. Journal of Experimental Botany 56 : 3083 3092.
53. Reymond M, Muller B, Leonardi A, Charcosset A, Tardieu F. 2003. Combining quantitative trait loci analysis and an ecophysiological model to analyze the genetic variability of the responses of maize leaf growth to temperature and water deficit. Plant Physiology 131 : 664 675.
54. Setter TL, Conocono EA, Egdane JA, Kropff MJ. 1995. Possibility of increasing yield potential of rice by reducing panicle height in the canopy. I. Effects of panicles on light interception and canopy photosynthesis. Australian Journal of Plant Physiology 22 : 441 451.
55. Setter TL, Peng S, Kirk GJD, Virmani SS, Kropff MJ, Cassman KG. 1994. Physiological considerations and hybrid rice. In : Cassman KG, ed. Breaking the yield barrier. Proceedings of a workshop on rice yield potential in favorable environments. Los Baños, Philippines : International Rice Research Institute, 39 62.
56. Sinclair TR, Horie H. 1989. Leaf nitrogen, photosynthesis, and crop radiation use efficiency: a review. Crop Science 29 : 90 98.
57. Sinclair TR, Purcell LC, Sneller CH. 2004. Crop transformation and the challenge to increase yield potential. Trends in Plant Science 9 : 70 75.
58. Sinclair TR, de Wit CT. 1975. Photosynthate and nitrogen requirements for seed production by various crops. Science 189 : 565 567.
59. Song X-J, Huang W, Shi M, Zhu M-Z, Lin H-X. 2007. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nature Genetics 39 : 623 630.
60. Spiertz JHJ, Struik PC, van Laar HH. 2007. Scale and complexity in plant systems research: gene-plant-crop relations. Dordrecht, the Netherlands : Springer.
61. Struik PC, Cassman KG, Koornneef M. 2007. A dialogue on interdisciplinary collaboration to bridge the gap between plant genomics and crop sciences. In : Spiertz JHJ, Struik PC, van Laar HH, eds. Scale and complexity in plant systems research: gene-plant-crop relations. Dordrecht, the Netherlands : Springer, 319 328.
62. Tamaki S, Matsuo S, Wong HL, Yokoi S, Shimamoto K. 2007. Hd3a protein is a mobile flowering signal in rice. Science 316 : 1033 1036.
63. Tardieu F. 2003. Virtual plants: modelling as a tool for the genomics of tolerance to water deficit. Trends in Plant Science 8 : 9 14.
64. Tuberosa R, Salvi S. 2006. Genomics-based approaches to improve drought tolerance of crops. Trends in Plant Science 11 : 405 411.
65. Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J. 2006. A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 314 : 1298 1301.
66. Weiss A. 2003. Introduction to the papers presented at the symposium 'Crop Modeling and Genomics'. Agronomy Journal 95 : 1 3.
67. Welch SM, Roe JL, Dong Z. 2003. Genetic neural network model of flowering time control in Arabidopsis thaliana. Agronomy Journal 95 : 71 81.
68. White JW, Hoogenboom G. 1996. Simulating effects of genes for physiological traits in a process-oriented crop model. Agronomy Journal 88 : 416 422.
69. White JW, Hoogenboom G. 2003. Gene-based approach to crop simulation: past experiences and future opportunities. Agronomy Journal 95 : 52 64.
70. White JW, McMaster GS, Edmeades GO. 2004. Physiology, genomics and crop response to global change. Field Crops Research 90 : 1 3.
71. de Wit CT. 1965. Photosynthesis of leaf canopy. Agricultural Research Report 663. Wageningen, the Netherlands : Pudoc.
72. de Wit CT. 1978. Simulation of assimilation, respiration and transpiration of crops. Wageningen, the Netherlands : Pudoc.
73. Wollenweber B, Porter JR, Lubberstedt T. 2005. Need for multidisciplinary research towards a second Green Revolution. Current Opinion in Plant Biology 8 : 337 341.
74. 2 concentrations on plants. Current Opinion in Plant Biology 5 : 207 211.
75. Yan L, Fu D, Li C, Belchl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J. 2006. The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proceedings of the National Academy of Sciences, USA 103 : 19581 19586.
76. Yano M, Kojima S, Takahashi Y, Lin H, Sasaki T. 2001. Genetic control of flowering time in rice, a short-day plant. Plant Physiology 127 : 1425 1429.
77. Yin X, Chasalow S, Stam P, Kropff MJ, Dourleijn CJ, Bos I, Bindraban PS. 2002. Use of component analysis in QTL mapping of complex crop traits: a case study on yield in barley. Plant Breeding 121 : 314 319.
78. 3 photosynthesis under limiting light. Plant, Cell & Environment 29 : 1771 1782 (corrigendum in 29: 2252).
79. 3 photosynthesis: development and applications. In : Laisk A, Nedbal L, Govindjee, eds. Photosynthesis in silico: understanding complexity from molecules to ecosystems. Advances in Photosynthesis and Respiration. Dordrecht, the Netherlands : Springer.
80. Yin X, Kropff MJ, Ynalvez MA. 1997. Photoperiodically sensitive and insensitive phases of preflowering development in rice. Crop Science 37 : 182 190.
81. Yin X, van Laar HH. 2005. Crop systems dynamics: an ecophysiological simulation model for genotype-by-environment interactions. Wageningen, the Netherlands : Wageningen Academic Publishers.
82. Yin X, Schapendonk AHCM, Kropff MJ, van Oijen M, Bindraban PS. 2000. A generic equation for nitrogen-limited leaf area index and its application in crop growth models for predicting leaf senescence. Annals of Botany 85 : 579 585.
83. Yin X, Stam P, Dourleijn CJ, Kropff MJ. 1999. AFLP mapping of quantitative trait loci for yield-determining physiological characters in spring barley. Theoretical and Applied Genetics 99 : 244 253.
84. Yin X, Struik PC. 2007. Crop systems biology: an approach to connect functional genomics with crop modelling. In : Spiertz JHJ, Struik PC, van Laar HH, eds. Scale and complexity in plant systems research: gene-plant-crop relations. Dordrecht, the Netherlands : Springer, 61 71.
85. Yin X, Struik PC, van Eeuwijk FA, Stam P, Tang J. 2005. QTL analysis and QTL-based prediction of flowering phenology in recombinant inbred lines of barley. Journal of Experimental Botany 56 : 967 976.
86. Yin X, Struik PC, Kropff MJ. 2004. Roles of crop physiology in predicting gene-to-phenotype relationships. Trends in Plant Science 9 : 426 432.
87. Zhu X-G, Ort DR, Whitmarsh J, Long SP. 2004. The slow reversibility of photosystem II thermal energy dissipation on transfer from high to low light may cause large losses in canopy gain by crop canopies: a theoretical analysis. Journal of Experimental Botany 55 : 1167 1175.