Developmental Dynamics and Early Growth Vigour in Rice 2. Modelling Genetic Diversity Using Ecomeristem

Journal of Agronomy and Crop Science

Volumn 198, Issue 5, 2012, Pages 385-398

  Luquet, D ^a   Soulie J C ^a   Rebolledo, M C ^a   Rouan, L ^a   Clement Vidal A ^a   Dingkuhn, M ^a  

^a UMR AGAP   (France)

Author keywords

Development rate; Early vigour; Genetic diversity; Modelling; Morphogenesis; Oryza sativa L; Sensitivity analysis

Indexed keywords

AGRICULTURAL MODELING; DEVELOPMENTAL BIOLOGY; GENETIC VARIATION; MORPHOGENESIS; REPRODUCTIVE BEHAVIOR; RICE; SENSITIVITY ANALYSIS; SOURCE-SINK DYNAMICS; VIGOR;

ORYZA SATIVA;

EID: 84866167040     PISSN: 09312250     EISSN: 1439037X     Source Type: Journal    
DOI: 10.1111/j.1439-037X.2012.00527.x     Document Type: Article

References (66)

1. Ahmadi, N., D. Luquet, B. Courtois, and M. Dingkuhn, 2008: Mapping QTL involved in rice early morphogenesis as described by the process based parameters of EcoMeristem model. In: D. Luquet, ed. Whole Plant Physiology Modelling Project: Final Meeting. Generation challenge programme, Johnston, IA, USA.
2. Andrieu, B., J. Hillier, and C. Birch, 2006: Onset of sheath extension and duration of lamina extension are major determinants of the response of maize lamina length to plant density. Ann. Bot. 98, 1005-1016.
3. Asai, K., N. Satoh, H. Sasaki, H. Satoh, and Y. Nagato, 2002: A rice heterochronic mutant, mori1, is defective in the juvenile-adult phase change. Development 129, 265-273.
4. Asseng, S., N. C. Turner, J. D. Ray, and B. A. Keating, 2002: A simulation analysis that predicts the influence of physiological traits on the potential yield of wheat. Eur. J. Agron. 17, 123-141.
5. Asseng, S., N. C. Turner, T. L. Botwright, and A. G. Condon, 2003: Evaluating the impact of a trait for increased specific leaf area on wheat yields using a crop simulation model. Agron. J. 95, 10-19.
6. Beemster, G. T. S., and J. Masle, 1996: Effects of soil resistance to root penetration on leaf expansion in wheat (Triticum aestivum L.): composition, number and size of epideraml cells in mature blades. J. Exp. Bot. 47, 1651-1662.
7. Birch, C. J., J. Vos, J. Kiniry, H. J. Bos, and A. Elings, 1998: Phyllochron responds to acclimation to temperature and irradiance in mairze. Field Crops Res. 59, 187-200.
8. Boote, K. J., J. W. Jones, W. D. Batchelor, E. D. Nafziger, and O. Myers, 2003: Genetic coefficients in the CROPGRO-Soybean model: links to field performance and genomics. Agron. J. 95, 32-113.
9. Brisson, N., B. Mary, D. Ripoche, M. H. Jeuffroy, F. Ruget, P. Gate, and F. Devienne-Barret, 1998: STICS: a generic model for the simulation of crops and their water and nitrogen balance. I- Theory and parameterization applied to wheat and corn. Agron. 18, 311-346.
10. Chapman, S., M. Cooper, D. Podlich, and G. Hammer, 2003: Evaluating plant breeding strategies by simulating gene action and dryland environment effects. Agron. J. 95, 99-113.
11. Chenu, K., S. Chapman, G. L. Hammer, G. McLean, and F. Tardieu, 2007: Translating short-term environmental effects on leaf growth rate into differences in whole-plant profiles of maize leaf area: impact of temperature, evaporative demand and soil water status. Agronomics. Supagro, Montpellier.
12. Chenu, K., S. C. Chapman, F. Tardieu, G. McLean, C. Welcker, and G. L. Hammer, 2009: Simulating the Yield Impacts of Organ-Level Quantitative Trait Loci Associated With Drought Response in Maize: A "Gene-to-Phenotype" Modeling Approach. Genetics 183, 1507-1523.
13. Clerget, B., M. Dingkuhn, E. Goze, H. F. W. Rattunde, and B. Ney, 2008: Variability of phyllochron, plastochron and rate of increase in height in photoperiod-sensitive sorghum varieties. Ann. Bot. 101, 579-594.
14. Cooper, M., and O. S. Smith, 2005: Gene to phenotype models and complex trait genetics. Aust. J. Agric. Res. 56, 895-918.
15. Dingkuhn, M., 1996: Modelling concepts for the phenotypic plasticity of dry matter and nitrogen partitioning in rice. Agric. Syst. 52, 383-397.
16. Dingkuhn, M., D. E. Johnson, A. Sow, and A. Y. Audebert, 1999: Relationships between upland rice canopy characteristics and weed competitiveness. Field Crops Res. 61, 79-95.
17. Dingkuhn, M., C. Baron, V. Bonnal, F. Maraux, B. Sarr, B. Sultan, A. Clopes, and F. Forest (2003) Decision support tools for rainfed crops in the Sahel at the plot and regional scales. In: T. Wopereis, ed. Decision Support Tools for Smallholder Agriculture in Sub-Saharian Africa - A Practical Guide, pp. 127-139. IFDC & CTA, Wageningen, the Netherland.
18. Dingkuhn, M., D. Luquet, B. Quilot, and P. D. Reffye, 2005: Environmental and genetic control of morphogenesis in crops: towards models simulating phenotypic plasticity. Aust. J. Agric. Res. 56, 1-14.
19. Dingkuhn, M., D. Luquet, H. K. Kim, L. Tambour, and A. Clément-Vidal, 2006: Ecomeristem, a model of morphogenesis and competition among sinks in rice: 2. simulating genotype responses to phosphorus deficiency. Funct. Plant Biol. 33, 325-337.
20. Drenth H., F. Berge, and J. J. M. Riethoven (eds), 1994: Oriza Simulation Modules for Potential and Nitrogen Limited Rice Production. SARP Research Proceedings. Wageningen, the Netherland.
21. Drouet, J. L., and L. Pagès, 2003: GRAAL: a model of Growth, Architecture and carbon ALlocation during vegetative phase of the whole plant: model description and parameterisation. Ecol. Model. 165, 147-173.
22. Fiorani, F., T. Beemster, L. Bultynck, and H. Lambers, 2000: Can meristematic activity determine variation in leaf size and elongation rate among Poa species? A kinematic study. Plant Physiol. 124, 845-855.
23. Fourcaud, T., X. Zhang, A. Stokes, H. Lambers, and C. Körner, 2008: Plant growth modelling and applications: the increasing importance of plant architecture in growth models. Ann. Bot. 101, 1053-1063.
24. Granier, C., and F. Tardieu, 1999: Leaf expansion and cell division are affected by reducing absorbed light before but not after the decline in cell division rate in sunflower leaf. Plant Cell Environ. 22, 1365-1376.
25. Granier, C., and F. Tardieu, 2009: Multi-scale phenotyping of leaf expansion in response to environmental changes: the whole is more than the sum of parts. Plant Cell Environ. 62, 1175-1184.
26. Hammer, G. L., M. J. Kropff, T. R. Sinclair, and J. R. Porter, 2002: Future contributions of crop modelling - from heuristics and supporting decision making to understanding genetic regulation and aiding crop improvement. Eur. J. Agron. 18, 15-31.
27. Hammer, G. L., S. Chapman, E. Van Oosterom, and D. W. Poldich, 2005: Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems. Aust. J. Agric. Res. 56, 947-960.
28. Hammer, G., E. van Oosterom, G. McLean, C. Chapman, I. Broad, P. Harland, and R. C. Muchow, 2010: Adapting APSIM to model the physiology and genetics of complex adaptive traits in field crops. J. Exp. Bot. 61, 2185-2202.
29. Heinemann, A. B., M. Dingkuhn, D. Luquet, J. C. Combres, and S. Chapman, 2008: Characterization of drought stress environments for upland rice and maize in central Brazil. Euphytica 162, 395-410.
30. Hemmerling, R., O. Kniemeyer, D. Lanwert, W. Kurth, and G. Buck-Sorlin, 2008: The rule-based language XL and the modelling environment GroIMP illustrated with simulated tree competition. Funct. Plant Biol. 35, 739-750.
31. Hammer, G., E. van Oosterom, G. McLean, C. Chapman, I. Broad, P. Harland, and R. C. Muchow, 2010: Adapting APSIM to model the physiology and genetics of compledx adaptive traits in field crops. J. Exp. Bot. 61, 2185-2202.
32. Hoogenboom, G., and J. W. White, 2003: Improving physiological assumptions of simulation models by using gene-based approaches. Agron. J. 95, 82-113.
33. Itoh, J. I., A. Hasegawa, H. Kitano, and Y. Nagato, 1998: A recessive heterochronic mutation, plastochron 1, shortens the plastochron and elongates the vegetative phase in rice. Plant Cell 10, 1511-1521.
34. Jones, J. W., G. Hoogenboom, C. H., Porter, K. J. Boote, W. D. Batchelor, L. A. Hunt, P. W. Wilkens, U. Singh, A. J. Gidjsman, and J. T. Ritchie, 2003: The DSSAT cropping system model. Eur. J. Agron. 18, 235-265.
35. Jullien, A., A. Mathieu, J. M. Allirand, A. Pinet, P. H. Cournède, and B. Ney, 2010: Characterization of the interactions between architecture and source-sink relationships in winter oilseed rape (Brassica napus) using the GreenLab model. Ann. Bot. 107, 765-779. Online.
36. Kimmel, P., 2001: Building Delphi 6 Applications. McGraw-Hill Eds, p. 774.
37. Komatsu, K., M. Maekawa, S. Ujiie, Y. Satake, I. Furutani, and H. Okomato, 2003: LAX and SPA: major regulators of shoot branching. PNAS 100, 11765-11770.
38. Kouressy, M., M. Dingkuhn, M. Vaksmann, A. Clément-Vidal, and J. Chantereau, 2008: Potential contribution of dwarf and leaf longevity traits to yield improvement in photoperiod sensitive sorghum. Eur. J. Agron. 28, 195-209.
39. Lafarge, T., C. Seassau, M. Martin, C. Bueno, A. Clément-Vidal, E. Shrek, and D. Luquet, 2010: Regulation and recovery of sink strength in rice plants grown under changes in light intensity. Funct. Plant Biol. 37, 418-423.
40. Luquet, D., M. Dingkuhn, H. K. Kim, L. Tambour, and A. Clément-Vidal, 2006: Ecomeristem, a model of morphogenesis and competition among sinks in rice. 1. concept, validation and sensitivity analysis. Funct. Plant Biol. 33, 309-323.
41. Luquet, D., Y. H. Song, S. Elbelt, D. This, A. Clément-Vidal, C. Périn, D. Fabre, and M. Dingkuhn, 2007: Model-assisted physiological analysis of Phyllo, a rice architectural mutant. Funct. Plant Biol. 34, 11-23.
42. Miyamoto, N., Y. Goto, M. Matsui, Y. Ukai, M. Morita, and K. Nemoto, 2004: Quantitative trait loci for phyllochron and tillering in rice. Theor. Appl. Genet. 109, 700-706.
43. Miyoshi, K., B. O. Ahn, T. Kawakatsu, Y. Ito, J. I. Itoh, Y. Nagato, and N. Kurata, 2004: PLASTOCHRON1, a timekeeper of leaf initiation in rice, encodes cytochrome P450. PNAS 101, 101, 875-880.
44. Morita, M., D. Tang, N. Miyamoto, Y. Goto, Y. Ukai, and K. Nemoto, 2005: Quantitative trait loci for rice phyllochron in Lemont × IR36 cross. Plant Prod. Sci. 8, 199-202.
45. Osone, Y., A. Ishida, and T. Masaki, 2008: Correlation between relative growth rate and specific leaf area requires associations of specific leaf area with nitrogen absorption rate of roots export by: Yoko Osone, Atsushi Ishida, Masaki Tateno. New Phytol. 179, 417-427.
46. Ouknider, M., P. Jacquard, and D. Elkhyari, 1991: Concurrence chez Vicia sativa L et Avena sativa L. I. Effets des contraintes hydriques et nutritionnelles sur la morphogenèse et la démographie des organes. Agronomie 11, 447-456.
47. Poorter, H., 1999: Growth responses of 15 rain-forest tree species to a light gradient: the relative importance of morphological and physiological traits. Funct. Ecol. 13, 396-410.
48. Pradal, C., S. Dufour-Kowalski, F. Boudon, C. Fournier, and C. Godin, 2008: OpenAlea: a visual programming and component-based software platform for plant modelling. Funct. Plant Biol. 35, 751-760.
49. R Development C-T, 2005: R: A Language and Environment for Statistical Computing, Reference Index Version 2.9.2. R Foundation for Statistical Computing, Vienna, Austria.
50. Rebetzke, G. J., and R. A. Richards, 1999: Genetic improvement of early vigour in wheat. Aust. J. Agric. Res. 50, 291-302.
51. Rebetzke, G. J., T. L. Botwright, C. S. Moore, R. A. Richards, and A. G. Condon, 2004: Genotypic variation in specific leaf area for genetic improvement of early vigour in wheat. Field Crops Res. 88, 179-189.
52. Rebetzke, G. J., R. A. Richards, N. A. Fettell, M. Long, A. G. Condon, R. I. Forrester, and T. L. Botwright, 2007: Genotypic increases in coleoptile length improves stand establishment, vigour and grain yield of deep-sown wheat. Field Crops Res. 100, 10-23.
53. Rebolledo, M. C., M. Dingkuhn, K. Mc Nally, and D. Luquet, 2012: Developmental dynamics and early growth vigour in rice. I. Relationship between development rate (1/Phyllochron) and growth. J. Agron. Crop Sci. 198, 374-384.
54. Rognoni, S., S. Teng, L. Arru, S. C. M. Smeekens, and P. Perata, 2007: Sugar effects on early seedling development in Arabidopsis. Plant Growth Regul. 52, 217-228.
55. Rolland, F., E. Baena-Gonzalez, and J. Sheen, 2006: Sugar sensing and signaling in plants: conserved and novel mechanisms. Annu. Rev. Plant Biol. 57, 675-709.
56. Saltelli, A., S. Tarantola, and K. Chan, 1999: A quantitative, model independent method for global sensitivity analysis of model output. Technometrics 41, 39-56.
57. Sekhon, S., and W. R. Mebane, Jr, 2011: Genetic optimization using derivatives: The rgenoud package for R. Journal of Statistical Software, 42, p. 26.
58. Shipley, B., 2006: Net assimilation rate, specific leaf area and leaf mass ratio: which is most closely correlated with relative growth rate? A meta-analysis. Funct. Ecol. 20, 565-574.
59. Steege, M. W., F. M. den Ouden, H. Lambers, P. Stam, and A. J. M. Peeters, 2005: Genetic and physiological architecture of early vigor in Aegilops tauschii, the D-Genome donor of hexaploid wheat. A Quantitative Trait Loci Analysis. Plant Physiol. 139, 1078-1094.
60. Stitt, M., Y. Gibon, J. E. Lunn, and M. Piques, 2007: Multilevel genomics analysis of carbon signalling during low carbon availability: coordinating the supply and utilisation of carbon in a fluctuating environment. Funct. Plant Biol. 34, 526-549.
61. Tisné, S., M. Reymond, D. Vile, J. Fabre, M. Dauzat, M. Koornneef, and C. Granier, 2008: Combined genetic and modeling approaches reveal that epidermal cell area and number in leaves are controlled by leaf and plant developmental processes in Arabidopsis. Plant Physiol. 148, 1117-1127.
62. Wang, E., M. J. Robertson et al., 2002: Development of a generic crop model template in the cropping system model APSIM. Eur. J. Agron. 18, 121-140.
63. Xu, L., M. Henke, J. Zhu, W. Kurth, and G. Buck-Sorlin, 2011: A functional structural model of rice linking quantitative genetic information with morphological development and physiological processes. Ann. Bot. 107, 817-828.
64. Yan, H. P., M. Z. Kang, P. D. Reffye, and M. Dingkuhn, 2004: A dynamic, architectural plant model simulating resource-dependent growth. Ann. Bot. 93, 591-602.
65. Yin, X., P. Stam, M. J. Kropff, and A. H. C. M. Schapendonk, 2003: Crop modeling, QTL mapping, and their complementary role in plant breeding. Agron. J. 95, 90-113.
66. Zou, J., Z. Chen, S. Zhang, W. Zhang, G. Jiang, X. Zhao, W. Zhai, X. Pan, and L. Zhu, 2005: Characterizations and fine mapping of a mutant gene for high tillering and dwarf in rice (Oryza sativa L.). Planta 222, 604-612.