Crops in silico

Generating virtual crops using an integrative and multi-scale modeling platform

Amy Marshall-Colon, Stephen P Long, Douglas K. Allen, Gabrielle Dawn Allen, Daniel A. Beard, Bedrich Benes, Susanne Von Caemmerer, A. J. Christensen, Donna J Cox, John C Hart, Peter M. Hirst, Kavya Kannan, Daniel S Katz, Jonathan P. Lynch, Andrew J. Millar, Balaji Panneerselvam, Nathan D. Price, Przemyslaw Prusinkiewicz, David Raila, Rachel G. Shekar & 9 others Stuti Shrivastava, Diwakar Shukla, Venkatraman Srinivasan, Mark Stitt, Matthew J Turk, Eberhard O. Voit, Yu Wang, Xinyou Yin, Xin Guang Zhu

Research output: Contribution to journalArticle

Abstract

Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (cropsinsilico.org), an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop.

Original languageEnglish (US)
Article number786
JournalFrontiers in Plant Science
Volume8
DOIs
StatePublished - May 15 2017

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crops
engineering
ecosystems
plant biology
climate models
plant breeding
food security
biochemical pathways
crop yield
weather
physiology
protein synthesis
prediction

Keywords

  • Computational framework
  • Crop yield
  • Integration
  • Model
  • Multiscale

ASJC Scopus subject areas

  • Plant Science

Cite this

Crops in silico : Generating virtual crops using an integrative and multi-scale modeling platform. / Marshall-Colon, Amy; Long, Stephen P; Allen, Douglas K.; Allen, Gabrielle Dawn; Beard, Daniel A.; Benes, Bedrich; Von Caemmerer, Susanne; Christensen, A. J.; Cox, Donna J; Hart, John C; Hirst, Peter M.; Kannan, Kavya; Katz, Daniel S; Lynch, Jonathan P.; Millar, Andrew J.; Panneerselvam, Balaji; Price, Nathan D.; Prusinkiewicz, Przemyslaw; Raila, David; Shekar, Rachel G.; Shrivastava, Stuti; Shukla, Diwakar; Srinivasan, Venkatraman; Stitt, Mark; Turk, Matthew J; Voit, Eberhard O.; Wang, Yu; Yin, Xinyou; Zhu, Xin Guang.

In: Frontiers in Plant Science, Vol. 8, 786, 15.05.2017.

Research output: Contribution to journalArticle

Marshall-Colon, A, Long, SP, Allen, DK, Allen, GD, Beard, DA, Benes, B, Von Caemmerer, S, Christensen, AJ, Cox, DJ, Hart, JC, Hirst, PM, Kannan, K, Katz, DS, Lynch, JP, Millar, AJ, Panneerselvam, B, Price, ND, Prusinkiewicz, P, Raila, D, Shekar, RG, Shrivastava, S, Shukla, D, Srinivasan, V, Stitt, M, Turk, MJ, Voit, EO, Wang, Y, Yin, X & Zhu, XG 2017, 'Crops in silico: Generating virtual crops using an integrative and multi-scale modeling platform', Frontiers in Plant Science, vol. 8, 786. https://doi.org/10.3389/fpls.2017.00786
Marshall-Colon, Amy ; Long, Stephen P ; Allen, Douglas K. ; Allen, Gabrielle Dawn ; Beard, Daniel A. ; Benes, Bedrich ; Von Caemmerer, Susanne ; Christensen, A. J. ; Cox, Donna J ; Hart, John C ; Hirst, Peter M. ; Kannan, Kavya ; Katz, Daniel S ; Lynch, Jonathan P. ; Millar, Andrew J. ; Panneerselvam, Balaji ; Price, Nathan D. ; Prusinkiewicz, Przemyslaw ; Raila, David ; Shekar, Rachel G. ; Shrivastava, Stuti ; Shukla, Diwakar ; Srinivasan, Venkatraman ; Stitt, Mark ; Turk, Matthew J ; Voit, Eberhard O. ; Wang, Yu ; Yin, Xinyou ; Zhu, Xin Guang. / Crops in silico : Generating virtual crops using an integrative and multi-scale modeling platform. In: Frontiers in Plant Science. 2017 ; Vol. 8.
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AU - Beard, Daniel A.

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AU - Shukla, Diwakar

AU - Srinivasan, Venkatraman

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AU - Turk, Matthew J

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