Biology Reference
In-Depth Information
Chapter 20
Arabidopsis as a Model for Systems
Biology
Philip N. Benfey 1 and Ben Scheres 2
1 Department of Biology and Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA, 2 Department of Biology, Utrecht University,
Padualaan 8, 3584 CH Utrecht, The Netherlands
Chapter Outline
Introduction
391
Mutual Support for Root Hair Patterning
399
Systems Analysis of Arabidopsis Development
392
Integrated Analysis of Shoot Development
399
Background
392
Gene Activity in Space and Time
399
Analysis of Gene Activity in Space and Time
393
Coupled Gene Regulatory Networks in the Shoot
400
The Use of Spatiotemporal Specific Expression Data to
Analyze Development
Modeling Regulatory Networks in the Shoot
400
393
Development and the Response to Environmental Stress
401
Toward an Understanding of the Dynamics of Asymmetric
Cell Division
Tissue-Specific Responses to Environment
401
397
A Major Challenge: The Transition to Flowering
402
Computational Modeling of Root Development
398
Conclusions and Perspective
403
Auxin Flow and Stem Cell Specification
398
References
404
INTRODUCTION
In this age of rapidly decreasing costs for genome-wide
assays, the question often arises, 'Are model systems still
all that useful?' The question is particularly raised for
plants, for which there are relatively few models and lots
of non-model plants that are valuable crops. At least in
the area of systems biology, the answer is still, 'Yes,
model systems are very useful.' Their utility arises from
the very nature of systems biology, which aims to
understand the dynamic connections among cellular
components. This is a very difficult problem to solve
owing to the number of components and the complexity
of their interactions. For the near future, at least, it is only
in model organisms that large quantities of information of
sufficient quality about cellular components can be
obtained. It is also of great benefit to have available
a broad and deep literature on a model organism to both
inform and potentially validate hypotheses generated
from systems level analyses.
Among plants, the leading model system for systems
biology work is Arabidopsis thaliana. It was originally
chosen as a favored model system for molecular genetic
analysis because of its rapid generation time, large number
of progeny and relatively small diploid genome. It was the
first plant to have its genome sequenced, and a large
number of genome-wide expression datasets have been
generated. An extensive library of insertional mutants has
facilitated the identification and characterization of many
genes. In the process, Arabidopsis research has contributed
to a vastly enhanced understanding of many basic plant
processes, including hormone production and response,
circadian rhythms, and plant growth and development. For
development, plants in general, and Arabidopsis in partic-
ular, have features that greatly simplify analysis. For
example, root and stem tissues are organized as concentric
cylinders of different types of cells ( Figure 20.1 ). Because
there is no cell movement, cellular positions are fixed with
respect to their neighbors.
In this chapter, we will not try to give an exhaustive
overview of systems-level analysis in Arabidopsis, but
instead discuss a few informative examples. We will focus
on the application of systems biology to development and to
the response to stress, in part because other productive areas,
such as circadian rhythm, are covered in other chapters.
 
 
 
 
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