Arabidopsis Functional Genomics:

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Arabidopsis Functional Genomics From Sequenced
Model Genome to Improved Crop Species Rebecca
Joy SEE Conference November 19, 2002
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What is Arabidopsis?
(and why should you care?)
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Brassicaceae Mustard Family
Over 100 other genera
Arabidopsis thaliana
Brassica
Raphanus
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• Small - 8 to 12 inches tall
• Fast life cycle - 6 weeks from seed to seed
• Self-fertilizing
• Makes thousands of seeds per plant
• Not particular about growth conditions
• Small, relatively succinct genome

Photo Credit Luca Comai
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DNA content
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Two Important Facts About Arabidopsis

• It can be transformed easily
• Its entire genome has been sequenced, and the
  sequence is freely available

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Transformation A Key Advantage
Transformation the ability to add heterologous
DNA to an organism and express it there
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Agrobacterium tumefaciens
Artificial T-DNA
Transformed Agrobacterium


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A Sequenced Genome
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Tool Satellite Imaging
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Tool The Sequence of Arabidopsis
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Sequence Transformation Reverse Genetics
Forward Genetics Phenotype (function) to Gene
(sequence)
Reverse Genetics Gene (sequence) to Phenotype
(function)
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Functional Genomics

• Using the sequence as a tool to discover the
  functions of all the genes in an organism
• Determining all the functions required for a
  plant to live, AND for any given process
• Process examples
• Biosynthesis
• Reproduction seed production
• Responses to stress

? ? ? Crop Improvements
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How will all of this lead to improved crops?

• Determination of gene functions in Arabidopsis
• Interactions between pathogens and plant
• Tolerance to environmental factors drought,
  high salinity, high CO2 levels
• Learning which versions of genes will help us to
  reach a particular goal with crop plants
• Learning what to look for to transform or
  introgress into crop varieties
• Testing the effect of different treatments and
  heterologous genes in plants
• Time scale and the model idea

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Examples
Glutamine Synthase (GS) Goal Improvement of
nitrogen use efficiency reduced dependence on
fertilizers, higher yields, higher protein
content in crops 20-fold increase in fertilizer
use in last 50 years Only 50 of N is recovered
in harvested crop GS identified as an important
enzyme in processes of nitrogen assimilation and
metabolism through work in Arabidopsis Breeding
and transgenesis now being successfully tested to
increase GS activity in plants
Miflin and Habash (2002), Journal of Exp. Bot.
53(370)979.
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Examples
Salt (NaCl) tolerance Goal Production of crop
species able to grow and produce in areas of high
soil salt concentration High soil salt
concentration affects about 1/5 of the worlds
irrigated land Until now the solutions have been
engineering-based, very expensive and impractical
for many farmers Breeding programs have met with
a lack of success multi-genic trait, lack of
good genes to introgress Some success with
transgenesis, and new work to find variations in
natural populations of Arabidopsis increasing
salt tolerance with an eye to transformation of
crop plants is promising
Quesada et al. (2002), Plant Phys. 130(2)951-63.
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• Research and development of new crop varieties is
  only the beginning of the process
• Obstacles include funding for work of improving
  crops, distribution and cost of improved lines,
  and public perception

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