Lecture 12 Chapter 8 Genomics and Genes and traits of interest I

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Lecture 12 Chapter 8 Genomics and Genes and
traits of interest I

• Neal Stewart

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Discussion questions

• What is genomics (and omics in general)? What
  are the tools for finding genes that might be
  useful in biotechnology.
• What is next-generation DNA sequencing? What is
  the impact or potential impact?
• Why is microarray analysis useful? What omics
  would it be applied to?
• 4. What are the differences between input and
  output traits? Considering the environmental
  and biological factors that limit production in a
  farmers field, what are some new input traits
  that might be good candidates for improvement
  using biotechnology?
• 5. Consider the possibility that you are
  employed by an agricultural biotechnology
  company, and they ask you to find a bacterial
  gene for resistance to a specific herbicide. The
  herbicide has been manufactured by the company
  for many years. Using a strategy similar to that
  used to find glyphosate resistance, where might
  you start to look for a bacterium resistant to
  that herbicide?

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Finding genes functional genomics

• Biochemistry
• Functional screens
• Hunting for specific genes cDNAs
• Searching databases for similar genes
• Omics e.g.,
• Genomic sequencing projects
• Microarrays for finding upregulated genes
• Extremophiles unusual genes from unusual
  organisms

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How plant genome sizes compare with other
organisms
http//fig.cox.miami.edu/cmallery/150/gene/genome
2.jpg
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Creating cDNAscomplementary DNA from mRNA
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Next-generation DNA sequencing technology

• Finding more genes than youd ever imagined

http//www.youtube.com/watch?vbFNjxKHP8Jc
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Microarrays
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Sample preparation
Reference material
Test material
Source Murali Rao
Total RNA isolation
mRNA purification
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Image Collection
Sample Array Data
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Progression of GM plants

• 1st Generation Input traits (herbicide
  tolerance, insect resistance, etc.)
• 2nd Generation Output traits (pharmaceuticals,
  enhanced nutrition, etc.)
• 3rd Generation Non-traditional
  (pharmaceuticals, phytoremediation, phytosensors,
  next-generation biofuels)

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First generation

• Input traits

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Herbicide-resistant crops
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Figure 8.1
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Finding a glyphosate resistance gene

• Discovery of glyphosatekills most plants
• Knowledge of shikimate pathway
• Targeting enyzme (gene) for resistance
• Functional screen for resistance
• Clone resistance gene
• Overexpress gene in plants

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Figure 8.2
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Discussion question

• Consider the possibility that you are employed by
  an agricultural biotechnology company, and they
  ask you to find a bacterial gene for resistance
  to a specific herbicide. The herbicide has been
  manufactured by the company for many years. Using
  a strategy similar to that used to find
  glyphosate resistance, where might you start to
  look for a bacterium resistant to that herbicide?

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Transgenic disease resistance

• Viruses (yes)
• Bacteria (no)
• Fungi (no)
• Nematodes (no)

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Photo by Dennis Gonsalves.
Stewart, 2004. Genetically Modified Planet 2004
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Biotechnologist of the dayDennis Gonsalves

• From Hawaii
• At USDA-ARS in Hilo, Hawaii
• Humbolt Prize 2002
• Virus resistant papaya credited for saving papaya
  industry in Hawaii