Lecture 12 Chapter 8
Genomics and
Genes and traits of interest I
Neal Stewart
Discussion questions
1.
What is genomics (and “omics” in general)? What are the tools for
finding genes that might be useful in biotechnology.
2.
What is next-generation DNA sequencing? What is the impact or
potential impact?
3.
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 farmer’s 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?
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
How plant genome sizes compare
with other organisms
http://fig.cox.miami.edu/~cmallery/150/gene/genome2.jpg
Creating cDNAs
complementary DNA from mRNA
Next-generation DNA
sequencing technology
Finding more genes than you’d
ever imagined
454 sequencing: http://www.youtube.com/watch?v=bFNjxKHP8Jc
Illumina sequencing: http://www.youtube.com/watch?v=l99aKKHcxC4
Microarrays
Test material
Sample preparation
Reference material
Source: Murali Rao
Total RNA isolation
mRNA purification
Image Collection
Sample Array Data
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)
First generation
Input traits
Herbicide-resistant crops
Figure 8.1
Finding a glyphosate resistance gene
•
•
•
•
•
•
Discovery of glyphosate—kills most plants
Knowledge of shikimate pathway
Targeting enyzme (gene) for resistance
Functional screen for resistance
Clone resistance gene
Overexpress gene in plants
Figure 8.2
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?
Transgenic disease resistance
•
•
•
•
Viruses (yes)
Bacteria (no)
Fungi (no)
Nematodes (no)
Photo by Dennis Gonsalves.
Stewart, 2004. Genetically Modified Planet 2004
Biotechnologist of the day
Dennis Gonsalves
• From Hawaii
• At USDA-ARS in
Hilo, Hawaii
• Humbolt Prize
2002
• Virus resistant
papaya credited
for saving papaya
industry in Hawaii