Photo by Dennis Gonsalves. - Department of Plant Sciences

workkinkajouBiotechnology

Dec 5, 2012 (4 years and 8 months ago)

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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



http://fig.cox.miami.edu/~cmallery/150/gene/genome2.jpg

How plant genome sizes compare
with other organisms

Creating cDNAs

complementary DNA from mRNA

Next
-
generation DNA
sequencing technology

Finding more genes than you’d
ever imagined

http://www.youtube.com/watch?v=bFNjxKHP8Jc


Microarrays

Sample preparation

Reference material

Test material

Total RNA isolation

mRNA purification

Source: Murali Rao

Image Collection

Sample Array Data

Progression of GM plants


1
st

Generation: Input traits (herbicide
tolerance, insect resistance, etc.)


2
nd

Generation: Output traits:
(pharmaceuticals, enhanced nutrition, etc.)


3
rd

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)






Stewart, 2004. Genetically Modified Planet 2004

Photo by Dennis Gonsalves.

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