Transcript Understanding Biotechnology

Understanding
Biotechnology
Steve Strauss, Professor, OSU
Forest Science, Genetics, Molecular and
Cellular Biology
Director, Outreach in Biotechnology
http://wwwdata.forestry.oregonstate.edu/orb/
[email protected]
Outreach website
http://wwwdata.forestry.oregonstate.edu/orb/
Educational activities
Food for Thought Lecture Series / 2005-2008
Streaming video - OPAN/OPB usage
The plan
• What is biotechnology
• GMOs
– State of usage in the world
– How it works
– The general concerns surrounding them
• Non-GMO biotechnologies (Dave Harry)
– Genomics and DNA markers
• Break-outs for grass seed specifics
– Commercialization issues, GMO testing, grass
industry biotechnologies
What is biotechnology?
Amer. Heritage Dictionary (2000)
• 1. The use of microorganisms or biological
substances such as enzymes, to perform
industrial processes.
• 2a. The application of the principles of
engineering and technology to the life
sciences; bioengineering.
A more crop oriented definition
of biotechnology
• Use of technologies that affect physiology,
genetics, management, or propagation
• Most common uses
– Microorganisms for fermentation of plant
products
– Plant tissue culture for propagation
– DNA sequencing and indexing for
identification (DNA fingerprinting)
– Gene isolation, modification, and insertion
(genetic engineering, “modern biotechnology”)
• GE, GEO or GM, GMO
Why emphasize GE forms of
biotechnology?
GE crops have been taken up rapidly
by farmers when available, have had
large benefits, and have great
economic and humanitarian potential
Exploding science of genomics fuels
rapid discovery, innovation
Rapid rise of GE crops in
developed and developing world
http://www.isaaa.org
Many social issues with major
impacts on use / acceptance
• Few GMO crop types in production
– Maize, soy, cotton, canola
– Insect, herbicide tolerance traits
– Small amounts of viral resistance (squash,
papaya)
• Benefits of reduced tillage, reduced pesticide
use, improved yields, reduced costs
• But other traits and crops mostly on hold
– Substantial social resistance and obstacles to
their use
Defining GMOs
• GEO / GMO = creation of a
“recombinant DNA modified organism”
– It’s the method, can use native or foreign genes
• DNA isolated, changed/joined in
a test tube, and re-inserted asexually
– Vs. making crosses or random mutations in
conventional breeding
• Powerful breeding tool but can generally handle
one to a few genes at a time
– Simple traits can be designed, but without constraints
from native gene pools
– That’s why its called genetic engineering, though we
are modifying, not building, a new organism
Assembling a gene
Promoter
Coding sequence
Terminator
Protein
Controls level of
expression, and
 Where and when
expressed

Provides stability to
messenger RNA, and
 Guides processing into
protein

Can mix and match parts & can
change sequences to improve
properties
Examples of promoter : gene
combinations produced via
recombinant DNA methods
Promoter
(controls expression)
35S-CAMV
(plant virus)
Gene
(encodes protein)
Phenolic pathway enzyme (bacteria)
Herbicide tolerant
Pollen sac (tobacco)
RNA degrading enzyme (bacteria)
Male-sterile
FMV (plant virus)
Insect toxin protein (bacteria)
Insect resistance
Oilseed (canola)
Improved nutrition
Insulin (human)
Recombinant DNA modification
of native plant genes
How are GE plants produced?
Step 1
Getting whole plants back from cultured
cells = cloning
Differentiation of new plant organs
from single cells
First step is dedifferentiation
into “callus”
after treatment
with the plant
hormone auxin
Leaf-discs
Shoots, roots, or embryos
produced from callus cells using
plant hormones
Step 2
Getting DNA into plant cells
Main methods
- Agrobacterium tumefaciens
- Biolistics [gene gun]
Agrobacterium is a natural plant
genetic engineer
Agrobacterium gene insertion
Gene of interest
T-DNA
Ti Plasmid
Engineered
plant cell
Agrobacterium tumefaciens
Only a few cells get modified so
need to identify and enrich for the
engineered cells
Not all cells are engineered, or engineered the
same. Thus need to recover plants from that
one cell so the new plant is not chimeric (i.e.,
not genetically variable within the organism)
Hormones in plant tissue culture
stimulate division from plant cells
Antibiotics in plant tissue culture
limit growth to engineered cells
Other kinds of genes can also be used to favor transgenic cells
(e.g., sugar uptake, herbicide resistance)
Transformation of bentgrass
(Wang and Ge 2006)
Glyphosate-tolerant Fescue
Conventionally-bred Patented Varieties
GE traits under development in
forage and turfgrasses
Wang and Ge, In Vitro Cell Develop. Biol. 42, 1-18 (2006)
• Nutritional quality
– Lignin reduction, increase of sulfur-rich proteins
• Abiotic stress tolerance
– Drought, frost, salt
• Disease/pest management
– Fungal, viral, herbicide tolerance
• Growth and nutrient use
– Flowering time, phosporus uptake
• Hypoallergenic pollen
• Bioethanol processability
Problems and obstacles to wider
use of GE crops
• Regulations complex, uncertain, changing, and
very costly
– Three agencies can be involved
– Environmental and food/feed acceptability criteria
complex, stringent compared to all other forms of
breeding
• Unresolved legal issues of
gene spread, safety assessment, liability,
marketing, and trade
restrictions
Legal actions
• USDA sued over process for granting field
trial permit for GE bentgrass and GE
biopharma crops
• USDA sued over deregulated Roundupresistant alfalfa
– First time an authorized crop forced to be
removed from market
• USDA required to do EIS for alfalfa, one
was already underway for bentgrass
• Scotts fined $ 500K over Roundup Ready
bentgrass field trial
Strong and well funded political
and legal resistance
Intellectual property issues
• New, costly, overlapping “utility patents” issued
for genes and crops since 1980
• Patent “anticommons”
– Major costs, uncertainties for use of best technologies
and usually need several licenses for an improved
crop
• Major litigations ongoing for years to decades
– Basic Agrobacterium gene transfer method
– Bt insect resistance gene innovations
• Regulatory risks make large companies very
reluctant to license to small companies,
academics
• Public sector, small companies find it very hard
to cope with the costs, obstacles
Varied public approval
• Strong polarization on benefits vs. risks
– A highly vocal, concerned minority (~20%)
• A majority whose level of acceptance
varies widely among applications
depending on benefits and ethical views
– Strong resistance to animal applications, and
to impacts that appear to harm biological
diversity
• Very low knowledge of the science,
technology
Rutgers survey data - USA (2005)
http://www.foodpolicyinstitute.org/resultpub.php
http://www.foodpolicyinstitute.org/docs/reports/NationalStudy2003.pdf
• Seven in ten (70%) don't believe it is possible
to transfer animal genes into plants
• Six in ten (60%) don't realize that ordinary
tomatoes contain genes
• More than half (58%) believe that tomatoes
modified with genes from a catfish would
probably taste fishy
• Fewer than half (45%) understand that eating a
genetically modified fruit would not cause their
own genes to become modified
Education needs: Gullibility
• "People seem to have a great number of
misconceptions about the technology. As a
result, they seem to be willing to believe
just about anything they hear about GM
foods.“
• Very few universities take an active role in
outreach, education
– University of California system an exception
Summary
• GE is a method, not a product
• GE crops a major presence and with major
science and technology push forward
• GE method highly regulated, causing great
costs and uncertainties both for field
research and commercial development
• Social/legal obstacles slowing or blocking
investment outside of the major crops and
large corporations
Understanding
Biotechnology
Part 2:
Genomics and DNA Markers
David Harry
Department of Forest Science
Assoc. Director, Outreach in Biotechnology
http://wwwdata.forestry.oregonstate.edu/orb/
[email protected]
DNA-based Biotechnologies
• Genetic engineering (GE, GMO)
– direct intervention and manipulation
– gene manipulation and insertion through an
asexual process
• Genomics & DNA markers
– are generally descriptive, examining the
structure and function of genes and genomes
– manipulating genes and genomes is indirect,
through selection and breeding
Some definitions
• Genes
– a piece of DNA (usually 100’s to 1000’s of bases long)
– collected together along chromosomes
– serves as a structural blueprint or a regulatory switch
• Genome
– an entire complement of genetic material in the nucleus of an
individual (excluding mitochondria and chloroplasts)
– genes, regulatory elements, non-coding regions, etc
– tools for describing genomes include maps and sequence
• DNA marker
– some type of discernable DNA variant (variation, or
polymorphism) that can be tracked
– tracking the +/- of markers offers powerful tools for managing
breeding populations and, increasingly, for predicting offspring
growth performance
For today:
• Basics of DNA markers
• DNA markers & fingerprints
– are fixed for the life of an individual
– can be used to identify individuals
• Marker inheritance (parent to offspring)
– nuclear markers
– parentage verification
– genome mapping
• Associating markers and traits
– maps and associations
– marker breeding (MAS/MAB)
Genomes, genes, and DNA
Genes are located on
packaging platforms called
chromosomes
DNA markers reveal subtle
differences in DNA sequence
Marker “1”
A
T
C
A
A
T
C
G
A
C
G
A
T
G
A
T
T
A
C
T
A
C
Marker “2”
G
G
T
C
G
C
T
G<>T
T
C
C
G<>C
A DNA fingerprint is fixed
throughout an individual’s life
Age
DNA Fingerprints to Verify Identities
22 Paired Samples Collected at Different Times
MCW-305
MCW-184
MCW-087
Pedigree errors: “non-parental”
marker types
S D
Progeny
Genetic Map:
Perennial Ryegrass
Gill et al. 2006
How might genetic markers
accelerate breeding?
X
X
First, associate performance and
genetic makeup
X
X
Then, evaluate genetic
makeup early to select
young birds
Linkage Map
k Trait 2
d
a
g
h
b
Trait 1
e
c
l
i
f
m
j
1
2
3
Hypothetical genes (QTLs)
affecting economic traits
4
Mapping loci affecting quantitative
traits (QTL) in chickens
Genes in the circled
region appear to affect
breast-meat yield
Distance along chromosome Gga 3 (cM)
High-throughput Genotyping
Illumina- BeadStation500G-BeadLab
~150,000 data points per week at UCDavis Genome Center
Marker Assisted Breeding
in Conifers
• Quantitative Trait Locus (QTL) Mapping
• Association Mapping
Pinus taeda
(loblolly pine)
Pinus elliottii
(slash pine)
Pseudotsuga menziesii
(Douglas-fir)
Genomics & DNA Markers:
Summary
• DNA markers can be used as fingerprints to
distinguish individuals, and
– cultivars, varieties, etc
– increasingly used to protect intellectual property
(utility patents, PVP)
• Marker inheritance allows parentage to be
verified, facilitating pedigree control
• DNA markers can be associated with phenotypic
traits
• Once marker-trait associations have been
established, marker data can augment
phenotypic observations to accelerate breeding