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Presentation made by Andy Jarvis in the Latin American Congress of Chemistry on 30th September 2010, in the symposium on Biodiversity and Ecosystems: the role of the chemical sciences.
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draws attention to deliberate efforts of breeders and
the specific techniques they have used in creating and
harnessing desired variation in developing elite breeding
lines and cultivated varieties.
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Mutagenesis is the process by which the genetic information
of an organism is changed in a stable manner.
The term ‘mutation breeding’ has become popular as it
draws attention to deliberate efforts of breeders and
the specific techniques they have used in creating and
harnessing desired variation in developing elite breeding
lines and cultivated varieties.
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Abstract
Many agriculturally important traits such as grain yield, protein content and relative disease resistance are controlled by many genes and are known as quantitative traits (also polygenic or complex traits). A quantitative trait depends on the cumulative actions of many genes and the environment. The genomic regions that contain genes associated with a quantitative trait are known as quantitative trait loci (QTLs). Thus, a QTL could be defined as a genomic region responsible for a part of the observed phenotypic variation for a quantitative trait. A QTL can be a single gene or a cluster of linked genes that affect the trait. The effects of individual QTLs may differ from each other and change from environment to environment. The genetics of a quantitative trait can often be deduced from the statistical analysis of several segregating populations. Recently, by using molecular markers, it is feasible to analyze quantitative traits and identify individual QTLs or genes controlling the traits of interest in breeding programs.
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6. GM will be part of the solution
1973: First recombinant organism
1975: Asilomar Conference
1978: Genentech founded
1986: - First field trial with Ice-Minus by Lindow S.
- Coordinated Regulatory Framework
1994-97: First commercially available GM crop: Flavr Savr Tomato
1998: Transgenic Papaya in HI
FAO definition: Genetically engineered/modified organisms, and products thereof, are produced through techniques
in which the genetic material has been altered in a way that does not occur naturally by mating and/or natural
recombination. (Definition not agreed by the Codex Alimentarius Commision).
EFSA: genetically modified organism (GMO)" means an organism, with the exception of human beings, in which the
genetic material has been altered in a way that does not occur naturally by mating and/or natural recombination
7. What drives GM development?
Profitability
Scientific curiosity
Disaster
8. What are the big hurdles?
Market Size
Intellectual Property
Regulatory
Public Acceptance
9. Commodity Crops in the Private Sector
R&D
Regulatory Affairs
Business
Development/Marketing
Legal/IP
$Cost: $70 million
Time: 10 years
$
US Revenues from major GM crops (Carlson R., 2009)
22 x
10. Specialty Crops in the Public Sector
Research IP? Regulatory?
Business
Development?
Corn = $40B
Grape
= $3BPIPRA
$
$
45%
(2004)
11. Transgrafting: Hope in deregulation?
“GM, or not GM?”
In vino veritasBenefits:
• Reduction in cost/time
for regulatory approval
• Pollen containment
• Public acceptance
Trans-grafting: a wild type scion grafted onto transgenic rootstock .
May confer a benefit to rootstock only or both rootstock and scion.
12. Who will benefit from this technology?
• Fruit tree crops
• Middle East/Europe (watermelons, tomatoes)
Papaya:
$13 Million
13. Industry Threats vs. Public Research
Fruit/Nut
Crop
Disease of Interest
No. GM
articles on
disease
Total No. Pest-
related GM
strategies
Grape Pierce's Disease 4 24
Powdery Mildew 4
Eutypa Dieback 1
Mealybug 0
Nematode 0
Citrus Canker 10 43
Greening (HLB) 2
Phytophthera Root Rot 2
Asian Citrus Psyllid 0
Thrips 0
Almond Anthracnose 0 1
Brown Rot 0
Rust 0
Scab 0
Shothole 0
Apple Fireblight 6 18
Scab 6
Codling Moth 2
Oblique Banded Leaf Roller 0
Powdery Mildew 0
15. USDA/APHIS/BRS
“Protecting American agriculture”
Notification and Permit
for Interstate Movement
and Release into the
Environment
Petition for Deregulation
of Regulated Article
the Animal and Plant Health Inspection Service (APHIS)
is responsible for protecting agriculture from pests and
diseases.
16. EPA
• The EPA through a
registration process
regulates the
sale, distribution and use of
pesticides in order to
protect health, and the
environment, regardless of
how the pesticide was made
or its mode of action
• IR-4 can help in the process
17. FDA
• The FDA is responsible for
ensuring the safety and proper
labeling of all plant-derived
foods and feeds, including those
developed through
bioengineering.
• Voluntary consultation process:
nutritional composition &
allergenicity
18. How will agencies consider transgrafting?
• No official opinion on this paradigm
• Depends on the trait/species combination
• If movement to the scion: risk assessment on
rootstock + scion combination
• Case by case
19. •Grafted plants traditionally thought of as
maintaining own genetic identity
•What defines identity?
•DNA, RNA, proteins, miRNAs?
•Epigenetic changes?
?
DNA
RNA
protein
miRNA
GM or non-GM?
20. Transgrafting experiments initiated here at UCD
•Aguerro- pPGIP grape
activity detected, protein not shown
•Escobar- RNAi expressing walnut
tomato scion tested for microRNA, walnut not examined
•Comprehensive follow up
•Establishing if tomato is a good model system
•Analysis of genetic components:
•iaaM, ipt: smRNA from hairpin
•GUS, NPTII: cytosolic proteins
•pPGIP: apoplast targeted protein
•mRNA and gDNA component for all
21. Plastid DNA can “cross” the graft junction
WT Pt-spec:gfp Nuc-kan:yfp YG-29
Stegemann 2009
Stegemann 2003
•Chloroplast
transformed with
nuc:nptii and
recombination sites
present in cassette
•1 in 5 million gene transfer events
•Incorporation of transgene and
segments of flanking pDNA
22. Walnut
•Utilized available grafted saplings
•2-4 nuts/plant
•Only Wt/Wt control available
•4 unique transformation events
-greenhouse inoculation data
-field testing
GM
WT WT (+)ctrl
(-)ctrl
23. Tomato & Grape
•Propagated seeds or cuttings
•Grafted and included “logical “controls
GM
WT
fruit
scion
rootstock
(-)ctrl
ctrls
27. Certain types of RNA are mobile
Kudo, Harada 2007
Probing Scion material
WT ctrls
tomato
potato
Differential
splicing
Me tomato
•Bill Lucas @ UCD
selective delivery of RNAs to scions through
vascular system
• “Zip codes” in the 3’UTR
•Targeting to shoots or roots
30. mRNA analysis- grape vs. tomato
NPTII
pPGIP
ACTIN
pPGIP
NPTII
ACTIN
•Transgenes active in GM portions; no mobility detected
GM
WT
31. •5 fold serial dilutions starting with ~10,000/rxn
-30 cycles
•Background of 100ng of WT DNA
-walnut
-grape
-tomato
•Similar ranges of 4-22 copies of gene/rxn
PCR-based Detection Limits: 4-22 copies
nptII
ipt
iiaM
gus
105
104
2740
548
109
22
4.4
0.8
(-)ctrl
pPGIP
32. Proteins can mobile
•100’s…some larger than 100kDA
•GFP expressed (CC-promoter) found in sink tissues
•GFP fusions at least 50kdA, <67kDA can diffuse into the SE
“Non specific macromolecular trafficking a
general feature of plasmodesmata in sink
tissues”—Oparka 1999
7 hours and 2 days post bombardment
Imlau 1999
33. NPTII analysis- Grape vs. Tomato
•5X loading in tissues where abundance may
be low
•Obtaining purified NPTII for detection limit
34. NPTII analysis- Walnut vs. Tomato
Ongoing with GUS as well
•Obtaining purified GUS for detection limit
35. 1ug 333ng 111ng 37ng 12ng 4ng
•Dilution of GM in WT background
•Purified pPGIP would be ideal
pPGIP analysis- Tomato & Grape
Preliminary blots in tomato and grape leaf
5X “overloading” in red boxed regions
•Consider using dilutions of
GM for GUS and NPTII
36. Molnar, 2010
•21-24 nt smRNAs mobile across graft junctions in
Arabidopsis
•Some associated with epigenetic effects
•Used deep sequencing
Small RNAs can be mobile
•Most miRNA are probably cell-autonomous or localized
(Voinnet 2009)
•Nutrient signaling, defense probably are systemic (Pant 2008)
GFP target
GFP-derived hairpin to silence
37. •Sense/co-suppression was graft
transmissible but antisense was
not
Palauqui 1996, Crete 2001
Shaharuddin 2006
•Antisense silencing can be transmitted to scions but at slower rate
• Target is necessary
Transmissibility of sense, antisense, and co-suppressed signal
38. smRNA detection in walnut and tomato
•Tomato grafts >12 weeks old
•Walnut grafts ~7 years old
•Ribonuclease protection assay (RPA)
Ambion’s mirVana series reagents
•Can be up to 100X more sensitive than Northern blot
•Deep-sequencing as an alternative
39. Summarizing Mobility
•DNA can cross organelle and even cell boundaries
•low frequencies
•probably not relevant to grafting scenarios
•RNA can cross cell boundaries and enter vascular system
•correct “zip codes”
•unless designed a priori, not likely to happen
•Proteins can “leak” into the vascular system
• Especially if expressed in companion cells
•Dependant on size, may degrade
•smRNAs can enter vascular system
•sense, antisense, or hairpin origin
•likely requires a target to obtain high levels
•may be time dependant
•Sensitivity is key to detection, case-by-case scenario
40. •Single Molecule ELISA (Nature
Biotech 2010)
Single Molecule Detection
•Single Molecule Real Time Sequencing
-Pacific Bioscience
-Helicos
•RNAseq
•Direct Real-Time RNA sequencing (Nature, 2009)
41. •RNAs, protein present
in scion?
•What if microRNAs
are present in scion?
•What about
epigenetic changes?
•How will this affect
commercialization?
•Would you grant
deregulation?
Transgrafting Considerations
??
? ?