Excluded methods discussion

Michael Hansen, Ph.D.

Senior Scientist

Consumers Union

NOSB meeting

Washington, D.C.

April 26, 2016
Codex Alimentarius

• Food safety standard setting organization of the 

United Nations. Joint World Health Organization 

(WHO) and Food and Agriculture Organization (FAO)

• Set up in 1963 to help developing countries with 

range of voluntary standards, guidelines and 

recommendations associated with food safety

• 1996 Uruguay Round of General Agreement on 

Tariffs and Trade sets up World Trade Organization 

(WTO)

• Codex standards, guidelines and recommendations 

considered “trade legal,” and are referenced by WTO
Codex Alimentarius

• Ad Hoc Intergovernmental Task Force on Foods 

Derived from Biotechnology (2000 – 2003; 2005-2008)

• Hosted by Japan 

• Developed 4 key documents:

• CAC/GL 44 Principles for Risk Analysis of Foods 

Derived from Modern Biotechnology (2003)

• CAC/GL 45 Guideline for the Conduct of Food Safety 

Assessment of Foods Derived from Modern 

Biotechnology (2003, 2008)

• CAC/GL 46 Guideline for the Conduct of Food Safety 

Assessment of Foods Produced Using Recombinant- DNA Microorganisms (2003)

• CAC/GL 68 Guideline for the Conduct of Food Safety 

Assessment of Foods Derived from Recombinant-DNA 

Animals (2008)
Codex Alimentarius: Principles for the Risk Analysis of 

Foods Derived from Modern Biotechnology

(CAC/GL 44—2003) 

•“8. “Modern Biotechnology” means the application of: 

– i) In vitro nucleic acid techniques, including 

recombinant deoxyribonucleic acid (DNA) and direct 

injection of nucleic acid into cells or organelles, or

– ii) Fusion of cells beyond the taxonomic family,

• that overcome natural physiological reproductive or 

recombinant barriers and that are not techniques used in 

traditional breeding and selection” (Para 8, CAC/GL 44-2003)
Codex Alimentarius

• Technologies included under the Codex definition of 

“modern biotechnology,” aka GE or GM:

– Cisgenic, intragenic

– Reverse breeding

– ODM (oligonucleotide directed mutagenesis)

– TALEN (transcription activator-like effector nucleases )

– Meganucleases

– ZFN (zinc finger nucleases)

– CRISPR/Cas (clustered, regularly interspaced, short 

palindromic repeats )

– RNAi

• Not included under Codex definition:

– TILLING (targeting induced local leisons in genomes)
Osakabe Y and K Osakabe. 2015. Genome editing with 

engineered nucleases in plants. Plant Cell Physiology 56(3): 389-

400
Osakabe Y and K Osakabe. 2015. Genome editing with 

engineered nucleases in plants. Plant Cell Physiology 56(3): 389-

400
ODM (oligonucleotide directed mutagenesis) 
CIBUS
Osakabe Y and K Osakabe. 2015. Genome editing with 

engineered nucleases in plants. Plant Cell Physiology

56(3): 389-400
Approach used to target the EPSPS loci in flax. 

Noel J. Sauer et al. Plant Physiol. 2016;170:1917-1928

©2016 by American Society of Plant Biologists
Lee J et al. 2016. Designed nucleases for targeted genome editing. 

Plant Biotechnology Journal 14: 448-462.
Sauer NJ et al. 2016. Oligonucleotide-Mediated Genome Editing 

Provides Precision and Function to Engineered Nucleases and 

Antibiotics in Plants. Plant Physiology 170: 1917-1928
A novel technology for speeding the improvement of germplasm and 

varieties of tree fruits and other long-generation cycle crops. 

FASTRACK

BREEDING
Pollination

Field planting seedlings

Breeding, carried out in the field, is affected by climate, diseases, and insect pests. 

Not every year is successful.

Due to this year’s cold spring temperatures we lost most of our hybridizations.

Protecting pollinations
THE PROBLEM:

•Fruit trees like peach, plum, apricot and cherry, need to 

grow for at least three years and sometimes more than 

seven years before they flower and fruit.

•That means for a breeder to improve a trait such as 

disease resistance, it is necessary to wait 3-7 years to 

see the results of each cross. Several to many 

generations are needed to produce an improved 

variety. 

•In practice it can take anywhere from 15 -20 years to 

produce a new variety, longer when introgressing traits 

from unimproved genotypes.
One solution: 

Hire younger fruit tree breeders
Another Solution – FASTRACK

A breeding system that

utilizes GE for producing 

generation cycles of one 

year or less but does not

produce a GE final product.
We inserted the Flowering locus T gene from 

poplar trees into plum. The results were striking.

Plum transformation with early flowering 

(FT) gene from poplar: July year 1 

Harvesting of fully ripe plum fruits 

with viable seeds in the greenhouse: May year 2 (10 months)

One year from gene 

transfer to ripe fruit! 

Then, from seed to seed in less than 1 year

Instead of 4 years or more
The PtFT gene is inserted into a parent plum line through genetic 

engineering.

Genetic Transformation Transgenic tree regeneration

PtFT gene ready to 

be inserted into the plum tree PtFT gene is inserted 

into a plum plant 

PtFT plum

(the T indicates that 

it carries the PtFT gene)

T

An early flowering plum parent tree is produced that can 

flower and fruit within a year.

How does it work?
FasTrack Breeding 

program

Conventional 

Breeding 

program 

with 4yr/ 

generation 

cycle 

8 years

for 3 BC

20 years

for 3 BC

Using PtFT early flowering Plums for breeding 

disease resistant plum varieties 

25% of seedlings PtFT and disease

resistant – select for fruit traits

X

‘disease resistant’

plum

X

back

cross

Two additional backcrosses or modified backcrosses 

with high quality types 

T

PtFT plum

T

T

High fruit quality plum

T

T

disease resistant

high quality

(not GE)

PtFT+ disease resistant

PtFT + disease susceptible

T

disease susceptible

Markers?

Markers?

25% of seedlings PtFT and disease

resistant – select for fruit traits

PtFT and disease

resistant 

Now must wait 4 years for first fruit to check for variety potential. 

Years of conventional backcross breeding have been saved. 
Early Flowering clones in the greenhouse
Simultaneous Development 

of Flowers and Fruit
Six month old early flowering & normal fruiting transgenic plum 

A

B

C

D
‘FasTrack’ Breeding Advantages

‘FASTRACK’

- 1 year generation time

- can make crosses and produce fruit year-round

- avoids winter and spring injury in the field

- reduced insect and disease pressures 

CONVENTIONAL

- 4-6 year generation time

- one pollination/fruiting per year

- subject to seasonal climate extremes

- disease, insect, and weed pressures

The final products of FasTrack breeding not containing the transgenes are not considered different 

from those bred conventionally and could not be distinguished from conventional cultivars.
Dutch elm disease

Emerald ash borer

Citrus canker

Chestnut blight

Asian longhorn beetle

Plum pox virus

White pine blister rust

Citrus greening

Hemlock woolly 

adelgid

Spotted Wing Drosophila

African Fig Fly

Brown marmorated stink bug

One reason why we need more rapid tree breeding - rapid influx of new pests and diseases 

Pine Shoot Beetle

Oriental fruit fly