Genome Editing in Agriculture - Navigating the Challenges and Opportunities on Seed Industry Sector

1. Genome Editing in Agriculture
Navigating
Challenges and Opportunities on Seed Industry Sector
Dr. S.R.Rao
Former Sr. Advisor, Department of Biotechnology, Government of
India.
Vice President, Sri Balaji Vidyapeeth (Deemed University)
Pondicherry
Co-founder, Global Alliance on Pandemic Preparedness and
Response (APAR)
IFPRI -Regulations & Governance Issues in Indian Seed Sector. 26-27 September 2023
Courtesy : Syngenta

2. Topics
• The Technology
• The Regulation
• Genome edited crops and traits
• CHALLENGES
➢Access to technology, ownership and control :
➢The regulatory status of genome-edited crops under EU law
➢Regulatory challenges with SDN 2
➢The detection of genome-edited crops is problematic
➢Divergence in views and public debate
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3. The decision to regulate is based on a variety of
considerations
➢Legislations and provisions thereof
➢ Scientific Complexity and risk assessment
protocols
➢Policy of the country/region
➢Social/Ethical considerations
Regulation of Genome Edited products
2
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4. 30-09-2023 3
GENOME EDITS CLASSIFIED
ACCORDING TO THE EDIT TYPE AND MECHANISM OF REPAIR
SDN 1 SDN 2 SDN 3
Size of the edit A few base changes Defined point
mutation to a few
bases
Up to several
kilobases
Mechanism Spontaneous
mutations; deletions;
replacements addition
of sequences
Pre-defined
mutations; sequence
optimization, allele
replacements
Additions of
sequences at the
target genomic
location
Result Targeted but not
defined
deletions/mutations
Targeted and precise
mutations/ gene edits
No Insertion of
transgene sequence
Targeted insertion of
sequence
Insertion of cisgenic/
transgenic sequence

5. Three types of mutation
4
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6. 3. Review and Analysis of Risk Assessment of Genome Edited Crops
Natural mutations
Mutagenesis
SDN1
SDN 2 &
ODM
SDN3
Oligonucleotide Long template
GEOs/GMOs/LMOs
Gene of interest: Any source
Process complexity, Product features and traceability of Genome editing techniques relative to
unregulated techniques
Long sequences
inserted
Point mutations,
deletions
Resulting complexity At Genotype, Phenotype, Biochemical level
Regulations Not regulated Regulated
?
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7. India : Does the genome editing technologies governed by the existing rules ---- Rules
1989 of EPA act 1986
Under Rules 1989 of E(P)A 1986 definition of “Genetic Engineering” is:
“Gene Technology: “Gene Technology” means the formation of live cells with
new combinations of genetic material through the fusion of two or more cells
by means of methods which do not occur naturally.
Genetic engineering” means the technique by which heritable material, which
does not usually occur or will not occur naturally in the organism or cell
concerned, generated outside the organism or the cell is inserted into said cell
or organism.
It shall also mean the formation of new combinations of genetic material by
incorporation of a cell into a host cell, where they occur naturally (self cloning)
as well as modification of an organism or in a cell by deletion and removal of
parts of the heritable material;
In India, both the process as well as
product of recombinant DNA
technology is regulated
Hence , any product(s) arising out of
genome editing technology also trigger
the regulations in India.
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8. Genome edited plants falling under SDN-1 and SDN-2 type that differ significantly from
GE plants in several respects, and are exempted under Rule 20 of Rules 1989 as per the
MoEFF&CC vide Office Memorandum F. No. C -12013/3/2020-CS-III dated
30.03.2022.
Food/Feed and Environmental safety assessment may not be necessary, provided
that the technology developer provides sufficient molecular and other documentary
evidences to show that the genome edited plants carry proposed mutation(s) and
fall under SDN-1 or SDN-2 type as per the definitions in the guidelines.
Technology developer shall ensure that the SDN-1/SDN-2 type Genome edited plant
under consideration for environmental release does not contain any foreign
gene/DNA or sequences of vector used to create mutations and other components
used in the editing process.
Applicants’ shall submit application for Genome editing of plants in prescribed
forms at IBKP to seek approval of IBSC.
Exemption of SDN 1 and SDN 2 from EPA Act, 1986/GEAC approval
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Department of Biotechnology
Ministry of Science and Technology
Government of India

10. Off-target,
Unintentional
changes
Successive rounds of such
modifications leading to
substantial changes
Major changes in the ORF
Changes in the expression profile
Major changes leading to increased
weediness potential, Environmental fitness
Type of
genome
editing
Risk
level
SDN 1 Type
SDN 3 Type
Risk concern
Low
High
Risk scenarios in genome editing.
3. Review and Analysis of Risk Assessment of Genome Edited Crops
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11. Data requirement for Risk Assessment
IBSC & RCGM IBSC, RCGM
& GEAC
SDN1 SDN2 SDN3 GM organisms
Biology document : Biology of the parent organism √ √ √ √
Molecular characterization:
1. Design of Programmable nuclease/nickase
2. Type of Editing and Method of transformation/Mode of Delivery
3. Selection & stability of Genome Edited organism
4. Characterization of the target site and expression of resulting
protein
5. Stability of introduced trait
6. Characterization of off-target changes
√ √ √ √
Compositional and Equivalence - - √ √
Toxicity and Allergincity studies, on a case by case basis - - √ √
Trait Efficacy, Phenotypic and Agronomic characteristics
1. In-house selection to identify best line(s)
2. Multi-location trails for trait efficacy
√ √ √ √
Data requirements on genome edited Organisms for Risk Assessment
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12. IBSC
RCGM
Not subject to regulation as a GMO,
treat as conventionally bred crop
Has new
genetic
material
been
introduced?
Does the
breeding
method use
a transgene
temporarily?
Is the final
product free
of
transgenes?
Yes
Yes
Yes if SDN-2
No
No if SDN-1
No
May be
commercialised
No, RNP Yes if SDN-3
Regulation as a
GMO
Limited
regulation
as a GMO
case-by case
Path-to-market for genome edited products in India
IBSC : Institutional Biosafety Committees; RCGM : Review Committee on genetic manipulation ;
Substantial
equivalence
Phenotype and
composition
yes
NO
GEAC
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13. Genome Editing regulation across coutries
No hurdles Case by case yet not clear
Consider as conventional
breeding for base pair
editing and deletion
Clear rules and procedures
in place consider case by
case for mutagenesis and cis
genesis
Developing new regulatory
frame work
USA
BRAZIL
ARGENTINA
PARAGUAY
EQUADOR
COLUMBIA
ISRAEL
CHILE
CANADA
NIGERIA
RUSSIA
JAPAN
AUSTRALIA
INDIA
PAKISTAN
PHILLIPINES
INDONASIA
EUROPIAN UNION(EU)
MAIN LAND CHINA
UNITED KINGDOM
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15. Crop Trait
NIPGR, New Delhi
Indian Mustard Glufosinate alkaloid reduction to
tolerant level
Rice Disease resistance and herbicide
tolerance
Chickpea Seed size and quality
RICE/Maize- engineer and improve root
architecture and
stress/nutrient
response/abiotic stress
Crops and Traits at R&D Stage India
Developed Low Glucosinolate Mustard
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16. Crop Trait
Bose Institute, Kolkata
Tomato Regulation of gene expression for adjusting
complex traits via synthetic biology approach
Junagadh Agricultural University Kolkata
Groundnut high oleic acid and low linoleic acid
IARI—New Delhi
Rice Yield, NUE, WUE, abiotic and biotic stress
tolerance
Crops and Traits at R&D Stage India
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17. Crop Trait
ICGEB—New Delhi
Rice Low phytate ; Nutrient use efficiency;
Herbicide tolerance:
NRCPB, New Delhi
Mustard Seed meal quality in Indian mustard
Tamilnadu Agricultural University Coimbatore
Rice disease resistance and nutritional quality rice
National Agri-Food Biotechnology, Mohali
Banana GE-β-carotene rich banana
India- Crops and Traits at R&D Stage
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18. Crop Trait
Institute of Life Sciences (ILS) Bhubaneswar
Bhimkol (Musa
balbisiana)
Seedless
NBRI Lucknow
Tomato
Cotton and
Rice
Chickpea
postharvest shelf life tomato; tomato root
architecture Sympodial synchronous flowering;
low arsenic rice;
drought stress in chickpea
India- Crops and Traits at R&D Stage
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19. Genome Editing Across Crops
Crops Percent
activity
Grains and
oilseeds
55
vegetables 23
Fruits 07
Ornamentals
/legumes/for
ages/grasses
03
Others 12
Gamma – aminobutyric
acid (GABA) ENRICHED
TOMATO Commercialized
in Japan by SANATECH
seed Company in 2021
CRISPR Leafy
Greens Now
Available in US
Market
May 24, 2023
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20. Global distribution of market –oriented
genome editing applications
Agronomic value 61
Product quality 59
Biotic stress
tolerance
34
Herbicide
tolerance
24
Plant breeding for
improvement
23
Abiotic tolerance 14
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21. 30-09-2023 20
Gene edited products 2023

22. 30-09-2023 21
➢ Access to technology, ownership and control : Edited commercialisation
of genome-edited crops in most cases necessary to have a licence on
CRISPR-related intellectual property (IP)
➢ The regulatory status of genome-edited crops under EU law
➢ Regulatory challenges with SDN 2
➢ The detection of genome-edited crops is problematic
➢ Divergence in views and public debate
CHALLENGES

23. IP issues
Patents on Rice Transformation
Country Number of
patents
USA 44
Japan 21
China 11
South Korea 10
Brazil 10
Vietnam 9
Indonesia 6
India 5** No Indian
patents abroad
Philippines 1
- Nationwide more than 780
patent applications related to
transgenic plants.
- 162 granted patents related to
plant transgenic technology.
- Among granted patents twenty
five percent of patents i.e. 40
patents are from public
organisation(s).
- Around 20 patents
(Applications and Granted)
are with cry gene
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24. TOP COUNTRIES / REGIONS HOLDING CRISPER PATENT FILINGS IN INDIA 2020-2021
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25. World wide filings of PCT Patents on CRISPER
India shares 6 % of Them
Crisper Knock out kits
Notice to purchaser
1.This product is for research use only. Use in and/or for diagnostics
and therapeutics is strictly prohibited. By opening and using the
product, the purchaser agrees to the following: The plasmids may not
be distributed, resold, modified for resale or used to manufacture
commercial products without prior written approval from OriGene
Technologies, Inc. If you do not agree to the above conditions, please
return the UNOPENED product to OriGene Technologies, Inc. within
ten (10) days of receipt for a full refund.
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26. 30-09-2023 25
The NEW draft 2023. also allows researchers to use gene editing to add or move
genes, as long as the genes already exist within what is called the
breeder's gene pool. That flexibility is appealing because moving genes can lead
to much more sophisticated effects, such as changing expression patterns, than
simply knocking out a gene with a mutation,
Plants would be exempt if no more than 20 nucleotides were added or
replaced during the gene editing. This number comes from a 2011 study of the
model plant Arabidopsis in which detectable natural genetic variations among
individual plants were limited to this size.)
The limit of 20 nucleotides could restrict what scientists would be able to achieve
through gene editing.
The regulatory status of genome-edited crops under EU law

27. Challenges for SDN-2
Definition Regulatory status
Australia An organism modified by the repair of
single-strand or double-strand breaks
of genomic DNA induced by a site-
directed nuclease, if a nucleic acid
template was added to guide
homology-directed repair.
Regulated
Japan Change with template of 1 to a few bps Deregulated if the template DNA is from the
same species or from a sexually compatible
species.
India
SDN-2 involves a template-guided
repair of a targeted DNA break using
an externally supplied template
sequence.
Deregulated if free from exogenous DNA
Concern India No BP changes not prescribed
What will happen if template DNA crosses species barriers(transgene)? i.e. the plant will
get sequence from other gene pool/ transgenic origin
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28. Administrative change for faring fast
Ensuring Competence in RCGM and IBSCs
• IBSC should have expert(S) to appraise the proposal
• Informing RCGM on the presence of related subject matter
expert (External expert)
• In case of absence, invite subject matter expert as an additional
resource. Inform the same to RCGM while reporting.
• RCGM may think of creating database to help IBSC identify such
experts
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29. 30-09-2023 28
DETECTIONOF GENOME EDITS IN PLANTS –FROM EDITING TO
TECHNLOGY COST THROUGHP
UT
SENSITIVI
TY
A PRORI/
KNOWLED
GE
OF EDIT
SURROUNDIN
G SEQUENCE(
INDEPENDEN
CY)
PCR (gel based) + ++ + ++ ++
qPCR + ++ to +++ + to +++ +++ +++
ddPCR ++ to
+++
++ +++ +++ +++
Hybrid capture
sequencing
+++ +++ + to ++ + to ++ ++
Amplicon based
sequencing
+++ +++ ++ to +++ + to ++ ++
Isothermal PCR + ++ + to ++ +++ +++
LOW (+) to HIGH (+++) RELATIVE TO THE TECHNOLGIES INCLUDED IN THIS TABLE
A challenge is no currently available
analytical tool(s) are able to determine
whether a mutation occurred
spontaneously in the population, or
due to application of radiation or
mutagens.
Thus, there will always be a question
as to the background level of
“detection” of such changes that are
not induced by laboratory methods

30. Traceability and Trade implication
• Although the current lab R&D and resultant GEd plant have no
commercial values, it is expected that those lines will be introduced
for commercialization and trade. As such, there are long term
implications of such research and need attention.
• Genome editing regulation is not uniform across globe with some
nations still debating on it.
• Editing may be have long term consequence on international trade
especially with nations (Like EU) where GEd is still regulated.
• Defining the methods and parameters for traceability will be essential
in future.
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31. Position Bt cotton with
Cry1Ac
& Cry2ab
or both
Bt Brinjal HT/BT
cotton
GM Mustard
Approval by GEAC YES YES NO YES
Approval by
Government of the
Day
YES NO NO NO
Patent Issues YES NO YES NO
Supreme Court case NO YES YES YES
Activist Role MILD AGGRESSIVE AGGRESSIVE VERY
AGGRESSIVE
30
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32. Gene‐Edited Food Adoption Intentions and Institutional Trust in
the United States: Benefits, Acceptance, and Labeling☆
Rural Sociology, First published: 23 February 2023, DOI: (10.1111/ruso.12480)

33. Perceptions on Gene‐Edited Food In Japan
Gene editing compared with genetic modification and conventional breeding techniques
of Three groups : 11000 sample size on internet
➢ experts in molecular biology,
➢ experts in other fields,
➢ lay public) on
Findings
➢ Domain-specific scientific knowledge affects people’s risk, benefit, or value perceptions,
➢ The experts in molecular biology showed the highest benefit and lowest risk
perceptions compared to the other two groups
➢ The lay public consider gene editing as closer to genetic modification differentiating
the conventional breeding technique
➢ The influence of science literacy on the lay public’s attitudinal change toward
agricultural crops is confirmed all in benefit, value, and risk perceptions for the
conventional breeding technique.
Kato-Nitta, N., Maeda, T., Inagaki, Y. et al. ( 2019)
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34. Thanks for your patience Questions ???? please
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