exv10w21






Exhibit 10.21



Pages where confidential treatment has been requested are stamped ‘Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission,’ and the confidential section has been marked as follows: [***].




COLLABORATION AGREEMENT





	1.	 	THE PARTIES






	 	 	This Agreement is made effective November 15, 2007 (the “Effective Date”) by and between
Ceres, Inc., a Delaware corporation with principal offices at 1535 Rancho Conejo Blvd.,
Thousand Oaks, CA 91320, hereinafter “Ceres,” and the Institute of Crop Sciences of the
Chinese Academy of Agricultural Sciences, 12 South Zhongguanchun Street, Haidian District,
Beijing 100081, People’s Republic of China, hereinafter “ICS.”






	 	 	THE PARTIES HERETO COVENANT AND AGREE AS FOLLOWS:






	2.	 	PROGRAM






	 	2.1	 	Ceres will deliver to ICS material and information as described in ANNEX
I (jointly referred to as the “Ceres Material”). ICS will inform Ceres of and
obtain any permits or authorizations and proceed to any notifications which are
required to import the Ceres Material in China and transfer it to the premises of ICS.
Ceres will only deliver the Ceres Material after receipt of written notice from ICS
that all required permits, authorizations and notifications have been obtained, which
notice will include a copy of any such permits, authorizations and/or notifications.
Upon receipt of a delivery of Ceres Material, ICS will sign and return the Receipt Form
enclosed with the Ceres Material to Ceres, attn: Mr. Chuan-yin Wu.
	 
	 	2.2	 	ICS agrees to perform the activities defined in ANNEX I which shall be
referred to hereinafter as the “Program.” For all activities, ICS shall strictly
comply with the standard operating protocols referred to hereinafter as “SOPs”, which
will be provided by Ceres or jointly agreed upon by the Parties. Further, ICS shall
strictly comply with any Stewardship Guidelines which may be provided by Ceres. The
Stewardship Guidelines applicable as of the Effective Date are in ANNEX IV.
Ceres may provide written updated from time to time. The Program includes provision of
defined deliverables to Ceres.
	 
	 	2.3	 	In performing the Program activities ICS undertakes to comply with the work
plan and time schedule set forth in ANNEX I and with all applicable laws, rules
and regulations. Program activities will be performed by employees to be hired by ICS
or under ICS’ responsibility, by its Authorized Subcontractors in accordance with
Article 5. ICS will make available all laboratory, greenhouse, and field space and all
relevant equipment and supplies required to perform the Program, except that certain
chemicals and supplies not available in China will be provided by Ceres (delivery
conditions of Article 2.1 to apply), all as defined in ANNEX I.
	 
	 	2.4	 	ICS undertakes not to make any use of the Ceres Material which is not strictly necessary
for performing the Program activities in accordance with ANNEX I.










Page 1 of 47









 












	 	2.5	 	The Ceres Material will be used only at premises under the control of ICS or
its Authorized Subcontractors, located at Beijing, Hainan or Nanjing.
	 
	 	2.6	 	Upon termination of the Program, and except to the extent a different agreement
is reached pursuant to Article 7.4, ICS will destroy any remaining Ceres Material and
any material and information obtained under the Program, and will send Ceres forthwith
an attestation of such destruction.
	 
	 	2.7	 	ICS shall have the right, subject to compliance with all the conditions stated
hereinafter, to subcontract certain parts of the Program activities under its own
responsibility to the third parties identified hereinafter or otherwise agreed to in
writing by Ceres (“Authorized Subcontractors”).
	 
	 	 	 	South China University of Tropical Agriculture

Chinese Academy of Tropical Agriculture Sciences

Danzhou, Hainan 571737

China

Dongyi Huang, PhD, Professor, Dean
	 
	 	 	 	National Key Laboratory for Crop Genetics and Germplasm Enhancement

Nanjing Agricultural University

Nanjing 210095

China

Jianmin Wan, PhD, Professor
	 
	 	 	 	The following terms and conditions shall apply to ICS’ Authorized Subcontractors:
(a) the Authorized Subcontractors shall perform defined activities on behalf and for
the benefit of ICS in exchange for a fee or other tangible consideration; (b) the
Authorized Subcontractors shall deliver all the results of the Authorized
Subcontractors’ activities under the subcontract to ICS and Ceres only, and assign
ownership of any inventions made during the performance of the subcontracting
activities to Ceres or to ICS for further assignment to Ceres, without any further
remuneration; (c) the Authorized Subcontractors shall not have the right to use any
results, whether information or material, for any purpose whatsoever other than the
performance of the subcontract; (d) the Authorized Subcontractors shall be bound by
confidentiality obligations consistent with the terms and obligations of this
Agreement and shall be bound to comply with all SOP’s, Stewardship Guidelines, laws,
rules and regulations that govern their activities; and (e) ICS will provide to
Ceres a draft copy of any subcontract ICS is planning to conclude at least fifteen
(15) days before the scheduled signature date and will provide a true copy of any
subcontract to Ceres within thirty (30) days of its execution.






	3.	 	REPORTS






	 	3.1	 	During the entire Program, ICS and Ceres will participate in monthly conference
calls and provide detailed quarterly reports regarding Program progress, discoveries
made and results obtained during the implementation of the Program,




Page 2 of 47









 






	 	 	 	management, tracking and data transfer. The type of information to be included in
the reports and formatting is set forth in ANNEX I and ANNEX II.
Authorized Subcontractors may participate in conference calls as appropriate. The
reports provided by ICS will include the same information regarding Authorized
Subcontractors’ activities as for ICS’ own activities.
	 
	 	3.2	 	During the entire Program, ICS will promptly communicate to Ceres any
information on the Program activities or the results obtained or observed that Ceres
may ask. Between reports, ICS will also spontaneously communicate to Ceres any
unexpected observations or results.






	4.	 	REMUNERATION. PAYMENT






	 	4.1	 	Ceres will remunerate ICS as set forth in ANNEX I for the
implementation of the Program, in accordance with the payment schedule set forth in
such annex and the detailed Program budget in ANNEX III.
	 
	 	4.2	 	The payments will be made on the dates set forth in the payment schedule in
ANNEX I provided that Ceres has received a corresponding invoice from ICS
(detailing the actual resources used by ICS during the applicable period) at least
thirty (30) days in advance, by bank transfer to ICS’s account mentioned in its
invoice.






	5.	 	PROGRAM STAFFING






	 	5.1	 	ICS will hire employees with the qualifications set forth in ANNEX I,
to perform the Program activities on a full-time basis. Upon mutual agreement of the
Parties, one or more of said employees may be hired by Authorized Subcontractors
instead of ICS.
	 
	 	5.2	 	More detailed qualifications and criteria for hiring and evaluating the
performance of the employees referred to in Article 5.1 will be determined by mutual
agreement. Ceres will have the right to participate in the interview and performance
review process and a joint decision will be made on each person to be hired.
	 
	 	5.3	 	Subject to the prior written agreement of both Parties on a case-by-case basis,
ICS graduate students may be involved in certain Program activities.
	 
	 	5.4	 	ICS will provide quarterly updates to the Collaboration Committee on
anticipated personnel changes at ICS and its Authorized Subcontractors to the extent
relevant for the Program.






	6.	 	EXCHANGE OF SCIENTISTS






	 	6.1	 	From time to time, ICS employees who are scientists working on Program
activities may perform such activities temporarily at Ceres’ premises in Thousand Oaks,
California, U.S.A. (“Visiting Scientists”).




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	 	6.2	 	The Parties will mutually agree on each Visiting Scientist and the dates of
his/her stay at Ceres. Not more than one (1) Visiting Scientist will be at Ceres at
any given time, and the duration of each stay will not exceed three (3) months.
	 
	 	6.3	 	ICS shall bear the entire cost related to its Visiting Scientists, including
but not limited to salary, other allowances and benefits, social security, housing,
meals and travel, and shall be responsible for obtaining all necessary permits or
documents required for the stay and work abroad. However, for practical purposes
certain of such costs, to be mutually agreed, may be paid by Ceres and deducted from
payments due to ICS pursuant to this Agreement. Such costs to be deducted shall be
agreed to in writing by the Parties and properly documented.
	 
	 	6.4	 	ICS shall take out appropriate insurance for its Visiting Scientists, including
but not limited to health insurance, travel insurance and insurance for damages to
third parties and Ceres.
	 
	 	6.5	 	Visiting Scientists shall be subject to all internal rules applicable at Ceres
when working there and they will sign appropriate agreements prepared by Ceres to that
effect, including an amendment to their Agreement on Confidentiality and Assignment of
Inventions. Their access to Ceres’ premises shall be restricted to the normal working
hours applicable there. Their attendance of internal company seminars and meeting
shall be subject to prior approval of Ceres’ Chief Scientific Officer.
	 
	 	6.6	 	Visiting Scientists shall have no access to any Ceres technology apart from the
technology which is used in the Program.






	7.	 	COLLABORATION COMMITTEE






	 	7.1	 	The Parties shall establish a Collaboration Committee to oversee the
implementation of the Program. The Collaboration Committee will consist of four (4)
members, each Party to appoint two (2) members. The Collaboration Committee will meet
monthly by teleconference and quarterly at ICS.
	 
	 	7.2	 	The responsibilities of the Collaboration Committee will be as follows:






	 	7.2.1	 	Reviewing progress of work relative to timelines and deliverables.
	 
	 	7.2.2	 	Implementation and maintenance of process flows, SOPs,
Stewardship Guidelines and key performance indicators referred to hereinafter
as “KPIs”.
	 
	 	7.2.3	 	Recommending to the Parties actions as necessary to ensure
successful implementation of the Program.
	 
	 	7.2.4	 	Managing resources within the Program.
	 
	 	7.2.5	 	Discussing field trials and advancement of selected genes.





Page 4 of 47









 






	 	7.2.6	 	Recommending to the Parties corrective measures as appropriate
with respect to compliance shortfalls or failures.
	 
	 	7.2.7	 	Referring issues to designated senior technical and/or
business officers of Ceres and ICS where resolution is not obtainable.






	 	7.3	 	Any decision or recommendation of the Collaboration Committee will require the
consent of at least one (1) of the representatives appointed by either Party.






	8.	 	OWNERSHIP. INTELLECTUAL PROPERTY RIGHTS. EXPLOITATION






	 	8.1	 	This Agreement does not bring any change to the ownership and intellectual
property rights relating to the Ceres Material. ICS acknowledges that the Ceres
Material may be covered by patents or patent applications of Ceres.
	 
	 	8.2	 	Ceres will exclusively own any material, information, data, technology, or
other findings or inventions resulting from the Program (hereinafter “Results”).
Subject to Article 8.6, Ceres will have the exclusive rights to protect any of the
Results through patents or similar protection, and any intellectual property rights
arising therefrom will belong exclusively to Ceres. If ICS is prevented by law or
otherwise from assigning ownership or protecting all rights in the Results as
contemplated by this Article 8.2, ICS shall take all steps necessary to give effect to
this clause, including but without limitation procuring that its employees,
consultants, Authorized Subcontractors, agents or otherwise shall take all steps
necessary to give effect to this clause.
	 
	 	8.3	 	In case ICS or an Authorized Subcontractor has made or contributed to any
invention forming part of the Results, ICS shall promptly inform Ceres thereof, giving
detailed information in a confidential written report. ICS shall, to the extent that
rights do not automatically vest in Ceres by virtue of the forgoing, assign its rights
in any such invention to Ceres. ICS shall render such assistance as may be required
for assigning any rights ICS inventors may have in such invention to Ceres or Ceres’
designee and for protecting such invention, including but not limited to the signing of
documents. Any inventor of ICS will be recognized in patent applications on an
invention which is part of the Results in accordance with U.S. patent law. If ICS is
prevented by law or otherwise from assigning its rights in inventions to Ceres as
contemplated by Article 8.2, ICS hereby grants Ceres all licenses, to the fullest
extent possible, to effectuate the intent of this Agreement that Ceres be assigned such
inventions, and to otherwise effectuate the purposes of this Agreement. ICS will cause
its Authorized Subcontractors to comply with the provisions of Articles 8.1 through 8.3
as if they were ICS.
	 
	 	8.4	 	Subject to Article 8.5, Ceres will have the exclusive right to commercialize
any of the Results.
	 
	 	8.5	 	At any time during the term of this Agreement, if ICS is interested in
commercializing a selected Result or Results in rice in China, ICS will notify
Ceres thereof in writing. Subject to any obligations of Ceres vis-à-vis third




Page 5 of 47









 






	 	 	 	parties at the time of such notification, Ceres will negotiate with ICS in good
faith about the grant by Ceres to ICS of a royalty-bearing license to commercialize
such selected Result(s) in rice in China and/or potential collaborative business
approaches for the commercialization of such selected Result(s) in rice in China.
The terms and conditions of such agreement may include the filing by ICS of patent
applications or other intellectual property rights on selected Results in China. If
no such agreement is signed six (6) months after the aforementioned notification by
ICS, neither Party shall have any obligation to enter into such an agreement.






	9.	 	CONFIDENTIALITY






	 	9.1	 	ICS will treat any and all information and material communicated or transferred
to it by Ceres pursuant to this Agreement (including but not limited to the Ceres
Material) and any Results as strictly confidential and will not use the same for any
purpose other than as expressly allowed by this Agreement nor disclose or transfer the
same to any third party other than its employees or other collaborators or Authorized
Subcontractors (or graduate students, if decided by the Parties jointly) necessary to
carry out the Program and bound by appropriate secrecy and non-use undertakings.
	 
	 	9.2	 	The obligations of ICS in Article 9.1 shall not apply to any information,
material or Results which ICS can demonstrate by competent evidence:






	 	- 	 	were lawfully in ICS’s possession without restriction prior to
disclosure by Ceres, as evidenced by written records of ICS;
	 
	 	- 	 	were in the public domain prior to disclosure by Ceres, or
subsequently comes in the public domain through no fault, action or
omission of ICS; or
	 
	 	- 	 	are made available to ICS, without any restriction, by a third party
who had the right to do so.






	 	9.3	 	If ICS wishes to disclose certain information relating to the Program to
Chinese government authorities with a view to obtaining a grant, ICS will inform Ceres
thereof, and the Parties will jointly define the information to be submitted to such
authorities. To the extent feasible under applicable law, ICS will make a reasonable
effort to obtain a protective order or other confidential treatment requiring that the
information so disclosed be used only for the purposes for which disclosure was made.
	 
	 	9.4	 	ICS will require all individuals performing Program activities to sign a
confidentiality agreement with Ceres, as per the model agreement in ANNEX V.






	10.	 	PUBLICATIONS






	 	10.1	 	“Publication” and “Publish” shall include any discussion with or presentation
to a third party, other than parties referred to in Article 9.1. Examples of
Publications
include, without limitation: presentation at a conference, submission for




Page 6 of 47









 






	 	 	 	publication to a journal, submission of joint proposals, posting information on a
website, posters, abstracts, Ph.D. dissertations, and informal oral discussions.
	 
	 	10.2	 	Subject to Ceres prior written approval, which will not unreasonably be
withheld, ICS may proceed to Publication of selected Results provided that: (i) no
confidential information of Ceres is revealed thereby, (ii) ICS shall take into account
any suggestions which may be formulated by Ceres, and (iii) at least thirty (30) days
prior to the submission to a publisher or presentation to any third party, ICS delivers
copies of the proposed Publication to Ceres for review. At Ceres’ request, ICS shall,
for a reasonable period up to ninety (90) days from initial delivery to Ceres, delay
revealing any patentable subject matter in the disclosure in order to permit the filing
of patent applications. In any Publication, the Parties shall consider joint
authorship and acknowledge the contributions and publications of the other as
scientifically appropriate.






	11.	 	WARRANTIES. LIMITED LIABILITY






	 	11.1	 	ICS acknowledges that the Ceres Material is of an experimental nature and will
take all reasonable precautions to prevent any damage or injury by the Ceres Material.
ICS will use its best efforts to prevent any theft or unauthorized use of the Ceres
Material or any Results.
	 
	 	11.2	 	ICS warrants that the Ceres Material will exclusively and restrictedly be used
under suitable containment conditions, and in accordance with all applicable
regulations, SOP’s and Stewardship Guidelines, and it will not be used on human
subjects. ICS will be responsible for obtaining any authorizations or permits or
proceeding to any notifications which may be required for its activities with the Ceres
Material.
	 
	 	11.3	 	ICS warrants that its Authorized Subcontractors will comply with the terms and
conditions of this Agreement.
	 
	 	11.4	 	Ceres declines any liability for any damage which may be caused by the Ceres
Material or the Program activities to ICS or any Authorized Subcontractor or any third
party. If Ceres is held to indemnify a third party for any damage related to the
conduct of the Program activities, ICS will indemnify and hold Ceres harmless for the
amounts paid by Ceres to such third party.
	 
	 	11.5	 	Neither Party shall be liable for indirect, special, remote, incidental or
consequential damages or loss of profit in connection with this Agreement or its
implementation.






	12.	 	GENERAL CONDITIONS






	 	12.1	 	Amendments: This Agreement, including its annexes, may only be amended
by a written document signed by duly authorized representatives of the Parties.
	 
	 	12.2	 	Ambiguities: In case of ambiguity between this Agreement and its
annexes, the contents of this Agreement shall prevail.




Page 7 of 47









 






	 	12.3	 	Number of copies: This Agreement including its annexes is being made
in two (2) copies, one for each Party.
	 
	 	12.4	 	Assignment / Subcontracts: Ceres has concluded this Agreement with ICS
in view of ICS’s specific qualifications and ICS shall not have the right to assign any
of its rights or obligations under this Agreement nor to sub-contract any part of the
Program activities to any third party, except with the prior written approval of Ceres
as provided in Article 2.7 on Authorized Subcontractors. Ceres has the right to assign
its rights and obligations under this Agreement to any third party. Further, Ceres has
the right to entrust the implementation of all or part of its obligations under this
Agreement to any of its affiliates.
	 
	 	12.5	 	Invalid provisions: If any provision of this Agreement is or becomes
invalid, is ruled illegal by a court of competent jurisdiction or is deemed
unenforceable under the current applicable law from time to time in effect during the
term of this Agreement, the remainder of this Agreement will not be affected or
impaired thereby and will continue to be construed to the maximum extent permitted by
law. In lieu of each provision which is invalid, illegal or unenforceable, there will
be substituted or added as part of this Agreement by mutual written agreement of the
Parties, a provision which will be as similar as possible in economic and business
objectives as intended by the Parties to such invalid, illegal or unenforceable
provision, but will be valid, legal and enforceable.
	 
	 	12.6	 	Equitable Remedies: It is understood and agreed that money damages
would not be a sufficient remedy for any breach of this Agreement by ICS and that Ceres
is entitled to equitable relief, including injunction and specific performance, as a
remedy for any such breach. Such remedies shall not be deemed to be the exclusive
remedies for a breach by ICS of this Agreement but shall be in addition to all other
remedies available at law or equity to Ceres.
	 
	 	12.7	 	Governing Law / Jurisdiction: This Agreement shall be governed by, and
construed and interpreted in accordance with, the laws of the State of California
without regard to principles of conflicts of law. The Parties agree that any dispute
regarding the interpretation or validity of, or otherwise arising out of this
Agreement, shall be subject to the exclusive jurisdiction of the California State
Courts of San Francisco County or, in the event of federal jurisdiction, the United
States District Courts of the Northern District of California, and each Party agrees to
submit to the personal and exclusive jurisdiction and venue of the courts and not to
seek the transfer of any case or proceeding out of such courts.
	 
	 	12.8	 	Notices: Any notice, notification or report permitted or required by
this Agreement shall be sent by (i) facsimile with written confirmation copy, (ii)
registered mail or (iii) a recognized private mail carrier service, and such notice
shall be effective on the date received as indicated by the facsimile imprint date in
the case of (i), or the carrier receipt of delivery to the addressee in the case of
(ii) and (iii), if sent and addressed as follows or to such other address as may be
designated by a Party in writing:




Page 8 of 47









 











	 	 	 	 	 

	 

	 	If to Ceres:
	 	Ceres, Inc.
	 

	 	 	 	1535 Rancho Conejo Blvd.
	 

	 	 	 	Thousand Oaks, California, 91320
	 

	 	 	 	USA
	 

	 	 	 	Attention: Vice President of Product Development
	 

	 	 	 	cc: Legal Department
	 

	 	 	 	Telephone Number: (805) 376-6500
	 

	 	 	 	Facsimile Number: (805) 376-6549
	 
	 	 	 	 
	 

	 	If to ICS:
	 	Institute of Crop Sciences
	 

	 	 	 	Chinese Academy of Agricultural Sciences
	 

	 	 	 	12 South Zhongguanchun Street
	 

	 	 	 	Haidian District
	 

	 	 	 	Beijing 100081
	 

	 	 	 	People’s Republic of China
	 

	 	 	 	Attention: Mr. Jian-Min Wan, Director
	 

	 	 	 	Telephone number:
	 

	 	 	 	Facsimile number:







	13.	 	DURATION






	 	13.1	 	This Agreement will enter into force on the date first written hereinabove and
will remain in full force and effect until the delivery by ICS of the last report
provided for in this Agreement, or until the last payment is due by Ceres pursuant to
this Agreement is made, whatever is later. Notwithstanding the foregoing, Ceres will
have the right to terminate this Agreement unilaterally at any time by giving sixty
(60) days’ prior written notice to ICS.
	 
	 	13.2	 	Either Party will have the rights to terminate this Agreement unilaterally by
registered letter addressed to the other Party in case such other Party has committed a
breach of any of its obligations under this Agreement and has failed to remedy such
breach within thirty (30) days from the receipt of a registered letter specifying the
breach.
	 
	 	13.3	 	Expiration or termination of this Agreement will not relieve either Party of
any obligation accruing prior to such expiration or termination. The provisions of
Articles 8, 9, 10, 11, 12.5, 12.6 and 12.7 will survive the expiration or termination
of this Agreement.





Page 9 of 47









 




Made in two (2) copies.




	 	 	 	 	 	 	 	 	 

	Institute of Crop Sciences 


Chinese Academy of Agricultural 

Sciences	 	Ceres, Inc.	 	 
	 
	 	 	 	 	 	 	 	 
	By: 

Name:

	 	/s/ Jian-Min Wan
 

Jian-Min Wan
	 	By:

Name:
	 	/s/ Peter Mascia
 

Peter Mascia
	 	 
	Title:

	 	Director
	 	Title:
	 	Vice President of Product
Development	 	 
	 
	 	 	 	 	 	 	 	 
	By: 

Name:

	 	/s/ Hu-Qu Zhai
 

Hu-Qu Zhai
	 	By:

Name:
	 	/s/ Richard Flavell
 

Richard Flavell, CBE, FRS
	 	 
	Title:

	 	President
	 	Title:
	 	Chief Scientific Officer	 	 






Page 10 of 47









 





ANNEX I




to the Collaboration Agreement between Ceres, Inc. and ICS



Program Plan




	1.	 	CERES MATERIAL






	 	 	Within 30 days from the Effective Date Ceres will provide approximately [***] gene
constructs in vectors designed for Agrobacterium-mediated rice transformation. At the
beginning of each calendar quarter thereafter, for a total of 12 quarters or as otherwise
agreed by Ceres and ICS, Ceres will provide approximately an additional [***] gene
constructs. Each group of constructs delivered to ICS will also contain target trait
information. In addition, within 30 days from the Effective Date Ceres will provide a list
of up to [***] pairs of selected events for which it would like the corresponding transgenes
combined into a single rice line using genetic crossing. At the beginning of each calendar
year thereafter, for a total of four years or as otherwise agreed by Ceres and ICS, Ceres
will provide an additional list of up to [***] pairs of selected events to be crossed. The
total number of slots for constructs to be transformed into rice and multiple-transgene
lines to be generated by genetic crossing is [***]. The rice lines generated will be
phenotyped and assayed for selected traits. At its option, Ceres can increase the number of
gene constructs for transformation to [***] per quarter and [***] crosses per year. In
addition, ICS and Ceres will collaborate on the QTL analysis of biomass in rice. The Program
will continue for 24 months after the final delivery of gene constructs. ICS will submit a
final report within 30 days after the end of such 24-month period.






	2.	 	PROGRAM ACTIVITIES






	 	 	The goal of the program is to generate and evaluate carefully selected plant gene constructs
of various origins under field conditions and under selected assay conditions by using a
high through-put rice transformation system. A second goal is to combine transgenes and
stack selected transgene-induced traits using genetic crosses between transgenic rice
plants. A third goal is to perform a QTL analysis of biomass in rice to determine the
identity of sequences that are associated with target biomass traits. Information generated
from this program is intended to be used for crop improvement.






	 	2.1	 	CERES ACTIVITIES






	 	2.1.1	 	High throughput cloning (HTPC): Selection and
construction of genes, transformation of Agrobacterium cells, delivery of
constructs to ICS in Agrobacterium (or transgenic seeds) and quality control of
the HTPC pipeline on a quarterly basis.






	 	2.1.1.1	 	Generate construct tracking numbers for all constructs, e.g.
CW00001.
	 
	 	2.1.1.2	 	List of target traits or predicted phenotype for each construct.











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Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission












 












	 	2.1.2	 	Prioritization: Prioritization of delivered
constructs for transformation, prioritization of existing events for genetic
crossing, and prioritization of existing events for plant assay.
	 
	 	2.1.3	 	Quality control: Deliver gene-specific primers and
vector primer sequences to ICS for use in quality control experiments using
gene-specific PCR. Verify quality control processes at ICS and at SCUTA as per
SOP R1 and R2 in ANNEX IV.
	 
	 	2.1.4	 	Data formats: Prescribe data formats for recording
phenotyping results, assay results and data transfer (ANNEX II).
	 
	 	2.1.5	 	Internet server: Establish and maintain an
independent web-accessible server for use by ICS, SCUTA and Ceres.
	 
	 	2.1.6	 	IT support: Establish a Program database. Provide
expertise and training for electronic data capture and for database management.






	 	2.2	 	ICS ACTIVITIES






	 	2.2.1	 	Rice transformation and rice genetic crosses: Perform
transformation and genetic crosses in rice, approximately [***] per year, for a
total of [***] for this Agreement. Written SOPs for all phenotyping and assays
will be provided by Ceres or developed by ICS in consultation with Ceres Trait
Managers by the end of year two of the Agreement. ICS will also track and
deliver quarterly updates for selected Program KPIs (ANNEX II).






	 	2.2.1.1	 	Transformation: Transform up to [***]constructs per quarter
and produce and collect seeds from [***] independent events (T0 plants)
for each construct (SOP R1). Maintain updated Program database that
includes articles 2.2.1.1.1 to 2.2.1.1.5. Update Ceres monthly.






	 	2.2.1.1.1	 	T0 production: See the Transformation Table and
KPI 1.1 (ANNEX II).
	 
	 	2.2.1.1.2	 	T0 plant phenotyping: See SOP R1. Include
descriptions, images and dates.
	 
	 	2.2.1.1.3	 	T1 seed production: See SOP R3, the Seed
Production Table and KPI 1.3 (ANNEX IV).
	 
	 	2.2.1.1.4	 	Quality control: See SOP R1 and R2, the
Transformation Table, the Quality Control Table and KPI 1.2
(ANNEX IV).
	 
	 	2.2.1.1.5	 	OPTION: Ceres can elect to exercise an option to
increase the number of constructs from [***] to [***] per
quarter.













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Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission











 












	 	2.2.1.2	 	T1 phenotyping — plant growth and development: Analyze T1
progeny from all events from article 2.2.1.1 for growth and development
phenotypes. Maintain updated Program database that includes articles
2.2.1.2.1 to 2.2.1.2.2. Update Ceres monthly.






	 	2.2.1.2.1	 	T1 plant phenotyping: See SOP R2 (ANNEX
IV). Include descriptions, coded comments, images and data
entry dates. Maintain a phenotype tracking database.
	 
	 	2.2.1.2.2	 	T2 seed production: See SOP R3 and the Seed
Production Table (ANNEX II, Table 3).






	 	2.2.1.3	 	T2 phenotyping: Upon request selected lines will be chosen
for additional phenotyping. Resources used for T2 plant phenotyping
should not exceed prescribed Program resources without the consent of
the Collaboration Committee. See SOP R2 (ANNEX IV).
	 
	 	2.2.1.4	 	Trait assays: Selected lines will be assayed for drought
tolerance, low N tolerance or composition by NIR. SOPs are presented in
ANNEX II.






	 	2.2.1.4.1	 	Drought tolerance: See the drought tolerance assay
SOP R4 (ANNEX IV).
	 
	 	2.2.1.4.2	 	Low N tolerance: See the low nitrogen assay SOP R5
(ANNEX IV).
	 
	 	2.2.1.4.3	 	NIR analysis: See SOP R6 (ANNEX IV).
Analyze plant material selected by Ceres for composition using
NIR.
	 
	 	2.2.1.4.4	 	Genotyping quality control: All events that are
selected for assaying will be sequence validated using
gene-specific PCR. In addition, Ceres may request plant material
or plant DNAs for QC analysis.
	 
	 	2.2.1.4.5	 	Images: Photographs will be taken of all plants
that display a distinct morphological phenotype or response to
assay conditions affecting plant growth, development, biomass,
fertility, stem morphology, tiller number or leaf morphology.
Images with and without labels and plant descriptions will be
stored in an image database and the Image Log Table (ANNEX
II, Table 6).






	 	2.2.1.5	 	OPTION: Ceres can elect to exercise an option to increase
the repertoire of measurements and assays.




Page 13 of 47









 












	 	2.2.1.5.1	 	New SOPs can be developed at ICS in consultation with Ceres
as authorized by the Collaboration Committee.
	 
	 	2.2.1.5.2	 	Resources for trait assay development and utilization
should not exceed prescribed resources without the consent of
the Collaboration Committee.






	 	2.2.1.6	 	Genetic crossing of transgenics: Perform up to [***]
crosses per year to stack and combine selected transgenes into a single
line. Crosses and events will be requested and prioritized by Ceres.
Crosses will be reviewed and scheduled by the Collaboration Committee.
The parent lines for crosses will be germinated two times each year —
in April for crosses made by ICS and in October for crosses made by
SCUTA.






	 	2.2.1.6.1	 	Homozygous T2 lines for crossing will be identified using
herbicide treatments at ICS or SCUTA.
	 
	 	2.2.1.6.2	 	Each cross requested will be given a unique CW
identification number, e.g. CW50001, CW50002. Parents, F1 and F2
seeds will be tracked in the Genetic Crossing Table (ANNEX
II).
	 
	 	2.2.1.6.3	 	Ceres Trait Managers will specify the number of F1 seeds
that need to be produced for each trait assay.
	 
	 	2.2.1.6.4	 	OPTION: Ceres can elect to exercise an option to increase
the number of crosses to [***] per year.






	 	2.2.1.7	 	F1 phenotyping: Grow F1 progeny and parents in the field
side-by-side, e.g. row 1, parent 1; row 2, F1; row 3, parent 2.
Phenotype as per SOP R2.






	 	2.3	 	QTL analysis of biomass: Genetically map quantitative trait loci
responsible for target biomass traits in rice.






	 	2.3.1	 	Target traits for QTL analysis. Plant height, growth rate,
flowering time, productive tiller number, stem thickness, biomass, and stem
composition (as determined by NIR).
	 
	 	2.3.2	 	Select parent lines and crosses for biomass QTL analysis.
Parent lines, descriptions and available crosses are listed in ANNEX
II. Screen parents for usable marker polymorphisms.
	 
	 	2.3.3	 	F2 analysis. [***] ([***]) F2 populations, [***] individuals in size, will be
used for QTL analysis. Identify the [***] top biomass producing plants from
each cross. Extract DNAs and map major QTLs. The estimated number of







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	 	 	 	project samples to be analyzed is [***]. Save seeds from all top
biomass plants.
	 
	 	2.3.4	 	Analyze composition of parent lines, F1 and F2 plants using
NIR. Save stem samples from all parents, F1 and selected F2 plants. Perform NIR
analysis on samples at ICS or at Ceres using SOP R6 (ANNEX IV).






	 	2.4	 	Quarterly delivery of transgenic rice seeds and biological materials to Ceres.






	 	2.4.1	 	ICS will work in good faith to obtain phytosanitary
certification and ship seeds requested by Ceres to the USDA in Maryland for
inspection and release to Ceres. This should take no more than three (3)
months.






	3.	 	Reports






	 	3.1	 	Deliver Program Reports to the Collaboration Committee on a quarterly basis at
the end of each calendar quarter. Reports shall include, but not be limited to:






	 	3.1.1	 	KPI summary. Gather KPI data according KPIs listed in
Section 1 ANNEX II and improve underlying processes.
	 
	 	3.1.2	 	Transformation update: Updated Transformation Table
including the identification and number of constructs transferred to rice and
summary of T0 QC analysis (ANNEX II, Table 1 and 2).
	 
	 	3.1.3	 	T1 and T2 seed production update: Updated Seed
Production Table (ANNEX II, Table 3).
	 
	 	3.1.4	 	T1 plant phenotyping update: Summary of T1 plant
phenotyping including descriptions, measurements and images.






	 	3.1.4.1	 	Phenotyping descriptions to be based on articles 2.2.1.2 and 2.2.1.3
of this ANNEX and in accordance with a coded comments system (SOP R2).






	 	3.1.5	 	Trait assay update: Summary of trait assay results,
measurements and images.
	 
	 	3.1.6	 	Genetic crossing update: Updated Genetic Crossing
Table (ANNEX II,Table 4) including crosses made and F1 seed
collected.
	 
	 	3.1.7	 	Summary of QTL Mapping: markers used, measurements,
mapping results, major loci identified.






	4.	 	Resources to be made available by the Parties






	 	4.1	 	ICS will make available the following resources for the implementation of the
Program (in addition to employees):




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	 	4.1.1	 	Laboratory space, fully equipped, installed and operational:
At least [***] square meters ([***] square feet) for media preparation and
molecular studies
	 
	 	4.1.2	 	Tissue culture space: At least [***] square meters ([***]
square feet) for tissue culture.
	 
	 	4.1.3	 	Screenhouse and droughthouse space for growing primary
transgenics and T1 plants: At least [***] square meters ([***] square feet).
	 
	 	4.1.4	 	Greenhouse space for germination, hydroponic assays, sample
drying and crosses: At least [***] square meters ([***] square feet).
	 
	 	4.1.5	 	Field space for evaluation of T1 and T2 plants: at least [***]
square meters ([***] square feet).
	 
	 	4.1.6	 	Supplies, chemicals, utilities as required.






	 	4.2	 	SCUTA will make available the following resources for the implementation of the
Program (in addition to employees):






	 	4.2.1	 	Laboratory space, fully equipped, installed and operational:
at least [***] square meters ([***] square feet) for seed storage and molecular
studies
	 
	 	4.2.2	 	Screenhouse space for growing primary transgenic plants and T1
plants: At least [***] square meters ([***] square feet).
	 
	 	4.2.3	 	Supplies, chemicals, utilities as required.






	 	4.3	 	At the request of ICS and SCUTA, Ceres will provide chemicals, supplies and IT
training required for the Program activities which are not available in China.
Delivery conditions of Article 2.1 of the Agreement to apply.






	5.	 	Remuneration and payment schedule






	 	5.1	 	Ceres will pay for employees for the Program referred to in Article 5.1 of the
Agreement at the rates indicated below (including salary, benefits and partial support
for apartment rental).






	 	5.1.1	 	IT specialist, $[***]
	 
	 	5.1.2	 	Post-doctoral fellow, $[***]
	 
	 	5.1.3	 	PhD student, $[***]
	 
	 	5.1.4	 	BS/MS level, $[***]
	 
	 	5.1.5	 	Technical/field staff, $[***]







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	 	5.2	 	Ceres will pay for use of [***] square feet of laboratory space at ICS at a
rate of $[***] per 10 square feet per year (approximately $[***] per year), including
water, electricity and other utilities.
	 
	 	5.3	 	Ceres will pay for use of [***] square feet of laboratory space at SCUTA at a
rate of $[***] per 10 square feet per year (approximately $[***] per year), including
water, electricity and other utilities.
	 
	 	5.4	 	Ceres will pay for use of [***] square feet of tissue culture room at a rate of
$[***] per 10 square feet per year (approximately $[***] per year), including water,
electricity, utilities and maintenance.
	 
	 	5.5	 	Ceres will pay for use of [***] square feet of ICS greenhouse space at a rate
of $[***] per 10 square feet per year (approximately $[***] per year), including water,
electricity, heating and others.
	 
	 	5.6	 	Ceres will pay for the installation of greenhouse lights at ICS at a one time
cost of $[***].
	 
	 	5.7	 	Ceres will pay for the use of [***] square feet of ICS screenhouse and
droughthouse space at a rate of $[***] per 10 square feet per year (approximately
$[***] per year). Includes screening film, soil preparation, water, plant care and pest
control.
	 
	 	5.8	 	Ceres will pay for the use of up to [***] square feet of specially segregated
and controlled access field space at Langfang Field Station for transgenic rice plants
at a rate of $[***] per 10 square feet per year plus room, board and transportation for
ICS breeder and field staff (approximately $[***] per year). Space has already been
approved by the Ministry of Agriculture for the growth of transgenic rice. Includes
soil preparation, water and pest management.
	 
	 	5.9	 	Ceres will pay for the use of [***] square feet of SCUTA screenhouse at a rate
of $[***] per 10 square feet (approximately $[***] per year). Includes soil
preparation, water and pest management.
	 
	 	5.10	 	Ceres will pay $[***] per year for growth media, supplies for QC, supplies for
Southerns, northerns, PCR, RT-PCR, assays, QTL mapping, chemicals and utilities for ICS
(including direct purchases by Ceres outside China).
	 
	 	5.11	 	Ceres will pay $[***] per year for supplies, chemicals and utilities for SCUTA
(including direct purchases by Ceres outside China).
	 
	 	5.12	 	Ceres will pay $[***] per year for 5 round trips travel to Hainan for ICS @
[***] CNY airfare, [***] CNY for 3 days hotel and meals and [***] CNY for ground
transportation.
	 
	 	5.13	 	Ceres will pay $[***] per year for 5 round trips travel to Beijing for SCUTA @ [***]
CNY airfare [***] CNY for 3 days hotel and meals, [***] CNY for ground transportation.












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	 	5.14	 	Ceres will pay $[***] per year to support ICS research activities.
	 
	 	5.15	 	Ceres will pay $[***] per year to support SCUTA research activities.
	 
	 	5.16	 	Payments to ICS will be made quarterly, within 30 days of Ceres’ receipt of an
invoice from ICS. An initial quarterly payment of $[***] will be made after the
Effective Date within 30 days of Ceres’ receipt of an invoice from ICS. Disbursement
of Program funds to SCUTA is the responsibility of ICS.
	 
	 	5.17	 	Budget summary






	 	5.17.1	 	Table 1: Budget summary for Program.
	 
	 	5.17.2	 	Table 2: Budget summery for Program Option.
	 
	 	5.17.3	 	Detailed Program budget: see ANNEX III, Table 1.
	 
	 	5.17.4	 	In the case that the exchange rate for one USD to RMB (RENMINBI), as quoted
by the Financial Management Service (FMS) of the U.S. Department of the
Treasury (DOT), and monitored by ICS on each anniversary of the effective date,
declines by 10 percent from 7.544 to less than 6.790 or increases by 10 percent
to greater than 8.300, then ICS or Ceres can propose that the payment schedule
in Table 1 be recalculated by Ceres and that future payments in USD be adjusted
based on the then current USD to RMB exchange rate.




Such payment adjustment can be requested one time during the Agreement.



Table 1. Program budget summary.




	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	5 YEAR
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	TOTAL IN
	 	 	Year 1	 	Year 2	 	Year 3	 	Year 4	 	Year 5	 	USD
	Lab space, plant growth, expendables, administration
	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 
	Project FTEs
	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 
	TOTAL CONTRACT
	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 	 	 	[***]	 






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ANNEX II




to the Collaboration Agreement between Ceres, Inc. and ICS



Reports and Report Format



Table 1. Transformation Table.




	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	DATE	 	SHIPME	 	 	 	 	 	 	 	 	 	NUM_RE	 	 	REGENE	 	 	PLANTLE	 	 	SOIL_TR	 	 	 	 	 	 	 	 	 	 	T0_PHEN	 	 	T1_SEED	 	 	T1_EVEN	 
	TRAN	 	 	 	RECEI	 	NT_NU	 	 	 	 	 	AGRO_G	 	INFECTIO	 	SISTANT	 	 	RATION	 	 	TS_GENE	 	 	ANSPLAN	 	 	T0_TO_S	 	 	T0_LOCA	 	 	OTYPING	 	 	_HARVE	 	 	TS_HARV	 
	S_ID	 	CW_LINE	 	VED	 	MBER	 	STATUS	 	REASON	 	ROWTH	 	N_DATE	 	_CALLI	 	 	DATE	 	 	RATED	 	 	T_DATE	 	 	OIL	 	 	TION	 	 	_NOTES	 	 	ST_DATE	 	 	ESTED	 
	1
	 	CW00001	 	12/1/04	 	01	 	FINISHED	 	INSUFFICIENT T1 EVENTS	 	Yes	 	12/18/04	 	 	23	 	 	 	2/26/05	 	 	 	18	 	 	 	5/15/05	 	 	 	 	 	 	ICS	 	 	Broad leaves	 	 	 	9/28/05	 	 	 	8	 
	2
	 	CW00002	 	12/1/04	 	01	 	FINISHED	 	INSUFFICIENT T1 EVENTS	 	Yes	 	12/18/04	 	 	20	 	 	 	2/26/05	 	 	 	15	 	 	 	5/15/05	 	 	 	 	 	 	ICS	 	 	 	 	 	 	 	9/28/05	 	 	 	7	 
	3
	 	CW00003	 	12/1/04	 	01	 	FINISHED	 	INSUFFICIENT T1 EVENTS	 	Yes	 	12/18/04	 	 	21	 	 	 	2/26/05	 	 	 	10	 	 	 	5/15/05	 	 	 	 	 	 	ICS	 	 	 	 	 	 	 	9/28/05	 	 	 	6	 
	4
	 	CW00004	 	12/1/04	 	01	 	FINISHED	 	INSUFFICIENT T1 EVENTS	 	Yes	 	12/18/04	 	 	21	 	 	 	2/26/05	 	 	 	9	 	 	 	5/15/05	 	 	 	 	 	 	ICS	 	 	 	 	 	 	 	9/28/05	 	 	 	6	 






Table 2. Transformation Table description of contents.




	 	 	 
	Column	 	Description
	TRANS_ID

	 	Unique barcode for a particular transformation event
	CW_LINE

	 	CW identifier supplied by Ceres
	DATE_RECEIVED

	 	Date constructs were received by ICS
	SHIPMENT_NUMBER

	 	Batch number of shipment
	STATUS

	 	Current status of construct: Received, In Process, Finished, Failed
	REASON

	 	Only for Failed constructs, explain why they failed
	AGRO_GROWTH

	 	Yes/No — did Agro grow
	INFECTION_DATE

	 	Date calli infection was performed
	NUM_RESISTANT_CALLI

	 	Number of resistant calli resulting from infection
	REGENERATION_DATE

	 	Date plantlet regeneration started
	PLANTLETS_GENERATED

	 	Number of plantlets resulting from regeneration
	SOIL_TRANSPLANT_DATE

	 	Date plantlets were transplanted to soil
	T0_TO_SOIL

	 	Number of T0 plants transplanted to soil
	T0_LOCATION

	 	Location of T0 plants (ICS, SCUTA)
	T0_PHENOTYPING_NOTES

	 	Any observations made while T0 plants are in soil
	T1_SEED_HARVEST_DATE

	 	Date of T1 seed harvest
	T1_EVENTS_HARVESTED

	 	Number of T1 seed lots harvested





Table 3. Seed Production Table.




	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Date of	 	 	 	Generation of	 	 	 	 	 	 	 	Container	 	Amount	 	 
	CW_ID	 	Harvest	 	Harvested By	 	Seed	 	Location	 	Building	 	Room	 	(Barcode)	 	(g)	 	Notes
	CW00006

	 	1/1/2006
	 	LZ
	 	T1
	 	SCUTA
	 	AAA
	 	XXX
	 	 	123456	 	 	 	2	 	 	Notes on
germination, amount
used (2.1.2006)
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	CW00003

	 	1/1/2006
	 	LZ
	 	T1
	 	SCUTA
	 	BBB
	 	XXX
	 	 	123457	 	 	 	3	 	 	Poor germination
(1.1.2007)
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	CW00006-01

	 	6/1/2006
	 	 	 	T2
	 	ICS
	 	 	 	YYY
	 	 	123458	 	 	 	4	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	CW00010

	 	7/1/2007
	 	CYW
	 	F1
	 	ICS
	 	 	 	YYY
	 	 	123459	 	 	 	0.5	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	CW00010-01

	 	10/1/2007
	 	XZ
	 	F2
	 	ICS
	 	 	 	YYY
	 	 	123460	 	 	 	2	 	 	 






Page 19 of 47









 




Table 4. Genetic Crossing Table.




	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Pollination	 	 	 	 	 	P1	 	 	 	P2	 	 	 	 	 	Deliver	 	Harvest	 	 
	CW_ID	 	Date	 	Crosser	 	Parent 1 	 	Trait	 	Parent 2  	 	Trait	 	Requester	 	Reason	 	By	 	Date	 	Project
	CW50010

	 	4/1/2007
	 	CYW
	 	CW00006-01-01
	 	Drought
	 	CW00003-01-01
	 	Drought
	 	JKO
	 	Stacking test
	 	6/1/2007
	 	4/1/2007
	 	Product Development
	CW50011

	 	4/1/2007
	 	CYW
	 	CW00006-01-01
	 	Drought
	 	CW00002-01-01
	 	Drought
	 	JKO
	 	Stacking test
	 	6/1/2007
	 	4/1/2007
	 	Product Development
	CW50012
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	CW50013
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 





Table 5. Available Parents for Biomass QTL Analysis.




	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Parent	 	Plant Height (m)	 	Tillers	 	Flowering time
	P1

	 	KN
	 	 	2	 	 	Less
	 	Late
	P2

	 	DWR-4
	 	 	N/A	 	 	Fast growing, stem elongation
	 	Average
	P3

	 	Nanjing 6
	 	>1.7
	 	High, strong stems
	 	Late
	P4

	 	Kuidao
	 	 	2	 	 	N/A
	 	N/A
	P5

	 	 	601	 	 	 	0.8	 	 	N/A
	 	Average





Table 6. Image Log Table.




	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	Image	 	 	 	 	 	 	 	 
	CW_ID	 	Image _ID	 	Description	 	Trait	 	Phenotype	 	Image Type	 	Location
	CW00196-04

	 	 	87654321	 	 	Whole plant and
controls
	 	Biomass
	 	Increased biomass
	 	Phenotype
	 	SCUTA
	CW00006-01

	 	 	87654322	 	 	Plot image
	 	Drought
	 	Drought tolerance
	 	Assay Result
	 	ICS
	CW00006-01-01

	 	 	87654323	 	 	Field shot
	 	Drought
	 	Drought tolerance
	 	Field Trial
	 	CHANGPING






Table 7. Data Collection Table.




	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	Measurement	 	 	 	 	 	 	 	 	Plant Position	 
	Block	 	Row	 	CW_Event	 	Measurement	 	_Code	 	 	Name	 	 	Date	 	 	1	 	 	2	 	 	3	 	 	4	 	 	5	 	 	6	 	 	7	 	 	8	 	 	9	 	 	10	 
	10
	 	1	 	CW00222-01	 	Plant_Status	 	 	1	 	 	 	 	 	 	 	5/31/2007	 	 	bugs	 	 	 	 	 	 	blight	 	 	 	 	 	 	 	 	 	 	sick	 	 	 	 	 	 	 	 	 	 	 	 	 	 	yellow	 
	10
	 	1	 	CW00222-01	 	Is this KI?	 	 	2	 	 	 	 	 	 	 	5/21/2007	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Y	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	10
	 	1	 	CW00222-01	 	Height	 	 	3	 	 	 	 	 	 	 	6/1/2007	 	 	 	72	 	 	 	68	 	 	 	59	 	 	 	68	 	 	 	66	 	 	 	60	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	10
	 	1	 	CW00222-01	 	Flowering_Time	 	 	4	 	 	 	 	 	 	 	6/1/2007	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	y	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	y	 	 	 	 	 	 	 	 	 
	10
	 	1	 	CW00222-01	 	Flowering_Time	 	 	4	 	 	 	 	 	 	 	6/2/2007	 	 	 	y	 	 	 	 	 	 	 	y	 	 	 	 	 	 	 	y	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	y	 	 	 	 	 
	10
	 	1	 	CW00222-01	 	Flowering_Time	 	 	4	 	 	 	 	 	 	 	6/3/2007	 	 	 	 	 	 	 	y	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	y	 	 	 	y	 	 	 	 	 	 	 	 	 	 	 	 	 
	10
	 	1	 	CW00222-01	 	QC_result	 	 	7	 	 	 	 	 	 	 	6/7/2007	 	 	 	 	 	 	 	+	 	 	 	 	 	 	 	 	 	 	 	—	 	 	 	 	 	 	 	 	 	 	 	+	 	 	 	 	 	 	 	 	 
	10
	 	1	 	CW00222-01	 	Biomass	 	 	5	 	 	 	 	 	 	 	6/28/2007	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 






Page 20 of 47









 







	1.	 	Key Performance Indicators (KPIs)






	 	1.1.	 	Number of constructs yielding >10 T0 plants delivered each quarter vs. all
constructs delivered each quarter.
	 
	 	1.2.	 	Number of constructs sequence validated in T0 plants each quarter vs. all constructs
assayed in T0 each quarter.
	 
	 	1.3.	 	Number of constructs yielding T1 seeds from >10 events each quarter vs. all T1 seeds
delivered each quarter.
	 
	 	1.4.	 	Number of constructs sequence validated in T1 events each quarter vs. all events
assayed in T1.
	 
	 	1.5.	 	Time from infection to T1 seed harvest each quarter.
	 
	 	1.6.	 	Number of constructs evaluated for predicted phenotype or trait.
	 
	 	1.7.	 	Number of constructs yielding predicted phenotype or trait vs. all constructs
phenotyped or assayed.
	 
	 	1.8.	 	Number of constructs yielding novel phenotypes vs. all constructs phenotyped and
assayed.
	 
	 	1.9.	 	Number of constructs showing yield drag or negative traits vs. all constructs analyzed.






	2.	 	Screenhouse Maps






	 	2.1.	 	Plot map for Screenhouse 1 and Screenhouse 2 at SCUTA










Page 21 of 47









 





ANNEX III




to the Collaboration Agreement between Ceres, Inc. and ICS



Program Budget


Table 1. Detailed Program budget.




[***]






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Table 1 (continued)




[***]






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Table 2. Budget for lab space and expendables.




[***]






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ANNEX IV




to the Collaboration Agreement between Ceres, Inc. and ICS



Stewardship Guidelines


The purpose of these guidelines is to prevent the pilferage, vandalism, or escape of transgenic
rice in China.





	1.	 	Plantlet transport. Transgenic rice plantlets will be transported by ICS personnel
from the lab to the field in a clearly labeled, secured and sealed container. Unused plants
will be destroyed by autoclaving according to SOP R7.






	2.	 	Plant growth. Transgenic rice will be grown in a secure and contained growth room,
greenhouse, screenhouse or in a field approved for the growth of transgenic rice. No
commercial rice plants will be grown in the same greenhouse, screenhouse or approved field
with transgenic rice.






	3.	 	Seed storage. Each seed line will be contained within a sealed clearly labeled
envelope or a sealed paper bag. Each seed line is inventoried and stored inside a locked
cabinet inside a secure room. Access to the seed storage cabinets is limited to those
involved in the experiments. Seed utilization and disposal will be tracked using a log system.
Unused seeds will be destroyed by autoclaving according to SOP R7.






	4.	 	Seed transport. Each seed line will be transported in a sealed, clearly labeled
envelope. Envelopes will be shipped in a clearly labeled, secured and sealed container within
a shipping box to prevent spillage if the outside packaging gets damaged.






	5.	 	Seed destruction. The maintenance of a transgenic rice seed log is the responsibility
of ICS. The inventory of transgenic seeds will be reviewed annually. Seed stocks designated by
Ceres as no longer needed will be destroyed by autoclaving as described in SOP R7. Their
destruction will be recorded in the seed log.




Page 25 of 47









 











SOPs (Standard Operating Protocols)




1. SOP R1: Agrobacterium-mediated Rice Transformation




					
	 	 	 	 	 
	
	 	Protocol Number:
	 	R1
	Property of Ceres, 

Inc.
	 	Protocol Name:
	 	Agrobacterium-mediated

Rice Transformation
	 	 	 	 	 
	          Authors: Chuan-yin Wu
	 	Date Issued:	 	 
	 	 	 	 	 
	Approved By:
	 	Version Number:
	 	1.0






	 	 	 

	Purpose:

	 	This protocol is established to produce a large number of
transgenic rice plants using Ceres’ promoter and selectable
marker gene.
	 
	 	 
	References:

	 	“Efficient transformation of rice (Oryza sativa L.) mediated
by Agrobacterium and sequence analysis of the boundaries of
the T-DNA.” Hiei, Y., Ohta, S., Komari, T. and Kumashiro, T.
Plant J. 6, 271-282 (1994).
	 
	 	 
	Safety:

	 	Follow universal lab safety technique. Properly dispose of
transgenic waste in designated receptacles.
	 
	 	 
	Stewardship:

	 	Properly manage and dispose of transgenic plant material.






	 	 	 
	Disposable Supplies:	 	Reagents and Stock Solutions:
	100 x 20 mm Petri dishes (25373-143; VWR)

	 	2,4-Dichlorophenoxyacetic acid

(Sigma) 2mg/mL
	 
	Disposable pipettes 10mL, 25mL (53106-431;
VWR)

	 	Kinetin (Sigma) 1mg/ml
	 
	Autoclave bags (11215-796; VWR)

	 	Naphthalene Acetic Acid (Sigma)
	 
	50 ml Corning conical tube (Fisher Scientific)

	 	Bialaphos 5mg/mL (Bialaphos; Shinyo
Sangyo)
	 
	Gloves (32916-532; Microflex Corp.)
Sundae Cup (Scott Naake Paper Co.)

	 	Carbenicillin (1000; Agribio) 250mg/mL
	 
	Whatman filter paper (VWR)

	 	Sucrose (S-0389; Sigma)
	 
	Eppendorf tubes

	 	N6 basal medium (Phytotechnology)
	 
	Pipette tips

	 	MS basal medium (Phytotechnology)
	 
	12 ml culture tubes (FALCON)

	 	Gelrite (Sigma)
	 
	 

	 	Agarose (EMD Chemicals Inc.)
	 
	 	 
	Capital Equipment:
	 	 
	Laminar Flow Hood (Nuaire)

	 	Non-disposable Supplies:
	66 Series Incubator (Percival Scientific)

	 	Magenta Boxes (GA7; Magenta Corp)
	Micro-centrifuge (Heraeus Instrument)
	 	 
	22°C growth chamber (Percival Scientific)
	 	 
	28°C growth chamber (Percival Scientific)
	 	 






Page 26 of 47









 






	 	 	 

	Start Product(s):

	 	Wild-type rice seeds
	End Product(s):

	 	Plants that have been genetically transformed with appropriate constructs







	A.	 	Induce calli of good quality from mature rice seeds






	 	1.	 	Dehusk mature seeds and discard any spotted ones. Do not use seeds which have been
stored for more than 2 years at room temperature. Do not use seeds harvested from plants
grown in high humidity and high temperature conditions.
	 
	 	2.	 	Transfer dehusked seeds to a 50 ml conical tube (such as CORNING 430290).
	 
	 	3.	 	Rinse seeds in 70% ethanol for 1 min.
	 
	 	4.	 	Pour out ethanol and rinse seeds with autoclaved distilled water.
	 
	 	5.	 	Add 24 ml autoclaved distilled water and then 6 ml Clorox Bleach (Chlorox contains 5.25
% sodium hypochlorite, so the final concentration is 1.05% ).
	 
	 	6.	 	Shake the tube occasionally for 30 min.
	 
	 	7.	 	Pour out the Clorox solution and rinse seeds with sterile water 4 times.
	 
	 	8.	 	Dry the seeds on autoclaved Kimwipes for a few minutes.
	 
	 	9.	 	Transfer seeds to semi-solid N6-P medium, 10 seeds in each Petri dish (100 x 20 mm,
FALCON). Each Petri dish contains 30 ml N6-P medium (see Appendix A for N6-P). Dishes are
sealed with surgical tapes to allow air exchange.
	 
	 	10.	 	Induce calli at 28°C under cold fluorescent light. Many granular calli should be formed
within 4 weeks on most of the seeds (Fig. 1). Calli of good quality consist of small
spherical cells with dense cytoplasm, which are competent for transformation (Fig. 2). The
calli can be used directly for Agrobacterium infection, or subcultured for later use. Do
not use calli older than 2 months (from the seed sterilization date).






	B.	 	Infection and co-cultivation of calli with Agrobacterium cells






	 	1.	 	Pick up a single Agrobacterium clone from plate and culture it in 2 ml YEB liquid
medium in a sterile tube on a shaker (140 rpm) overnight. Include appropriate antibiotics
depending on marker genes in a vector at 50 ug/ml.
	 
	 	2.	 	Transfer the liquid culture to 1.5 ml Eppendorf tube and centrifuge it at 7,000 rpm for
5 min.
	 
	 	3.	 	Discard the supernatant and resuspend cells in N6-AS liquid medium (see Appendix B for
N6-AS).
	 
	 	4.	 	Adjust cell density with the liquid N6-AS medium. The density can be measured by a
spectrometer. The optimal OD600 value varies significantly depending on Agrobacterium
strains and vectors. The optimal value means there is no over-growth of Agrobacterium cells
in 3-day co-cultivation.
	 
	 	5.	 	Mix rice calli with bacterium cells. This can be done in a 50 ml sterile conical tube.
Shake the tube by hand gently for 3 min. The ratio of calli to bacterium solution is not a
critical factor affecting transformation efficiency. Several grams of calli can be in 15 ml
bacterium suspension.





Page 27 of 47









 






	 	6.	 	Pour out bacterium solution. Transfer calli onto autoclaved Kimwipes paper to remove
extra solution.
	 
	 	7.	 	Culture calli on autoclaved filter paper placed on the N6-AS semi-solid medium. Each
100 x 20 mm dish contains 20 ml N6-AS. Seal the dish with surgical tape.
	 
	 	8.	 	Co-culture calli and bacterium cells at 22 °C in dark for 4-6 days.
	 
	 	9.	 	Note: Calli should remain healthy during co-cultivation (Fig. 3).
	 
	 	10.	 	Less than 10% of the calli should be over-infected at the end of co-cultivation (Fig.
4).
	 
	 	11.	 	Efficiency of Agrobacterium infection can be examined by using the GFP gene as a
reporter (Fig. 5).






	C.	 	Selection of transformed calli






	 	1.	 	Transfer the infected calli to a sterile 50 ml tube containing 35 ml sterile distilled
water.
	 
	 	2.	 	Shake the tube for a few seconds and pour out water. Repeat washing 6 times.
	 
	 	3.	 	For the final wash, add carbenicillin or cefotaxime at the concentration of 500
mg/ml.
	 
	 	4.	 	Transfer calli onto autoclaved Kimwipes paper to remove extra water.
	 
	 	5.	 	Culture calli on the semi-solid N6-P medium supplemented with 250 mg/ml
carbenicillin or cefotaxime at 28 °C under cold fluorescent light for 7 days. Each
100 x 20 mm dish contains 30 ml N6-P medium, 30 calli on each dish. Dishes are sealed with
surgical tape.
	 
	 	6.	 	Subculture calli on the N6-P medium supplemented with 250 mg/ml carbenicillin or
cefotaxime and 100 mg/ml paramomycin for 16 days. The Gelrite is replaced by Agarose
(7-8 g/l) in the N6-P medium.
	 
	 	7.	 	Subculture calli on the N6-P medium supplemented with 250 mg/ml carbenicillin or
cefotaxime and 100 mg /ml paramomycin for another 16 days. Use agarose to replace
Gelrite in N6-P medium. Paramomycin-resistant calli should start to be visible at the end
of the 2nd selection.
	 
	 	8.	 	Note: fast-growing transformed cells must be visible during second selection (Fig. 6).
Non-transformed wild-type calli must be completely killed by selection (Fig. 7).






	D.	 	Regeneration of transgenic plants






	 	1.	 	Transfer independent resistant calli to the N6-R plant regeneration medium (see
Appendix C for N6-R). Add 50 mg/l paramomycin to N6-R medium. Each 100 x 20 mm dish
contains 30 ml N6-R medium, 10 calli on each dish. Dishes are sealed with surgical tape.
Culture calli at 28 °C under cold fluorescent light for 2 weeks.
	 
	 	2.	 	Transfer calli to fresh N6-R medium. Do not add paramomycin to N6-R medium for this
subculture. Culture calli at 28 °C under cold fluorescent light until shoots and
roots are formed.
	 
	 	3.	 	Transfer plantlets to Magenta boxes containing 30 ml MS-F medium (see Appendix D for
MS-F). Grow plantlets at 28 °C under cold fluorescent light for 10-14 days.




Page 28 of 47









 












	 	4.	 	Acclimate in vitro regenerated plants. Plant containers will be opened 4 days before
transplanting in order to harden plantlets.
	 
	 	5.	 	Transfer plants to pots or to soil. Label T0 plants systematically with CW ID and event
number, e.g. CW00001-01. Generate and maintain greenhouse and field maps for all T0 plants.
Note: transformed plants must be resistant to paramomycin, and non-transgenic seedlings are
albinos when treated with kanamycin (Fig. 8).






	E.	 	Quality assurance






	 	1.	 	Validate transgene identity in transgenic calli or T0 regenerants for each construct
using gene-specific primers and PCR.
	 
	 	2.	 	Process three independent samples for each construct along with appropriate positive
and negative controls.






	F.	 	T0 plant phenotyping






	 	1.	 	Grow and maintain T0 plants normally throughout phenotyping.
	 
	 	2.	 	T0 observations and measurements include:






	 	a.	 	Fertility: No entry (normal), 1 (reduced). Include date of observation.
	 
	 	b.	 	Morphology: Morphological traits will be described using prescribed coded
comments (TBD).
	 
	 	c.	 	Images: Photographs will be taken of all T0 plants with distinctive
morphological phenotypes affecting plant growth, development, biomass and seed
production, including fertility, stem morphology, tiller number and leaf morphology.
Each photograph should include a Ceres white board labeled with construct name, event
number and date and be written with a black broad tip erasable marker.
	 
	 	d.	 	Labeled images with plant descriptions will be stored in the project database
and image log with the date of entry.






	G.	 	T1 seed harvest and tracking






	 	1.	 	T1 seed numbering. Assign a unique event number to each plant for T1 seed
harvesting, e.g. CW00001-01.
	 
	 	2.	 	Harvest T1 seeds on the panicle and placed into an envelope. Label the envelope with
the construct and event number, date of harvest and store individually.
	 
	 	3.	 	Log each envelope of seed collected in the Seed Production Table. Include the room and
storage container numbers.






	H.	 	Pest management






	 	1.	 	Spray low noxious pesticides to control the plant hoppers and borers 1-3 times during
the vegetative phase.






Page 29 of 47











 





Appendix A — N6-P medium (mg per liter)




	 	 	 

	N6 basal salt mixture (Sigma)
	 	1 bag (1 liter size)
	KI
	 	0.8
	CoCI2×6H2O
	 	0.025
	CuSO4×5H2O
	 	0.025
	NaMoO4×2H2O
	 	0.25
	Glycine
	 	2
	Myo-inositol
	 	100
	Thiamine HCI
	 	5
	Pyridoxine HCI
	 	1
	Nicotinic acid
	 	1
	Proline
	 	2,800
	Casamino acid
	 	300
	Sucrose
	 	30,000
	2.4-D
	 	2
	pH
	 	5.6
	Gelrite
	 	4,000
	(For Bar marker and Biolaphos selection)
Or
Agarose
	 	7,000-8,000
	(For NPT II marker and Paramomycin selection)
Autoclave at 121 °C for 15 min.
	 	 






Appendix B — N6-AS medium (mg per liter)




	 	 	 

	N6 basal salt mixture (Sigma)
	 	1 bag (1 liter size)
	KI
	 	0.8
	CoCI2×6H2O
	 	0.025
	CuSO4×5H2O
	 	0.025
	NaMoO4×2H2O
	 	0.25
	Glycine
	 	2
	Myo-inositol
	 	100
	Thiamine HCI
	 	5
	Pyridoxine HCI
	 	1
	Nicotinic acid
	 	1
	Casamino acid
	 	1,000
	Sucrose
	 	30,000
	Glucose
	 	10,000
	2.4-D
	 	2
	pH
	 	5.6
	Gelrite (semi-solid medium)
	 	4,000
	Autoclave at 121 °C for 15 min.
	 	 
	Add in acetosyringone at the final concentration of 200 mM just before use.
	 	 






Appendix C — N6-R medium (mg per liter)




	 	 	 

	N6 basal salt mixture (Sigma)
	 	1 bag (1 liter size)
	KI
	 	0.8






Page 30 of 47









 






	 	 	 

	CoCI2×6H2O
	 	0.025
	CuSO4×5H2O
	 	0.025
	NaMoO4×2H2O
	 	0.25
	Glycine
	 	2
	Myo-inositol
	 	100
	Thiamine HCI
	 	5
	Pyridoxine HCI
	 	1
	Nicotinic acid
	 	1
	Casamino acid
	 	1,000
	Sucrose
	 	25,000
	Sorbitol
	 	25,000
	Kinetin
	 	2
	NAA
	 	0.05
	pH
	 	5.6
	Agarose (Sigma Type I-A)
	 	8,000
	Autoclave at 121 °C for 15 min.
	 	 
	 
	Appendix D — MS-F medium (mg per liter)
MS basal salt mixture (Sigma)
	 	1/2 bag (1 liter size)
	Glycine
	 	2
	Myo-inositol
	 	100
	Thiamine HCI
	 	5
	Pyridoxine HCI
	 	1
	Nicotinic acid
	 	1
	Sucrose
	 	15,000
	pH
	 	5.6
	Gelrite
	 	2,500
	Autoclave at 121 °C for 15 min.
	 	 







[***]





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[***]






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2. SOP R2: Plant Growth and Development (PG&D) Phenotyping




	 	 	 	 	 	 	 	 	 

	

Property of Ceres, Inc.	 	 	 	 	 	 
	 	 	 	 	 	 
	 	Protocol Number:
	 	R2	 
	 	 	 	 	 	 
	 	Protocol Name:
	 	Plant Growth and 
Development Phenotyping

	 
	 	 	 	 	 	 	 	 
	Authors:

	 	Chuan-yin Wu
	 	Date Issued:
	 	July 16, 2007

	 
	 	 	 	 	 	 	 	 
	Approved By:

	 	 	 	Version Number:
	 	1.0	 






	 	 	 

	Purpose:

	 	This protocol is for the phenotyping of T1 and T2 transgenic rice plants.
	Safety:

	 	Follow universal lab safety techniques.
	Stewardship:

	 	Properly manage and dispose of transgenic plant material.






	 

	Stock Solution: herbicide

	0.4% Finale







A. Germinate seeds





	 	1.	 	Assign an experiment number to seedlings started together and record events included in
the experiment.
	 
	 	2.	 	Soak seeds in 2% limewater for 2-3 days at room temperature, and then wash them
completely using clean water.
	 
	 	3.	 	Sow seeds in flats.
	 
	 	4.	 	Herbicide selection — eight days (summer) or twelve days (winter) after germination,
spray seedlings with the herbicide Finale® to remove non-transgenic segregants.
Respray 5 days after the first spraying to minimize escapes.





B. Transplant seedlings to the field





	 	1.	 	Herbicide resistant seedlings at 4-5 leaf stage will be transplanted to field, ten
transgenic lines for each construct, fifteen plants for each line, one row wild type plants
every eleven rows as shown in Figure 1.
	 
	 	2.	 	Save and score at least 30 seedlings for herbicide tolerance after herbicide sensitive
plants have clearly died. Store numbers of herbicide sensitive and resistant seedlings in
the Data Collection Table (ANNEX II).
	 
	 	3.	 	Field layout — the distance between rows is 26.7 cm and the distance between plants
within a row is 13.4 cm. Two guard rows will be grown for each plot. Walk lane will be 50
cm wide.





Page 33 of 47









 






	 	4.	 	A plot map or a screenhouse map (ANNEX II) will be used to track each plant in
each experiment.





     Figure 1. Sample plot of transgenic plants.



     




	 	5.	 	Measurements to be taken for all T1 plants






	 	a.	 	Flowering time: Number of days from transplanting to heading of the earliest
panicle.
	 
	 	b.	 	Plant height: From the ground to the top of the tallest panicle.
	 
	 	c.	 	Effective tiller number: Number of tillers bearing a fertile panicle.
	 
	 	d.	 	Seed yield: Weight of seeds while still on panicles, including the or
envelope.






	 	6.	 	General observations 
To be noted in cases where the frequency is higher than expected based on control plants.
Use coded comments whenever possible to describe plants (see ANNEX IV, Data
Collection Table). A phenotyping update should be presented monthly to the Collaboration
Committee.






	 	a.	 	Growth vigor: Normal (no entry), improved (1), poor (2)
	 
	 	b.	 	Leaf color: Normal (no entry), darker green (1), yellow-green (2)
	 
	 	c.	 	Fertility: Normal (no entry), reduced (1).
	 
	 	d.	 	Lodging tolerance: Normal (no entry), increased lodging (1).
	 
	 	e.	 	Resistance to pests and diseases: Normal (no entry), increased resistance (1),
hypersensitive (2).
	 
	 	f.	 	Stress tolerance (drought, cold, heat): Normal (no entry), increased tolerance
(1), hypersensitive (2).
	 
	 	g.	 	Flag leaf color at maturity: Normal (no entry), more green than controls (1),
more yellow than controls (2).




Page 34 of 47









 






	 	h.	 	Flag leaf angle from vertical: Normal (no entry), decreased leaf angle (1),
increased leaf angle (2).






	 	7.	 	Optional measurements for selected events (upon request from Ceres)






	 	a.	 	Fertility2: Number of filled seeds divided by number of spikelets on a panicle
(average of 3 panicles).
	 
	 	b.	 	Panicle size: Number of seeds per panicle, averaged from three panicles.
	 
	 	c.	 	Seed yield2: Weight of total seeds less panicles and bag for lines showing 10
percent increase.
	 
	 	d.	 	Seed fill rate: Number of days from flowering to when 50% of seeds are yellow.





C. Genotype Confirmation





	 	1.	 	Events with highly penetrant phenotypes will be genotype confirmed using gene specific
PCR. New phenotypes will be reported monthly to the Collaboration Committee.
	 
	 	2.	 	Images. Photographs will be taken of T1 or T2 plants with distinctive morphological
phenotypes affecting plant growth, development, biomass and seed production including
fertility, stem morphology, tiller number and leaf morphology. Each photograph should
include a Ceres white board labeled with the construct name, the event number and date and
be written with a black broad tip erasable marker.
	 
	 	3.	 	Labeled images with plant descriptions will be stored in the project database and image
log with the date of entry.






Page 35 of 47











 






3. SOP R3: Rice Seed Harvesting




	 	 	 	 	 	 	 

		 	Protocol Number:	 	R3
	 
	 	 	 	 	 	 
	Property of Ceres, Inc.	 	Protocol Name:	 	Rice Seed Harvesting
	 
	 	 	 	 	 	 
	Authors:

	 	Chuan-yin Wu
	 	Date Issued:
	 	July 16, 2007
	 
	 	 	 	 	 	 
	Approved By:

	 	 	 	Version Number:
	 	 1.0






	 	 	 

	Purpose:

	 	Harvest and track seeds from transgenic T0, and T1 rice plants.
	 
	 	 
	Safety:

	 	Follow universal lab safety techniques.
	 
	 	 
	Stewardship:

	 	Properly manage and dispose of transgenic plant material.







	A.	 	T1 seed harvest






	 	1.	 	Harvest T1 seeds from individual T0 plants.
	 
	 	2.	 	Harvest seeds by removing whole panicles.
	 
	 	3.	 	Store in labeled envelopes with CW ID, event number and date, e.g. CW00001-01,
MM/DD/YY.
	 
	 	4.	 	Log harvested seed in the Seed Production Table (ANNEX II).






	B.	 	T2 seed harvest






	 	1.	 	Harvest T2 seeds from individual T1 plants.
	 
	 	2.	 	Harvest seeds by removing whole panicles.
	 
	 	3.	 	Store in appropriately labeled paper envelopes with CW ID, event number, progeny number
and date, e.g. CW00001-01-10, MM/DD/YY.
	 
	 	4.	 	Log harvested seed in the Seed Production Table.




Table 1. Seed Production Table.




	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	CW_ID	 	Date of Harvest	 	 	Harvested By	 	 	Generation of Seed	 	 	Location	 	 	Building	 	 	Room	 	 	Container

(Barcode)	 	 	Amount (g)	 	 	Notes	 
	CW00006
	 	 	1/1/2006	 	 	LZ	 	 	T1	 	 	SCUTA	 	AAA	 	XXX	 	 	123456	 	 	 	2	 	 	Notes on germination, amount used (2.1.2006)
	CW00003
	 	 	1/1/2006	 	 	LZ	 	 	T1	 	 	SCUTA	 	BBB	 	XXX	 	 	123457	 	 	 	3	 	 	Poor germination (1.1.2007)
	CW00006-01
	 	 	6/1/2006	 	 	 	 	 	 	 	T2	 	 	ICS	 	 	 	 	 	YYY	 	 	123458	 	 	 	4	 	 	 	 	 
	CW00010
	 	 	7/1/2007	 	 	CYW	 	 	F1	 	 	ICS	 	 	 	 	 	YYY	 	 	123459	 	 	 	0.5	 	 	 	 	 
	CW00010-01
	 	 	10/1/2007	 	 	XZ	 	 	F2	 	 	ICS	 	 	 	 	 	YYY	 	 	123460	 	 	 	2	 	 	 	 	 






Page 36 of 47









 







4. SOP R4: Drought Assay




	 	 	 	 	 	 	 	 	 

		 	Protocol Number:	 	 	R4	 
	 
	 	 	 	 	 	 	 	 
	Property of Ceres, Inc.	 	Protocol Name:	 	Rice Drought Assay

	 
	 	 	 	 	 	 	 	 
	Authors:

	 	Ning Su, Lifeng

Wang, Chuan-yin Wu
	 	Date Issued:
	 	July 16, 2007

	 
	 	 	 	 	 	 	 	 
	Approved By:

	 	 	 	Version Number:
	 	 	1.0	 






	 	 	 

	Purpose:

	 	Test selected transgenic rice lines for enhanced drought tolerance.
	 
	 	 
	Stewardship:

	 	Properly manage and dispose of transgenic plant material.
	 
	 	 
	Safety:

	 	Follow universal lab safety techniques. Properly dispose of transgenic waste.






	 	 	 

	Stock Solutions:

	 	 
	 
	 	 
	0.4% Finale
	 	 







	A.	 	Seedling Germination






	 	1.	 	Choose 50 seeds of good quality for each event to be assayed. The seeds of wild type should
be prepared at the same time as a control.
	 
	 	2.	 	Soak the seeds at room temperature for 3 days.
	 
	 	3.	 	Sow the seeds in flats and cover the flats with a net or plastic to protect from
animals.
	 
	 	4.	 	Check for seed germination every day. Make sure there is enough water and the
temperature is not too high.
	 
	 	5.	 	Spray the herbicide Finale at day 8 after seed sowing, or at the time >95% seeds
have germinated. (Add 4 ml Finale in one liter of water. Shake the solution thoroughly
before spraying). Note: Do not spray the wild type control.
	 
	 	6.	 	Spray the seedlings again with the Finale solution of the same concentration 5 days
after the first spraying.
	 
	 	7.	 	Count herbicide resistant and herbicide sensitive seedlings 8 days after the second
spraying. Then allow the seedlings to grow another week before transplanting to soil.






	B.	 	Transplant seedlings to pots






	 	1.	 	Transfer 2 transgenic (good resistance to herbicide) and 2 wild type seedlings to a
pot. Use four pots for each event tested. Water the plants daily until the second tiller is
visible. (2 cm long). Note: Soil must be mixed uniformly and each pot must contain the same
amount of soil.




Page 37 of 47









 






	 	2.	 	Stop watering plants. Record for each plant the date when leaves start to wilt (the
leaves start to roll up). Special attention should be paid to any difference between the
transgenic and control plants within a pot.
	 
	 	3.	 	Re-water the pot if all plants in a pot have wilted. Harvest grains and biomass (above
ground only) when the plants mature. Dry up and weigh grain yield and biomass.
	 
	 	4.	 	Take pictures for any observed phenotypes.






Page 38 of 47











 




5. SOP R5: Low N Assay




	 	 	 	 	 	 	 

	

	 	Protocol Number:
	 	R5 	 	 
	 
	 	 	 	 	 	 
	Property of Ceres,
Inc.
	 	 	 	 	 	 
	 

	 	Protocol Name:
	 	Low N Assay

	 
	 	 	 	 	 	 
	Authors: Chuan-yin Wu

	 	Date Issued:
	 	July 16, 2007

	 
	 	 	 	 	 	 
	Approved By:

	 	Version Number:
	 	1.0 	 	 






	 	 	 

	Purpose:

	 	Test selected transgenic rice lines for low N tolerance.
	 
	 	 
	Stewardship:

	 	Properly manage and dispose of transgenic plant material.
	 
	 	 
	Safety:

	 	Follow universal lab safety techniques. Properly dispose of transgenic waste.






	 

	Stock Solution: herbicide

	 

	0.4% Finale

	 

	Equipment:

	 

	SPAD 502 chlorophyll meter, Spectrum Technologies, Inc.

(http://www.specmeters.com/Chlorophyll_Meters/index.html)








	A.	 	Seed germination






	 	1.	 	Choose 50 seeds of good quality for each event to be assayed. The seeds of wild type
should be prepared at the same time as a control.
	 
	 	2.	 	Soak the seeds at room temperature for 3 days.
	 
	 	3.	 	Sow the seeds in flats and cover the flats with net or plastic to protect from animals.
	 
	 	4.	 	Check for seed germination every day. Make sure there is enough water and that the
temperature is not too high.
	 
	 	5.	 	Spray seedlings with the herbicide Finale at day 8 after seed sowing, or at the time
>95% seeds have germinated. Note: Do not spray the wild type control. (Add 4 ml Finale
in one liter of water. Shake the solution thoroughly before spraying).
	 
	 	6.	 	Spray the seedlings again with the Finale solution of the same concentration 5 days
after the first spraying.
	 
	 	7.	 	Count herbicide resistant and herbicide sensitive seedlings 8 days after the second
spraying. Then allow the seedlings to grow another week.
	 
	 	8.	 	Supply fertilizer in the field one day before transplanting.






	B.	 	Transplant seedlings to the field






	 	1.	 	Transplant 15 seedlings per row, 2 rows per event. Transplant one row of wild type
controls every 3 rows so that each row of transgenics has an immediate control neighbor.




Page 39 of 47









 











	 	2.	 	Supply fertilizer at day 5 and 10, respectively, after transplanting. Stop fertilizer
supply until plants mature.
	 
	 	3.	 	Observe plant growth daily and compare between transgenic and control plants to see if
there is any difference, especially on leaf color. Take pictures for any observed
phenotypes.
	 
	 	4.	 	Record chlorophyll levels regularly (Minolta SPAD-502 chlorophyll meter, Spectrum
technologies, Inc or a comparable instrument) until the termination of the experiment.
	 
	 	5.	 	When plants reach maturity measure shoot length, tiller number and yield.




Page 40 of 47









 










6. SOP R6: NIR Composition Analysis Assay




	 	 	 	 	 	 	 

	

	 	 Protocol Number:
	 	R6 		 
	Property of Ceres,
Inc.

	 	Protocol Name:
	 	NIR Composition Assay

	 
	 	 	 	 	 	 
	Authors: Bonnie Hames, Steve
Thomas

	 	Date Issued:
	 	July 16, 2007

	 
	 	 	 	 	 	 
	Approved By:

	 	Version Number:
	 	1.0 		 






	 	 	 

	Purpose:

	 	The following instructions describe a sample collection and
preparation protocol for collection of NIR spectra using the
Bruker Optics MPA FT-NIR.
	 
	 	 
	Safety:

	 	Follow universal lab safety techniques.
	 
	 	 
	Stewardship:

	 	Properly manage and dispose of transgenic plant material.






	 	 	 

	Capital Equipment:

	 	Disposable Supplies:
	Bruker Optics MPA
(www.brukeroptics.com).

	 	Bruker part number: 301061 (package of 10 glass petri dishes, 94x20 mm,
Schott DUROPLAN).
	Part number: IN312/C rotating sample
cup (www.brukeroptics.com).

	 	Standard NIST RM8491 sugarcane bagasse (see
https://srmors.nist.gov/view_detail.cfm?srm=8491; and
https://srmors.nist.gov/referencelinks/view_referencelinks.cfm?srm=8491)
	Part number: IN312-B adaptor for glass petri
dishes

(www.brukeroptics.com).
	 	 







	A.	 	Sample collection






	 	1.	 	Harvest fully senesced plants according to your region’s harvest time.
	 
	 	2.	 	Harvest 5 randomly selected individual plants from each variety at each test site (if
multiple reps, more samples are fine). Combine these plants into one sample. The target
amount for each sample is minimum 20 g dry weight.
	 
	 	3.	 	For very large plants, a sub-sample can be collected if care is taken to obtain a
representative sub sample of the entire plant.
	 
	 	4.	 	Freshly cut biomass samples should be placed in some sort of breathable bag or sack.
e.g. Brown paper, mesh, muslin or burlap.
	 
	 	5.	 	Each bag should be labeled with a Sample ID — a unique sample identifier, written ON
THE BAG (labels/tag, etc can fall off). For perennial species, record any information
about the sample collection process that will be needed if we wish to return to the same
plants in subsequent years.




Page 41of 47









 












	 	6.	 	Sample bags with cut biomass should bee sealed to prevent spilling — e.g. stapled ,
sewn, tied.






	B.	 	Drying






	 	1.	 	Samples should be dried to < 10% moisture content prior to milling.
	 
	 	2.	 	Ideally, samples should be dried for several days in a forced air oven set 45°C. **Keep
oven at or below 45°C to maintain sample integrity.
	 
	 	3.	 	Air drying is OK, provided the ambient relative humidity allows the samples to reach
moisture content <10%.






	C.	 	Milling






	 	1.	 	Mill dried biomass samples in a standard laboratory knife mill to pass a 2mm screen.
Collect the entire milled sample to minimize separation of plant tissues.
	 
	 	2.	 	Check blade sharpness periodically; dull blades cause temperatures to rise,
compromising sample integrity and yield large amount of fines, skewing chemistry &
conversion results); Ceres’ preferred mills are Wiley Model 4 mill or Cyclone mill (for
smaller sample amounts).
	 
	 	3.	 	Clean mill thoroughly between samples to avoid cross contamination of samples.
	 
	 	4.	 	Milled samples should be stored in sealed quart or gallon Ziploc freezer bag at room
temperature.
	 
	 	5.	 	After milling place sample ID and information inside each sample bag, include a 3” x 5”
index card with these six pieces of information. For handwritten cards — please use a
Sharpie or other permanent marker — preferably black. For printed labels, please use Ceres’
label template.






	 	•	 	Sample ID
	 
	 	•	 	Plant Number (1-5)
	 
	 	•	 	Variety
	 
	 	•	 	Location
	 
	 	•	 	Harvest Date (MM/YYYY)
	 
	 	•	 	Weight of milled sample






	D.	 	Spectroscopy






	 	1.	 	Turn on the instrument and lamp at least one hour prior to running samples
	 
	 	2.	 	Check instrument dessicant and replace if necessary.
	 
	 	3.	 	Run instrument diagnostics. Do not proceed until instrument passes all tests.
	 
	 	4.	 	Run the QC sample each day at the beginning and end of each batch of samples.
	 
	 	5.	 	Using a metal spatula, thoroughly mix the sample prior to removing a sample for
spectroscopy. Avoid shaking the sample or any actin that cause the sample to separate by
particle size.
	 
	 	6.	 	Using a small scoop spatula, take four aliquots of material from different parts of the
bag. Transfer each aliquot to a clean, dry Petri dish.




Page 42 of 47









 












	 	7.	 	**Close the Petri dish. Hold it by using your thumb on the cover and your middle finger
at the base it (such as when holding a CD disk)and mix the material by shaking from left to
right a couple of times. Avoid tapping or any action that causes the sample to separate by
particle size.
	 
	 	8.	 	Be careful at all times to avoid touching the Petri dish in areas within the
spectroscopic window.
	 
	 	9.	 	Make sure that your sample holder in the machine is free of any debris. Remove the top
of the Petri dish and place only the base of your dish with the sample in it in the sample
holder
	 
	 	10.	 	Scan the sample using the instrument method provided. Repeat from ** until three
spectra have been collected.
	 
	 	11.	 	Average the three spectra and save the averaged spectrum. Only this spectrum will be
forwarded to Ceres for analysis




Page 43 of 47









 











7. SOP R7: Destruction of Biomaterials




	 	 	 	 	 	 	 

	
Property of Ceres, Inc.

	 	Protocol Number:
	 	R7
	 	Protocol Name:	 	Destruction of Biomaterials
	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	Authors:

	 	Jack Okamuro
	 	Date Issued:
	 	July 16, 2007
	 
	 	 	 	 	 	 
	Approved By:

	 	 
	 	Version Number:	 	1.0






	 	 	 

	Purpose:

	 	Insure that all CW seed are eventually destroyed.
	 
	 	 
	Safety:

	 	Practice universal safety techniques in the lab.






	 	 	 

	Start Product(s):

	 	CW line seed stocks.
	 
	 	 
	End Product(s):

	 	All CW seeds should be destroyed by the end of the contract.







	1.	 	Must maintain a log of all CW seed stocks generated (see Seed Production Table, ANNEX
IV).
	 
	2.	 	Store individual stocks in a sealed clearly labeled envelope or a sealed paper bag. Each
seed line is logged and stored inside a locked metal cabinet inside a locked room. Access to
the seed storage cabinets is limited to those involved in the experiments.
	 
	3.	 	Track seed utilization in the seed log. Review list of CW seed stocks annually with Ceres.
Destroy unneeded seed stocks by autoclaving at 121 °C for 15 min.








Page 44 of 47












 





ANNEX V




to the Collaboration Agreement between Ceres, Inc. and ICS



MODEL AGREEMENT ON CONFIDENTIALITY AND ASSIGNMENT OF INVENTIONS



UNILATERAL — DISCLOSURE BY CERES


This Agreement (the “Agreement”) is made effective as of _____________________ (the “Effective
Date”), by and between

Ceres, Inc., 1535 Rancho Conejo Blvd, Thousand Oaks, California 91320 (“Ceres”) and

[NAME] ________________________, an individual, of [ADDRESS]




 





 





(the “Receiving Party”), as follows:





	 	1.	 	Purpose.
	 
	 	 	 	Ceres has entered into a Collaboration Agreement with ICS effective November 15, 2007
(the “Collaboration Agreement”). In the framework of the Collaboration Agreement, (i)
the Receiving Party may have access to certain information of a confidential or
proprietary nature of Ceres and (ii) the Receiving Party may make or contribute to
inventions that will be assigned to Ceres pursuant to such agreement.
	 
	 	2.	 	Confidential Information.
	 
	 	 	 	Confidential Information is any information disclosed by Ceres in the framework of the
Collaboration Agreement and any material, information, data, technology or other
findings or inventions resulting from the work performed under the Collaboration
Agreement. Confidential Information may be disclosed or provided in oral, written,
graphic, photographic or any other form or may be acquired by the Receiving Party
through inspection, observation or overhearing, whether advertent or inadvertent.
	 
	 	3.	 	Protection of Confidential Information.






	 	3.1	 	The Receiving Party agrees (i) to hold Ceres’ Confidential
Information in strict confidence and to take all reasonable precautions to
protect such
Confidential Information (ii) not to divulge any of the Confidential
Information or any information derived therefrom to any third person except ICS
employees, collaborators or graduate students performing work under the
Collaboration Agreement, and (iii) not to make any use whatsoever at any





Page 45 of 47









 





	 	 	 	time
of the Confidential Information except for the purpose of the implementation of
the Collaboration Agreement.
	 
	 	3.2	 	The obligations in Section 3.1 shall not apply with respect to any
information that the Receiving Party can demonstrate by competent evidence:






	 	-	 	was lawfully in his/her possession without restriction prior to
disclosure by Ceres, as evidenced by written records of the Receiving
Party;
	 
	 	-	 	was in the public domain prior to disclosure by Ceres, or subsequently
comes in the public domain through no fault, action or omission of the
Receiving Party; or
	 
	 	-	 	is made available to the Receiving Party, without any restriction, by a
third party who had the right to do so.






	 	4.	 	Ownership.
	 
	 	 	 	The Confidential Information including any material support containing Confidential
Information will remain the exclusive property of Ceres and the Receiving Party will not
acquire any right, title, license or interest on or to the Confidential Information, the
supports containing Confidential Information, or any patent covering Confidential
Information.
	 
	 	5.	 	Inventions.
	 
	 	 	 	Pursuant to the Collaboration Agreement, ICS shall promptly inform Ceres of, and assign
its rights in, any invention made or contributed to during the implementation of such
agreement. In order to enable ICS to comply with such obligation, the Receiving Party
shall promptly disclose to the Research Director at ICS and, to the extent that rights
do not automatically vest in ICS, assign to ICS any invention made or contributed to by
her/him in the framework of the implementation of the Collaboration Agreement. The
Receiving Party shall render such assistance to ICS and Ceres as may be required for
assigning the aforementioned rights to Ceres or Ceres’ designee and for protecting such
invention, including but not limited to the signing of documents. The Receiving Party
will be recognized in patent applications on the inventions referred to in this Article
5 in accordance with U.S. patent law.
	 
	 	6.	 	Term.
	 
	 	 	 	This Agreement will be valid until all Confidential Information is in the public domain.
	 
	 	7.	 	Notices.
	 
	 	 	 	Any notice or request delivered pursuant to this Agreement shall be deemed given when
actually received or three days after mailed first class postage prepaid or dispatched
by courier service to the Receiving Party’s address set forth hereinafter (whichever is
earliest):




Page 46 of 47









 







	 	 	 	 
	 	 	 	 
	If to Ceres, Inc.:

	 	Ceres, Inc.	 
	 

	 	1535 Rancho Conejo Blvd	 
	 

	 	Thousand Oaks, California 91320	 
	 

	 	Telephone Number: (805) 376-6500	 
	 

	 	Facsimile Number: (805) 376-6549	 
	 

	 	Attention: Vice President of Product Development	 
	 

	 	cc: Legal Department	 
	 
	 	 	 
	If to the Receiving Party:

	 	[NAME]	 
	 
	 	 	 
	 

	 	 	 
	 
	 	 	 
	 

	 	[ADDRESS]	 
	 
	 	 	 
	 

	 	 	 
	 
	 	 	 
	 

	 	 	 
	 
	 	 	 
	 

	 	 	 






	 		 	or at such address as shall be designated in writing by such Party to the other Party
upon at least ten (10) days prior notice thereof.






	 	8.	 	Governing Law/Jurisdiction.
	 
	 	 	 	This Agreement shall be governed by, and construed and interpreted in accordance with,
the laws of the State of California without regard to principles of conflicts of law.
The Parties agree that any dispute regarding the interpretation or validity of, or
otherwise arising out of this Agreement, shall be subject to the exclusive jurisdiction
of the California State Courts of San Francisco County or, in the event of federal
jurisdiction, the United States District Courts of the Northern District of California,
and each Party agrees to submit to the personal and exclusive jurisdiction and venue of
the courts and not to seek the transfer of any case or proceeding out of such courts.





	 	 	 	 	 	 	 
	CERES, INC.	 	 	 	RECEIVING PARTY
	Signature:

	 	 	 	Signature:	 	 
	 

	 	 
	 	 	 	 
	Name:

	 	Chuan-yin Wu
	 	Name:	 	 
	 

	 	 	 	 	 	 
	Title:

	 	Manager, Crop Transformation and Gene Evaluation
	 	Title:	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	Signature:
	 	 	 	 	 	 
	 

	 	 	 	 	 	 
	Name:

	 	Peter Mascia	 	 	 	 
	Title:

	 	Vice President of Product Development	 	 	 	 






Page 47 of 47









 







AMENDMENT I



to the Collaboration Agreement effective as of November 15, 2007 between Ceres, Inc. and the
Institute of Crop Sciences of the Chinese Academy of Agricultural Sciences (the “Agreement”).



WHEREAS, the Parties wish to substitute certain activities under the Program by new activities
relating to the development and evaluation of transgenic [***] plants;



WHEREAS, the Parties wish to add additional stewardship guidelines applicable to the performance of
the Program activities;



NOW THEREFORE, the Parties agree as follows:





	 	1.	 	The Parties agree that the activities defined in the [***] Program Plan in ANNEX
I-A attached hereto will be included in the Program. Activities under the Program Plan
in ANNEX I relating to rice will be decreased as directed by Ceres. Whenever
reference is made in the Agreement to ANNEX I, except in Article 5.1, this
reference shall forthwith read “ANNEX I and ANNEX I-A”.
	 
	 	2.	 	The Program Budget in ANNEX III remains unchanged and covers both the
activities defined in ANNEX I (as decreased pursuant to Ceres’ directors) and the
activities defined in ANNEX I-A. It is anticipated that the decrease of the
activities under ANNEX I for Years 3 through 5 will amount to approximately fifteen
percent (15%) of the Program Budget.
	 
	 	3.	 	The type of information with respect to [***] Program Plan activities to be included in
the reports and formatting is set forth in ANNEX I-A and ANNEX II-A
attached hereto.
	 
	 	4.	 	ICS agrees to comply with the Additional Stewardship Guidelines included in ANNEX
IV-A attached hereto. The Stewardship Guidelines in ANNEX IV and the
Additional Stewardship Guidelines in ANNEX IV-A apply to all activities under the
Agreement, whether defined in ANNEX I or in ANNEX I-A.
	 
	 	5.	 	The Parties agree that this Amendment I is effective as of March 5, 2009.
	 
	 	6.	 	For the remainder, the Agreement remains unchanged and this Amendment I shall form an integral
part thereof.




Made in two (2) copies



Page 1 of 28





Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission









 





	 	 	 	 	 	 	 

	Institute of Crop Sciences	 	Ceres, Inc.
	Chinese
Academy of Agricultural Sciences	 	 	 	 
	 
	 	 	 	 	 	 
	By:

	 	/s/
Jian-Min Wan	 	By:	 	/s/
Roger Pennell
	 

	 	 
	 	 	 	 
	Name:

	 	Jian-Min Wan
	 	Name:
	 	Roger Pennell
	Title:

	 	Director
	 	Title:
	 	Director of Trait Development
	 
	 	 	 	 	 	 
	By:

	 	/s/
Hu-Qu Zhai	 	By:	 	/s/
Richard Flavell
	 

	 	 
	 	 	 	 
	Name:

	 	Hu-Qu Zhai
	 	Name:
	 	Richard Flavell, CBE, FRS
	Title:

	 	President
	 	Title:
	 	Chief Scientific Officer







Page 2 of 28











 





ANNEX I-A





	 	 	to the Collaboration Agreement between Ceres and ICS dated November 15, 2007





[***] Program Plan




	1.1 [***] PROGRAM ACTIVITIES
	 
	 	 	The goal of the [***] PROGRAM ACTIVITIES project is to generate and evaluate selected [***]
gene constructs [***] .
	 
	 	 	CERES ACTIVITIES






	 	1.1.1	 	Design of constructs: Constructs will be made
according to the specifications below. Ceres will provide:






	 	1.1.1.1	 	The six [***] vectors (plasmid and map), and sequences for [***]
	 
	 	1.1.1.2	 	Protocol for establishing [***] for transformation
	 
	 	1.1.1.3	 	Protocol for T-DNA integration analysis
	 
	 	1.1.1.4	 	[***] protocol and [***] for [***] quantification
	 
	 	1.1.1.5	 	A list of [***] for [***] testing






	 	1.1.2	 	[***] Transformation: Ceres will [***] provide a
[***] transformation protocol.
	 
	 	1.1.3	 	Prioritization: Prioritization of constructs for
transformation, prioritization of existing events for genetic crossing, and
prioritization of existing events for plant assay.
	 
	 	1.1.4	 	Quality control: Suggest gene-specific primer
sequences and vector primer sequences for use in quality control experiments
using gene-specific PCR.
	 
	 	1.1.5	 	Data formats: Prescribe data formats for recording
results (ANNEX II).






	1.2	 	ICS ACTIVITIES






	 	1.2.1	 	Gene Construction: Develop up to 10 constructs based
on DNA sequence information and maps provided by Ceres. Ceres will provide the
following vectors: [***].




Page 3 of 28




Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission












 









	 	1.2.2	 	Perform transformation according to the [***] Transformation Protocol.
ICS will also track and deliver quarterly updates for selected Program KPIs
(ANNEX II).






	 	1.2.2.1	 	Transformation: Transform up to 5 constructs into [***]
lines provided by Ceres. Produce and collect seeds from up to 100
independent events (T0 plants) for each construct (SOP R1). Maintain
updated Program database that includes articles 2.2.1.1.1 to 2.2.1.1.5.
Update Ceres monthly.






	 	1.2.2.1.1	 	T0 production: See the Transformation Table and
KPI 1.1 (ANNEX II).
	 
	 	1.2.2.1.2	 	T0 plant phenotyping: See SOP R1. Include
descriptions, images and dates.
	 
	 	1.2.2.1.3	 	T1 seed production: See SOP R3, the Seed
Production Table and KPI 1.3 (ANNEX IV).
	 
	 	1.2.2.1.4	 	Quality control: See SOP R1 and R2, the
Transformation Table, the Quality Control Table and KPI 1.2
(ANNEX IV).






	 	1.2.2.2	 	T1 phenotyping — plant growth and development: Analyze T1
progeny from all events from article 2.2.1.1 for growth and development
phenotypes. Maintain updated Program database that includes articles
2.2.1.2.1 to 2.2.1.2.2. Update Ceres monthly.






	 	1.2.2.2.1	 	T1 plant phenotyping: See SOP R2 (ANNEX
IV). Include descriptions, coded comments, images and data
entry dates. Maintain a phenotype tracking database.
	 
	 	1.2.2.2.2	 	T2 seed production: See SOP R3 and the Seed
Production Table (ANNEX II, Table 3).






	 	1.2.2.3	 	T2 phenotyping: Upon request selected lines will be chosen
for additional phenotyping. Resources used for T2 plant phenotyping
should not exceed prescribed Program resources without the consent of
the Collaboration Committee. See SOP R2 (ANNEX IV).






	 	1.2.2.4	 	Trait assays: Selected lines will be assayed for [***].
SOPs to be discussed.






	 	1.2.2.4.1	 	[***]: Selected events will be assayed for [***].





Page 4 of 28




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	 	1.2.2.4.2	 	Genotyping quality control: All events that are
selected for assaying will be sequence validated using
gene-specific PCR.






	 	1.2.2.4.3	 	Images: Photographs will be taken of all plants
that display a distinct morphological phenotype. Images with
and without labels and plant descriptions will be stored in an
image database and the Image Log Table (ANNEX II, Table
6).






	2.	 	REPORTS






	 	2.1	 	Deliver Program Reports to the Collaboration Committee on a quarterly basis at
the end of each calendar quarter. Reports shall include, but not be limited to:






	 	2.1.1	 	KPI summary. Gather KPI data according KPIs listed in
Section 1 ANNEX II and improve underlying processes.
	 
	 	2.1.2	 	Transformation update: Updated Transformation Table
including the identification and number of constructs transferred to [***] and
summary of T0 QC analysis (ANNEX II, Table 1 and 2).
	 
	 	2.1.3	 	T1 and T2 seed production update: Updated Seed
Production Table (ANNEX II, Table 3).
	 
	 	2.1.4	 	T1 plant phenotyping update:






	 	2.1.4.1	 	Phenotyping descriptions






	 	2.1.4.1.1	 	Seedling emergence stand count 30 days post planting
	 
	 	2.1.4.1.2	 	Seeding vigor rating
	 
	 	2.1.4.1.3	 	Plant height in cm at flowering (if notably different from
parent)
	 
	 	2.1.4.1.4	 	Tillering (if notably different from parent)
	 
	 	2.1.4.1.5	 	Plant health rating (1-9) at flowering
	 
	 	2.1.4.1.6	 	Lodging
	 
	 	2.1.4.1.7	 	[***]
	 
	 	2.1.4.1.8	 	[***]
	 
	 	2.1.4.1.9	 	[***]





Page 5 of 28




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	 	2.1.5	 	Trait assay update: Summary of trait assay results,
measurements and images.






	3. RESOURCES AND WORK PLAN
	 
	 	 	Resources as specified in the Agreement will be allocated to this project as follows:
	 
	 	 	Ceres will deliver a vector backbone for [***] to China. The work will be divided into 2
phases. The first phase will include vector construction to preliminary event selection.
The second phase will be the testing and development phase.





	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	Duration	 
	Task	 	FTE	 	 	(months)	 
	Phase I — Vector construction to preliminary event
selection
	 	 	[***]	 	 	 	[***]	 
	[***] synthesis and cloning
	 	 	[***]	 	 	 	[***]	 
	[***] transformation protocol development and
validation in China
	 	 	[***]	 	 	 	[***]	 
	[***] transformation and plant regeneration (200 each)
	 	 	[***]	 	 	 	[***]	 
	Grow and observe primary transformants in ICS
greenhouse
	 	 	[***]	 	 	 	[***]	 
	Transgenic plant (seedlings) analysis and [***]
expression level measuring (RT-PCR, [***])
	 	 	[***]	 	 	 	[***]	 
	Test [***] efficacy with transgenic plants
	 	 	[***]	 	 	 	[***]	 
	Transgenic plant seed collection
	 	 	[***]	 	 	 	[***]	 
	Segregation analysis
	 	 	[***]	 	 	 	[***]	 
	Insert quality evaluation
	 	 	[***]	 	 	 	[***]	 
	Phase II — [***] development
	 	 	 	 	 	 	 	 
	[***]
	 	 	[***]	 	 	 	[***]	 
	[***]
	 	 	[***]	 	 	 	[***]	 
	[***]
	 	 	[***]	 	 	 	[***]	 
	[***]
	 	 	[***]	 	 	 	[***]	 
	Selection of preferred events
	 	 	 	 	 	 	[***]	 
	Additional [***] testing
	 	 	[***]	 	 	 	[***]	 
	[***] event selection and [***]
	 	 	 	 	 	 	 	 







	4. REMUNERATION AND PAYMENT SCHEDULE






	 	4.1	 	As specified in the Agreement.





Page 6 of 28






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ANNEX II-A




to the Collaboration Agreement between Ceres and ICS dated November 15, 2007



[***] Reports and Report Format


Table 1. Transformation Table.




	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	Number of	 	Regeneration	 	Plantlets	 	Soil Transplant	 	T0	 	 	 	T1 Harvest	 	T1 Events
	Trans ID	 	Construct ID	 	Construct Date	 	Made by	 	Agro Growth	 	Infection Date	 	Resistant [***]	 	date	 	Generated	 	date	 	location	 	Notes	 	Date	 	Harvested
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Notes on	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	germination, amount	 	 	 	 
	1
	 	 	 	1/1/2009
	 	LZ
	 	Yes
	 	2/1/2009
	 	50
	 	6/1/09
	 	40
	 	9/1/09
	 	ICS
	 	used (10/1/09)
	 	12/1/09
	 	30
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Poor	 	 	 	 
	2
	 	 	 	1/1/2009
	 	LZ
	 	Yes
	 	2/1/2009
	 	20
	 	6/1/09
	 	10
	 	9/1/09
	 	ICS
	 	germination (10/1/09)
	 	12/1/09
	 	9
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	3
	 	 	 	6/1/2009
	 	 	 	No
	 	7/1/2009
	 	21
	 	12/1/09
	 	10
	 	3/1/09
	 	ICS
	 	 	 	 	 	8
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	4
	 	 	 	7/1/2009
	 	[***]
	 	No
	 	8/1/2009
	 	21
	 	1/1/10
	 	9
	 	4/1/10
	 	ICS
	 	 	 	 	 	7
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	5
	 	 	 	10/1/2009
	 	XZ
	 	Yes
	 	11/1/2009
	 	60
	 	3/1/10
	 	50
	 	6/1/10
	 	ICS
	 	 	 	 	 	45





Table 2. Transformation Table description of contents.




	 	 	 
	Column N	 	Description
	Trans ID

	 	Unique number for a particular transformation event
	Construct ID

	 	Number assigned to the construct
	Construct date

	 	Date the construct was completed
	Made by

	 	Who made the construct
	Agro growth

	 	Yes/No did the agro grow
	Infection date

	 	Date [***] infection was performed
	Number of Resistant [***]

	 	Number of resistant [***] resulting from the infection
	Regeneration date

	 	Date plantlet regeneration started
	Plantlets regenerated

	 	Number of resistant [***] which give rise to plants
	Soil transplant date

	 	Date plantlets were transplanted to soil
	T0 location

	 	Location of T0 plants
	Notes

	 	Any observations made while T0 plants are in soil
	T1 harvest date

	 	Date of T1 seed harvest
	T1 events harvested

	 	Number of T1 seed lots harvested





Table 3. Seed Production Table.




	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Date of	 	 	 	Generation	 	 	 	 	 	 	 	Container	 	 	 	 
	[***]_ID	 	Harvest	 	Harvested By	 	of Seed	 	Location	 	Building	 	Room	 	(Barcode)	 	Amount (g)	 	Notes
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Notes on
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	germination, amount
	[***]
	 	1/1/2009
	 	LZ
	 	T1
	 	SCUTA
	 	AAA
	 	XXX
	 	123456
	 	[***]
	 	used (2.1.2006)
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Poor germination
	[***]
	 	1/1/2009
	 	LZ
	 	T1
	 	SCUTA
	 	BBB
	 	XXX
	 	123457
	 	[***]
	 	(1.1.2007)
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	[***]
	 	6/1/2009
	 	 	 	T2
	 	ICS
	 	 	 	YYY
	 	123458
	 	[***]	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	[***]
	 	7/1/2009
	 	CYW
	 	F1
	 	ICS
	 	 	 	YYY
	 	123459
	 	[***]	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	[***]
	 	10/1/2009
	 	XZ
	 	F2
	 	ICS
	 	 	 	YYY
	 	123460
	 	[***]	 	 





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Table 6. Image Log Table.




	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	Image	 	 	 	 	 	 	 	 
	[***]_ID	 	Image _ID	 	Description	 	Trait	 	Phenotype	 	Image Type	 	Location
	[***]
	 	87654321
	 	Whole plant and
controls
	 	[***]
	 	None observed
	 	Phenotype
	 	SCUTA
	[***]
	 	87654322
	 	Plot image
	 	[***]
	 	[***]
	 	Assay Result
	 	ICS
	[***]
	 	87654323
	 	Field shot
	 	[***]
	 	None [***]
	 	Field Trial
	 	CHANGPING






Table 7. Data Collection Table.






	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Plant Position
	 	 	 	 	 	 	 	 	 	 	Measurement	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Block	 	Row	 	CW Event	 	Measurement	 	Code	 	Name	 	Date	 	1	 	2	 	3	 	4	 	5	 	6	 	7	 	8	 	9	 	10
	10

	 	 	1	 	 	GW00222-01
	 	Plant Status
	 	 	1	 	 	 	 	5/31/2007
	 	 	[***]	 	 	 	 	 	 	 	[***]	 	 	 	 	 	 	 	 	 	 	sick
	 	 	 	 	 	 	 	yellow
	10

	 	 	1	 	 	GW00222-01
	 	Is this KI?
	 	 	2	 	 	 	 	5121/2007
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Y	 	 	 	 	 	 	 	 	 
	10

	 	 	1	 	 	GW00222-01
	 	Height
	 	 	3	 	 	 	 	6/1/2007
	 	 	72	 	 	 	68	 	 	 	59	 	 	 	68	 	 	 	66	 	 	 	60	 	 	 	 	 	 	 	 	 
	10

	 	 	1	 	 	GW00222-01
	 	Flowering Time
	 	 	4	 	 	 	 	6/1/2007
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Y	 	 	 	 	 	 	 	 	 	 	 	 	Y	 	 	 	 
	10

	 	 	1	 	 	GW00222-01
	 	Flowering Time
	 	 	4	 	 	 	 	6/2/2007
	 	 	Y	 	 	 	 	 	 	 	Y	 	 	 	 	 	 	 	Y	 	 	 	 	 	 	 	 	 	 	Y	 	 
	10

	 	 	1	 	 	GW00222-01
	 	Flowering Time
	 	 	4	 	 	 	 	6/3/2007
	 	 	 	 	 	 	Y	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	Y	 	 	Y	 	 	 	 	 	 
	10

	 	 	1	 	 	GW00222-01
	 	QC result
	 	 	7	 	 	 	 	6/7/2007
	 	 	 	 	 	 	+	 	 	 	 	 	 	 	 	 	 	 	-	 	 	 	 	 	 	 	 	+	 	 	 	 
	10

	 	 	1	 	 	GW00222-01
	 	Biomass
	 	 	5	 	 	 	 	6/28/2007	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 







	1.	 	Key Performance Indicators (KPIs)






	 	1.1.	 	Number of constructs yielding >10 T0 plants delivered each quarter vs. all
constructs delivered each quarter.
	 
	 	1.2.	 	Number of constructs sequence validated in T0 plants each quarter vs. all constructs
assayed in T0 each quarter.
	 
	 	1.3.	 	Number of constructs yielding T1 seeds from >10 events each quarter vs. all T1 seeds
delivered each quarter.
	 
	 	1.4.	 	Number of constructs sequence validated in T1 events each quarter vs. all events
assayed in T1.
	 
	 	1.5.	 	Time from infection to T1 seed harvest each quarter.
	 
	 	1.6.	 	Number of constructs evaluated for predicted phenotype or trait.
	 
	 	1.7.	 	Number of constructs yielding predicted phenotype or trait vs. all constructs
phenotyped or assayed.
	 
	 	1.8.	 	Number of constructs yielding novel phenotypes vs. all constructs phenotyped and
assayed.
	 
	 	1.9.	 	Number of constructs showing yield drag or negative traits vs. all constructs analyzed.






	2.	 	Screenhouse Maps






	 	2.1.	 	Plot map for Screenhouse 1 and Screenhouse 2 at SCUTA











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Page 9 of 28





 











 





ANNEX IV-A





	 	 	to the Collaboration Agreement between Ceres and ICS dated November 15, 2007





Additional Stewardship Guidelines




	1.	 	the Excellence Through Stewardship Quality Management Program Guide to Maintaining
Plant Product Integrity of Biotechnology-derived Plants (provided herewith).






	2.	 	Ceres has licensed in the bar gene from Bayer BioScience, N.V. (“Bayer”). Pursuant
to the License Agreement with Bayer Ceres has to comply with and charge its subcontractors
with the Stewardship Guidelines set forth hereinafter or any reasonable stewardship guidelines
as Bayer may provide.
	 
	 	 	BAYER and LICENSEE agree they have a common interest to ensure that any material containing
the bar Gene alone or in combination with the 35S Promoter is handled in such a way that no
safety or regulatory issues arise from its use. Therefore, the Parties agree that LICENSEE
will maintain an internal stewardship program ensuring the appropriate handling of the
aforesaid material in order to assure particularly, but not exclusively containment,
confinement and traceability.
	 
	 	 	The LICENSEE confirms that all employees and/or contractors working at any stage with the
Material will be trained to ensure compliance with the stewardship program and appropriate
documentation will be maintained as evidence of training and compliance.
	 
	 	 	The LICENSEE shall follow all necessary biosafety requirements during the handling and any
transportation of the Material.
	 
	 	 	The Parties agree that BAYER may request a stewardship audit to be conducted by an
independent auditor(s) agreed upon by both Parties, a maximum of one (1) time per calendar
year per location where research is taking place (except in case of default; see below). The
auditor(s) will, upon BAYER’s request, notify LICENSEE of desire to conduct an audit, giving
minimum of five (5) working days notice of such audit. It is expressly agreed upon by the
Parties that non-inspection or non-action on the part of BAYER shall not be construed in any
way as an approval of procedures and precautions practiced by LICENSEE and does not remove,
reduce or affect in any way the responsibility and liability of LICENSEE as set forth in the
Agreement.
	 
	 	 	BAYER will specify to the auditor(s) which aspects of LICENSEE’s use of the bar Gene alone
or in combination with the 35S Promoter are to be audited, and specifically what activities
in relation to such use must be taken into account. This can include specific handling,
containment and monitoring procedures (laboratory, greenhouse or field use, etc.); locations
(e.g. audit of all activities involving the bar Gene alone or in combination with the 35S
Promoter at a particular LICENSEE location); or combinations thereof, and will be
communicated to LICENSEE upon notification of an audit.
	 
	 	 	LICENSEE will provide to auditor access to any and all stewardship documentation (laboratory
notebooks, records of shipment, copies of legal permits for field trials, records of
monitoring, etc.) to allow auditor(s) to make a full assessment of LICENSEE’s compliance





Page 10 of 28









 






	 	 	with local requirements and use of the bar Gene alone or in combination with the 35S
Promoter. LICENSEE agrees to share other documentation (stewardship guidelines, best
practices, SOPs, etc.) with auditor(s), as requested. LICENSEE agrees to allow auditor(s) to
question LICENSEE’s staff concerning specific practices and procedures of relevance.
LICENSEE will also provide to auditor(s) access of reports of all external audits conducted
by regulatory authorities as part of their compliance procedures, the conclusions of which
will be transferred to BAYER subject to BAYER’s confidentiality obligations in Article 10.
	 
	 	 	Auditor(s) will prepare a report, to be provided simultaneously to both Parties, indicating
the following: Compliance with applicable legal requirements (Yes/No); if Yes, any specific
or general recommendations for improvements; if No, nature and location of defaults and
recommended actions to correct such. It is expressly understood that the auditor(s) will not
provide BAYER with any confidential information concerning LICENSEE’s use of the bar Gene
alone or in combination with the 35S Promoter.
	 
	 	 	LICENSEE will have sixty (60) days to remedy such default to BAYER’s satisfaction. BAYER has
the right to request a follow-up audit, at LICENSEE’s expense, to verify corrective action
has been taken and the default remedied.
	 
	 	 	Any deviation from these Stewardship Guidelines should be reported to Judith Rylott,
Telephone: +44(0)1787 880979, E-mail: Judith.Rylott@BAYERcropscience.com






	3.	 	the following guidelines are provided to prevent the pilferage, vandalism, or escape of
transgenic [***] in China.






	 	3.1	 	Plantlet transport. Transgenic [***] plantlets will be transported by
ICS personnel from the lab to the field in a clearly labeled, secured and sealed
container. Unused plants will be destroyed by autoclaving according to SOP R7.
	 
	 	3.2	 	Plant growth. Transgenic [***] will be grown in a secure and contained
growth room, greenhouse, screenhouse or in a field approved for the growth of
transgenic rice. No [***] rice plants will be grown in the same greenhouse,
screenhouse or approved field with transgenic [***] .
	 
	 	3.3	 	Seed storage. Each seed line will be contained within a sealed clearly
labeled envelope or a sealed paper bag. Each seed line is inventoried and stored
inside a locked cabinet inside a secure room. Access to the seed storage cabinets is
limited to those involved in the experiments. Seed utilization and disposal will be
tracked using a log system. Unused seeds will be destroyed by autoclaving according to
SOP R7.
	 
	 	3.4	 	
Seed transport. Each seed line will be transported in a sealed, clearly labeled
envelope. Envelopes will be shipped in a clearly labeled, secured and sealed container
within a shipping box to prevent spillage if the outside packaging gets damaged.






Page 11 of 28


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	 	3.5	 	

Seed destruction. The maintenance of a transgenic [***] seed log is the
responsibility of ICS. The inventory of transgenic seeds will be reviewed annually.
Seed stocks designated by Ceres as no longer needed will be destroyed by autoclaving as
described in SOP R7. Their destruction will be recorded in the seed log.





Page 12 of 28


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	 	Protocol

Number:
	 	Leave this blank.
	 
	 	 	 	 
	Property of Ceres, Inc.

	 	Protocol Name:
	 	[***] Transformation
	 
	 	 	 	 
	Authors: Anthony Trieu

	 	Date Issued:
	 	12/30/[***]
	Approved By: Chuan-Yin Wu

	 	Version	 	 
	 

	 	Number:	 	 






SOP [***]: [***] Transformation




“The materials and methods described in this SOP are Ceres Trade Secrets. Please treat this
proprietary information as Ceres Confidential.”




1. Purpose:




[***] by genetic engineering




2. References:




[***]




3. Safety:




3.1. Follow universal lab safety technique




3.2. Proper disposal of transgenic waste in designated receptacles





	 	3.2.1.	 	Dispose the unused Agrobacterium culture in the biological waste container
	 
	 	3.2.2.	 	Dispose all the excess [***] and plant materials in the biological waste
container





4. [***] Integrity Concerns




4.1. Misidentification





	 	•	 	To avoid misidentification, request HTPC group to use printed labels on tubes when
handing over Agrobacterium to transformation group. The label should contain Gemini
ID, date of inoculation and the initials of the person who inoculated the culture.





4.2. Mislabeling: To avoid mislabeling





	 	•	 	Agrobacterium culture tubes during re-inoculation, keep the tubes that belong to
the same Gemini ID together. Check the label on the tubes before each inoculation.
	 
	 	•	 	Always check the label on the lid of the Petri dish before subculturing.
	 
	 	•	 	Sub-culture just one construct at a time to avoid mix up. Once you finish
subculturing a construct, label the plates and then go on to the next construct.
	 
	 	•	 	Print labels to avoid mislabeling the Petri dish.





4.3. Errors in tracking





	 	•	 	Print labels to avoid mislabeling.
	 
	 	•	 	Count the number of plates used for sub-culturing each construct. In the next
stage, make sure that the count matches. For example, if you used 15 plates to
subculture one construct from co-cultivation to selection, make sure that there are 15
plates when you transfer the [***] from selection to regeneration.
	 
	 	•	 	Enter all the data in the work sheet, so it is easy to refer.






 Page 13 of 28



Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission









 








	 	 	 	 	 

	

	 	Protocol

Number:
	 	Leave this blank.
	 
	 	 	 	 
	Property of Ceres, Inc.

	 	Protocol Name:
	 	[***] Transformation
	 
	 	 	 	 
	Authors: Anthony Trieu

	 	Date Issued:
	 	12/30/[***]
	Approved By: Chuan-Yin Wu

	 	Version	 	 
	 

	 	Number:	 	 







4.4. Errors in disposition





	 	•	 	Check the database to verify if you are handing over the transformants for the
right person who requested the transformation of that particular construct.
	 
	 	•	 	Ask the requestor, to sign off those transformants to indicate that they have
received the plants.
	 
	 	•	 	Enter the hand off information in the oracle database and worksheets. The hand off
information should include the date of hand off, the person to whom the transformants
were delivered and the number of transformants that were delivered.





5. Critical Control Points




5.1. Confirm construct identity prior to transformation





	 	•	 	Request the HTPC group to send the list of constructs that have to be used for
transformation. The list should contain the following information






	 	•	 	Gemini ID
	 
	 	•	 	Name of the requestor
	 
	 	•	 	Project






	 	•	 	Target organism
	 
	 	•	 	Number of transformants needed
	 
	 	•	 	Selection marker





5.2. Confirm host material identity prior to transformation





	 	•	 	Refer to 5.1.





5.3. Transfer of transformants (e.g., containment growth chamber/greenhouse, field, or third party)





	 	•	 	Refer to 4.4.





5.4. Confirm transformation success rate




6. Critical limits




6.1. Establish the expected or current success rate for the process. Use this as a benchmark





	•	 	Refer to 5.4.





7. Preventive measures




7.1. Establish and implement labeling, tracking and, disposition as part of an inventory system





	 	•	 	Refer to [***] Integrity Concerns (No. 4)





7.2. Establish and implement procedures so that labels used to identify host material and
transformants are recorded and information pertinent to identity is retrievable





	 	•	 	Create worksheets for each transformation experiment.
	 
	 	•	 	Enter data in the worksheets immediately after a specific task has been completed.
	 
	 	•	 	Enter the data in oracle database.





 Page 14 of 28


Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission













 








	 	 	 	 	 

	

	 	Protocol

Number:
	 	Leave this blank.
	 
	 	 	 	 
	Property of Ceres, Inc.

	 	Protocol Name:
	 	[***] Transformation
	 
	 	 	 	 
	Authors: Anthony Trieu

	 	Date Issued:
	 	12/30/[***]
	Approved By: Chuan-Yin Wu

	 	Version	 	 
	 

	 	Number:	 	 






7.3. Establish and implement internal work processes and SOP for trace back





	•	 	Refer to 7.2.





8. Monitor control of the CCP




8.1. Prior to transformation, confirm identity of transforming DNA, host, and associated material
by documentation or confirm using diagnostic methods where appropriate





	 	•	 	Request the HTPC group to send a transformation request email with the list of
constructs that have to be used for transformation. The list should contain the
following information






	 	•	 	Gemini ID
	 
	 	•	 	Name of the requestor
	 
	 	•	 	Project
	 
	 	•	 	Target organism
	 
	 	•	 	Number of transformants needed
	 
	 	•	 	Selection marker






	 	•	 	Print the transformation request email and attach it to the worksheet.





8.2. Prior to transfer for further propagation, confirm identity of transformant by documentation
or confirm using diagnostic methods where appropriate





	•	 	Refer to 4.4.





9. Corrective action to be taken when monitoring indicates that a particular CCP is not under
control




9.1. In the event that host material or the transformant is found to be incorrectly identified or
where identity cannot be confirmed, the material and any derivatives should be reviewed and
appropriate disposition determined




9.2. Incorporate any corrective measures or procedural changes into SOP as appropriate




9.3. If the process efficiency falls below expected levels conduct root cause analysis and
implement corrective action plan





	 	•	 	Check the [***] of the [***] that was used for transformation.
	 
	 	•	 	Check if the right selection was used.
	 
	 	•	 	Check if a new vector was used.
	 
	 	•	 	Sequence the selection marker to confirm that it is intact
	 
	 	•	 	Analyze the promoter driving the selection marker gene
	 
	 	•	 	Analyze the effects of the trait gene





10. Verification to confirm that the HACCP system is working effectively




10.1. Confirmation of transforming DNA, host, and associated material identity prior to
transformation





	 	•	 	Refer to 5.1.





10.2. Confirmation of transformant identity prior to transfer of plants to containment facility





	•	 	Refer to 4.4.





 Page 15 of 28


Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission















 








	 	 	 	 	 

	

	 	Protocol

Number:
	 	Leave this blank.
	 
	 	 	 	 
	Property of Ceres, Inc.

	 	Protocol Name:
	 	[***] Transformation
	 
	 	 	 	 
	Authors: Anthony Trieu

	 	Date Issued:
	 	12/30/[***]
	Approved By: Chuan-Yin Wu

	 	Version	 	 
	 

	 	Number:	 	 






11. Documentation




11.1. Documentation of identity and trace back should be secure, accessible, and retained as
appropriate





	 	•	 	Refer to 7.2.






	11.2.	 	Document Process Improvement plans and results






	11.3.	 	Document handoff to PI






	 	•	 	Refer to 4.4.





Specifications and expectations: The following need to be documented in notebook
and [***] transformation database for each construct





	 	•	 	Construct ID
	 
	 	•	 	Person to whom you will deliver the transgenic plants
	 
	 	•	 	How many events were requested
	 
	 	•	 	How many events were delivered
	 
	 	•	 	Material destroyed
	 
	 	•	 	Attach spreadsheet template to this SOP— [***] transformation
database





CHANGE CONTROL




	 	 	 	 	 	 	 	 	 	 	 	 	 
	Revision	 	Date	 	Description of Change	 	Approval and Date





Flow chart of [***] Transformation process:




 Page 16 of 28


Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission













 








	 	 	 	 	 

	

	 	Protocol

Number:
	 	Leave this blank.
	 
	 	 	 	 
	Property of Ceres, Inc.

	 	Protocol Name:
	 	[***] Transformation
	 
	 	 	 	 
	Authors: Anthony Trieu

	 	Date Issued:
	 	12/30/[***]
	Approved By: Chuan-Yin Wu

	 	Version	 	 
	 

	 	Number:	 	 






[***]



	 	 	 

	MATERIALS
	 	 
	 
	 	 
	Disposable Supplies:

	 	Capital Equipment:
	 
	 	 
	100 x 20 mm Petri dishes (25373-143; VWR)

	 	Laminar Flow Hood (Nuaire)





 Page 17 of 28

Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission














 








	 	 	 	 	 

	

	 	Protocol

Number:
	 	Leave this blank.
	 
	 	 	 	 
	Property of Ceres, Inc.

	 	Protocol Name:
	 	[***] Transformation
	 
	 	 	 	 
	Authors: Anthony Trieu

	 	Date Issued:
	 	12/30/[***]
	Approved By: Chuan-Yin Wu

	 	Version	 	 
	 

	 	Number:	 	 






	 	 	 

	Gloves (32916-532; Microflex Corp.)

	 	66 Series Incubator (Percival Scientific)
	Whatman 113 filter papers (VWR)

	 	Micro-centrifuge (Heraeus Instrument)
	50 ml Corning conical tube (Fisher Scientific)

	 	Stock Solutions:
	3M first-aid tape (3M)

	 	[***]
	Sands

	 	[***]
	[***]
	 	[***]
	[***]
	 	[***]
	[***]
	 	[***]
	[***]
	 	[***]
	[***]
	 	[***]
	[***]
	 	[***]
	[***]

	 	Magenta Boxes (GA7; Magenta Corp),
	[***]

	 	Forceps
	[***]
	 	 
	[***]
	 	 
	[***]
	 	 
	[***]
	 	 
	[***]
	 	 
	 
	 	 
	[***]
	 	 
	[***]
	 	 
	 
	 	 
	[***]
	 	 






 Page 18 of 28

Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission

















 





	 	 	 	 	 

	

	 	Protocol
Number:
	 	Leave this blank.
	 	 	 	 
	 	 	 	 
	Property of Ceres, Inc.

	 	Protocol Name:
	 	[***] Transformation
	 
	 	 	 	 
	Authors: Anthony Trieu

	 	Date Issued:
	 	12/30/[***]
	Approved By: Chuan-Yin Wu

	 	Version Number:	 	 






	 	 	 	 	 
	[***]
	 	 	 	 
	[***]




    	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	 
	[***]

	 	[***]	 	 
	[***]

	 	[***]	 	 






PROCEDURE:




This protocol is subject to modification [***].



Make check mark in each box after each step of the SOP when carrying out the transformation
procedures



[***]





	 	 	o [***]
	 
	 	 	o [***]





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	 	Protocol
Number:
	 	Leave this blank.
	 

	 	 	 	 
	 
	 	 	 	 
	Property of Ceres, Inc.

	 	Protocol Name:
	 	[***] Transformation
	 
	 	 	 	 
	Authors: Anthony Trieu

	 	Date Issued:
	 	12/30/[***]
	Approved By: Chuan-Yin Wu

	 	Version Number:	 	 







	 	 	o [***]
	 
	 	 	o [***]
	 
	 	 	     [***]





[***]

[***]





	 	 	o [***]
	 
	 	 	o [***]
	 
	 
	 	 	o [***]




[***]





	 	 	o [***]
	 
	 	 	o [***]
	 
	 	 	o [***]
	 
	 	 	o [***]





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	 	 	 	Protocol
	 	Leave this blank.
	 	 	 	Number:


	 	 
	 
	 	 	 	 	 	 
	Property of Ceres, Inc.

	 	 	 	Protocol

Name:
	 	[***] Transformation
	 
	 	 	 	 	 	 
	Authors:

	 	Anthony Trieu
	 	Date Issued:
	 	12/30/[***]
	Approved By:

	 	Chuan-Yin Wu
	 	Version	 	 
	 

	 	 	 	Number:	 	 





o [***]



  [***]



  [***]



o [***]



o [***]



o [***]



o [***]



o [***]



o [***]



o [***]



  [***]



o [***]





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	 	 	 	Protocol
	 	Leave this blank.
	 	 	 	Number:


	 	 
	 
	 	 	 	 	 	 
	Property of Ceres, Inc.

	 	 	 	Protocol

Name:
	 	[***] Transformation
	 
	 	 	 	 	 	 
	Authors:

	 	Anthony Trieu
	 	Date Issued:
	 	12/30/[***]
	Approved By:

	 	Chuan-Yin Wu
	 	Version	 	 
	 

	 	 	 	Number:	 	 





o [***]



o [***]



o [***]



  [***]



o [***]



o [***]



o [***]



  [***]



o [***]



o [***]




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	 	 	 	Protocol
	 	Leave this blank.
	 	 	 	Number:


	 	 
	 
	 	 	 	 	 	 
	Property of Ceres, Inc.

	 	 	 	Protocol

Name:
	 	[***] Transformation
	 
	 	 	 	 	 	 
	Authors:

	 	Anthony Trieu
	 	Date Issued:
	 	12/30/[***]
	Approved By:

	 	Chuan-Yin Wu
	 	Version	 	 
	 

	 	 	 	Number:	 	 





o [***]



o [***]



o [***]



  [***]



o [***]



o [***]




     [***]


o [***]



o [***]



o [***]






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	 	Protocol Number: R2
	 	 	 
	Property of Ceres, Inc.
	 	Protocol Name: Plant Growth and
Development Phenotyping
	 	 	 
	Authors: Chuan-yin Wu
	 	Date Issued: December 30, 2008
	 	 	 
	Approved By:
	 	Version Number: 1.0






1. SOP S2: Plant Growth and Development (PG&D) Phenotyping




	 	 	 

	Purpose:

	 	This protocol is for the phenotyping of T1 and T2 transgenic [***] plants.
	 
	 	 
	Safety:

	 	Follow universal lab safety techniques.
	 
	 	 
	Stewardship:

	 	Properly manage and dispose of transgenic plant material.






B. Plant seed in the field




     Figure 1. Sample plot of transgenic plants.









	1.	 	Measurements to be taken for all T1 plants






	 	a.	 	Flowering time: Number of days from transplanting to heading of the panicle.
	 
	 	b.	 	Plant height: From the ground to the top of the panicle.
	 
	 	c.	 	Seed yield: Weight of seeds while still on panicles, including the envelope.






	2.	 	General observations


To be noted in cases where the frequency is higher than expected
based on control
plants. Use coded comments whenever possible to describe plants (see ANNEX IV, Data








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Commission








 








			
	
	 	Protocol Number: R2
	 	 	 
	Property of Ceres, Inc.
	 	Protocol Name: Plant Growth and
Development Phenotyping
	 	 	 
	Authors: Chuan-yin Wu
	 	Date Issued: December 30, 2008
	 	 	 
	Approved By:
	 	Version Number: 1.0








	 	 	Collection Table). A phenotyping update should be presented monthly to the Collaboration
Committee.







	 	a.	 	Growth vigor: Normal (no entry), improved (1), poor (2)








	 	b.	 	Leaf color: Normal (no entry), darker green (1), yellow-green (2)
	 
	 	c.	 	Fertility: Normal (no entry), reduced (1).
	 
	 	d.	 	Lodging tolerance: Normal (no entry), increased lodging (1).
	 
	 	e.	 	[***] to [***] and [***]: Normal (no entry), increased [***]
	 
	 	f.	 	Stress tolerance (drought, cold, heat): Normal (no entry), increased tolerance
(1), hypersensitive (2).
	 
	 	g.	 	Flag leaf color at maturity: Normal (no entry), more green than controls (1),
more yellow than controls (2).
	 
	 	h.	 	Flag leaf angle from vertical: Normal (no entry), decreased leaf angle (1),
increased leaf angle (2).






	7.	 	Optional measurements for selected events (upon request from Ceres)






	 	a.	 	Fertility: Number of filled seeds divided by number of spikelets on a panicle
(average of 3 panicles).
	 
	 	b.	 	Panicle size: Number of seeds per panicle, averaged from three panicles.
	 
	 	c.	 	Seed yield2: Weight of total seeds less panicles and bag for lines showing 10
percent increase.
	 
	 	d.	 	Seed fill rate: Number of days from flowering [***].





C. Genotype Confirmation





	1.	 	Events with acceptable phenotypes will be genotype confirmed using gene specific PCR.
	 
	2.	 	Images. Photographs will be taken of T1 or T2 plants with distinctive morphological
phenotypes affecting plant growth, development, biomass and seed production including






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Commission












 





	 	 	 	 	 	 	 

	 

	 	 	 	Protocol Number:
	 	 R2
	 
	 	 	 	 	 	 
	
	 	 
	 
	 	 	 	 	 	 
	Property of Ceres, Inc.
	 	Protocol Name:	 	Plant Growth and Development Phenotyping
	 
	 	 	 	 	 	 
	Authors:

	 	Chuan-yin Wu
	 	Date Issued:
	 	December 30, 2008
	 
	 	 	 	 	 	 
	Approved By:

	 	 	 	Version Number:
	 	 1.0








	 	 	fertility, stem morphology, tiller number and leaf morphology. Each photograph should
include a Ceres white board labeled with the construct name, the event number and date and
be written with a black broad tip erasable marker.
	 
	11.	 	Labeled images with plant descriptions will be stored in the project database and image
log with the date of entry.







2. SOP S3 [***] Seed Harvesting




	 	 	 

	Purpose:

	 	Harvest and track seeds from transgenic T0, and T1 [***] plants.
	Safety:

	 	Follow universal lab safety techniques.
	Stewardship:

	 	Properly manage and dispose of transgenic plant material.






A. T1 seed harvest





	 	1.	 	Harvest T1 seeds from individual T0 plants.
	 
	 	2.	 	Harvest seeds by removing whole panicles.
	 
	 	3.	 	Store in labeled envelopes with [***] ID (‘[***]’), event number and date, e.g.
[***]00001-01, MM/DD/YY.
	 
	 	4.	 	Log harvested seed in the Seed Production Table (ANNEX II).





B. T2 seed harvest





	 	1.	 	Harvest T2 seeds from individual T1 plants.
	 
	 	2.	 	Harvest seeds by removing whole panicles.
	 
	 	3.	 	Store in appropriately labeled paper envelopes with CW ID, event number, progeny number
and date, e.g. [***]00001-01-10, MM/DD/YY.
	 
	 	4.	 	Log harvested seed in the Seed Production Table.




Table 1. Seed Production Table.







	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	CW_ID	 	Date of Harvest	 	Harvested By	 	Generation of Seed	 	Location	 	Building	 	Room	 	Container (Barcode)	 	Amount (g)	 	Notes






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Commission










 






	 	 	 	 	 	 	 

	 

	 	 	 	Protocol Number:
	 	 R2
	 
	 	 	 	 	 	 
	
	 	 
	 
	 	 	 	 	 	 
	Property of Ceres, Inc.
	 	Protocol Name:	 	Plant Growth and Development Phenotyping
	 
	 	 	 	 	 	 
	Authors:

	 	Chuan-yin Wu
	 	Date Issued:
	 	December 30, 2008
	 
	 	 	 	 	 	 
	Approved By:

	 	 	 	Version Number:
	 	 1.0






	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	CW_ID	 	Date of Harvest	 	Harvested By	 	Generation of Seed	 	Location	 	Building	 	Room	 	Container (Barcode)	 	Amount (g)	 	Notes
	[***]
	 	1/1/2006
	 	LZ
	 	T1
	 	SCUTA
	 	AAA
	 	XXX
	 	123456
	 	[***]
	 	Notes on germination, amount used (2.1.2006)
	[***]
	 	1/1/2006
	 	LZ
	 	T1
	 	SCUTA
	 	BBB
	 	XXX
	 	123457
	 	[***]
	 	Poor germination (1.1.2007)
	[***]
	 	6/1/2006
	 	 	 	T2
	 	ICS
	 	 	 	YYY
	 	123458
	 	[***]	 	 
	[***]
	 	7/1/2007
	 	CYW
	 	F1
	 	ICS
	 	 	 	YYY
	 	123459
	 	[***]	 	 
	[***]
	 	10/1/2007
	 	XZ
	 	F2
	 	ICS
	 	 	 	YYY
	 	123460
	 	[***]	 	 














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7. SOP S7: Destruction of Biomaterials




	 	 	 	 	 	 	 

	 

	 	 	 	Protocol Number:
	 	 R7
	 
	 	 	 	 	 	 
	
	 	 
	 
	 	 	 	 	 	 
	Property of Ceres, Inc.
	 	Protocol Name:	 	Destruction of Biomaterials
	 
	 	 	 	 	 	 
	Authors:

	 	Chuan-Yin Wu
	 	Date Issued:
	 	July 16, 2007
	 
	 	 	 	 	 	 
	Approved By:

	 	Roger Pennell
	 	Version Number:
	 	 1.0









	 	 	 

	Purpose:

	 	Insure that all [***] seed are eventually destroyed.
	Safety:

	 	Practice universal safety techniques in the lab.
	Start Product(s):

	 	[***] line seed stocks.
	End Product(s):

	 	All [***] seeds should be destroyed by the end of the contract.







	1.	 	Must maintain a log of all [***] seed stocks generated (see Seed Production Table, ANNEX
IV).
	 
	2.	 	Store individual stocks in a sealed clearly labeled envelope or a sealed paper bag. Each
seed line is logged and stored inside a locked metal cabinet inside a locked room. Access to
the seed storage cabinets is limited to those involved in the experiments.




Track seed utilization in the seed log. Review list of [***] seed stocks annually with Ceres.
Destroy unneeded seed stocks by autoclaving at 121 °C for 15 min.







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