exv10w12







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: [***].



Exhibit 10.12



SPONSORED RESEARCH AGREEMENT

between

Ceres, Inc.

and

The Texas Agricultural Experiment Station

of The Texas A&M University System




     This agreement (“Agreement”) is made and entered into by and between Ceres, Inc., a
corporation with principal offices in Thousand Oaks, California, a Delaware corporation (“CERES”)
and The Texas Agricultural Experiment Station (“TAES”) with principal offices in College Station,
Texas, a member of The Texas A&M University System (“TAMUS”), an agency of the State of Texas,
collectively referred to as “Parties” and individually as “Party.”



WITNESSETH:



WHEREAS, TAES and CERES have in common the desire to encourage and facilitate the discovery,
dissemination and application of new knowledge, and CERES desires to support said research;



WHEREAS, the Parties desire to improve germplasm, develop lines and hybrids of sorghum and its
interbreeding species and develop DNA markers and marker platform technology to advance the
development of biomass/bioenergy crops;



WHEREAS, the Parties have agreed on guidelines setting forth how CERES and TAES will cooperate to
make the benefits of such crops available to the public.



NOW THEREFORE, in consideration of the mutual covenants and premises contained in this Agreement,
the receipt and sufficiency of which is acknowledged, the Parties agree as follows:




Article 1. Scope and Management of Work



A. TAES agrees to perform the work set forth in Appendix A (the “Program”) entitled “Crop
Development Using Marker-Assisted Breeding.” Any additional work not specifically identified in
the scope of work statement, but which is indicated during the course of the study shall be
separately negotiated and funded for the appropriate amounts to be agreed upon by CERES and TAES.



B. The work will be under the direction of TAES’ principal investigators, Prof. William Rooney and
Prof. John Mullet (each a “Principal Investigator”). No substitution may be made for TAES’
principal investigator without the prior written concurrence of CERES.



C. A committee of four members (the “Management Committee”) will oversee the




Page 1 of 45









 




implementation of the Program. Two members will be nominated by each Party to serve on the
Management Committee.



D. The Management Committee will be a forum for communication and exchange of information regarding
the implementation of the Program. It shall have no authority to make any modifications to this
Agreement, but may formulate recommendations to change the Program or to take advantage of
additional funding opportunities and present such recommendations to CERES and TAES for
consideration. TAES agrees to permit CERES representatives to confer as necessary with Principal
Investigators. It is understood and agreed that the Management Committee and CERES representatives
have no authority to supervise, direct or control the work performed hereunder.



E. Recommendations of the Management Committee shall be made by unanimous agreement and recorded in
a manner prescribed by the Management Committee as a true record of the recommendations. If the
Management Committee cannot come to a unanimous agreement on any matter then the Management
Committee shall make no recommendation on that matter.



F. TAES’ contact for administrative matters relating to the work performed hereunder is:



Diane Gilliland

Agriculture Program Contracts & Grants

2147 TAMU

College Station, TX 77843-2147

d-gilliland@tamu.edu

Phone: (979) 845-4761

Fax: (979) 862-7775



Physical Address:

3000 Briarcrest Dr. Suite 101

Bryan, TX 77802



G. Each Party will require any and all of its employees and researchers who will perform Program
activities to sign a statement stating that they have read and understand the obligations of TAES
under Article 11 (Confidentiality) and Article 15 (Materials). TAES affirms that, as per The Texas
A&M University System Policy 17.01, Subsection 2.2.1, intellectual property conceived or developed
with support from the System or any of its members in the form of administered funds shall be owned
by the System, and that the funding received from CERES will constitute such administered funds
under such policy.



H. Each Party will conduct Program activities exclusively in laboratories, greenhouses or fields
under full control of or owned by that Party. Each Party will take all reasonable precautions to
prevent damage to, or unintentional destruction of or release of any germplasm created in the
Program.




Page 2 of 45









 




I. Each Party will strictly comply, and use its best efforts to cause its employees and researchers
conducting Program activities to comply, with notebook and breeding book keeping policies of the
highest standards as applicable in the field. Each Party will record and keep all field evaluation,
composition and marker data in user-friendly electronic database format.



J. Each Party shall be responsible for its compliance with all applicable laws, rules and
regulations, including, without limitation, those relating to genetically modified organisms (to
the extent the Program involves such organisms), and for obtaining any and all permits or
authorizations or proceed to any notifications which may be required by such laws, rules and
regulations.



K. When contributing sorghum germplasm for Program activities, the contributing Party will verify
what the origin of the material is and inform the other Party in writing from whom/where and
approximately on what date such Party initially obtained such germplasm. If the germplasm
contributed is governed by the Convention on Biological Diversity (“CBD”), the contributing Party
will be responsible for obtaining all necessary authorizations to commercialize any progeny of such
material under defined financial terms and conditions, and neither Party will use any germplasm in
the Program for which the preceding condition is not satisfied. Further, each Party shall only
contribute germplasm to the Program for which such Party has breeding rights with the right to
commercialize the progeny.



L. Any subcontracting of Program activities to a third party by TAES will be subject to CERES’
prior written approval which will not be unreasonably withheld.



M. TAES agrees not to conduct Germplasm Improvement (as defined in Article 8.A.2) under a funding
or collaboration agreement which grants rights to any person or entity other than CERES in
Biomass/Bioenergy Sorghum (as defined in Article 8.A.2) during the term of this Agreement.




Article 2. Period of Performance



The period of performance for this Agreement shall begin on September 3, 2007, and shall end on
September 2, 2012 (“Program Term”). This period may be extended by mutual agreement of the Parties
in writing.




Article 3. Consideration and Payment



A. CERES agrees to pay for the direct and indirect cost of work of this Agreement to a maximum
amount of four million three hundred ninety three thousand one
hundred fifty eight dollars ($4,393,158) as described in the budget and attached as Appendix B. Twenty
payments in the amount of $193,157.90 shall be made quarterly with the first payment being due and
payable within thirty (30) days of execution of this Agreement. In addition to the quarterly
payments, CERES agrees to pay $470,000.00 within thirty







Page 3 of 45












 







(30) days
of execution of this Agreement and $60,000.00 upon the first anniversary of this Agreement
for the purchase of equipment as described in Appendix B. TAES will invoice CERES when the
payments become due. All payments to TAES under this Agreement shall be made payable to The Texas
Agricultural Experiment Station and forwarded to the address designated in Article 5.



B. TAES will expend these funds as needed for labor, equipment, travel, and other operating costs
in connection with the research. The unexpended balance or any unused supplies remaining at the
completion of the project shall remain the sole property of TAES. The Parties agree that
unexpended funds will be used to extend the term and/or scope of the Program and that they shall
amend this Agreement accordingly. Title to all equipment purchased under this Agreement shall
vest with TAES upon acquisition.



C. If, at any time, TAES has reason to believe that the cost of the work will exceed the amount set
forth in Article 3.A, TAES will notify CERES in writing, giving a revised budget for completion of
the work. CERES will not be obligated to reimburse TAES for any cost in excess of the amount set
forth in Article 3.A, and, subject to diligent performance of the Program activities, TAES will not
be obligated to continue the work or incur costs in excess of that amount unless and until this
Agreement is amended to increase the maximum amount.



D. CERES and TAES may jointly seek additional funding opportunities from Federal and State funding
sources in support of the Program or in support of expansion of the Program. Where accepting
funds from such additional sources would conflict with the obligations of TAES to CERES, such
acceptance of funds will be contingent upon the approval and subsequent amendment of the Agreement
by the Parties.




Article 4. Exchange of Information, Data and Germplasm



The Parties intend to reasonably share all information and data that they develop during the course
and for the purpose of the Program. At its sole discretion, CERES may designate information and
data that it develops and shares with TAES as CERES Confidential Information and such Confidential
Information shall be subject to the terms of Article 11. The Management Committee will meet at
least quarterly with additional meetings as mutually agreed upon and exchange information and data
regarding the implementation of the Program. At least one (1) week before each Management
Committee meeting, each Party will provide the other Party with a report on the Program activities
performed since the last Management Committee meeting. A preferred format for such reports will be
created by the Management Committee. Such reports will contain at least the following:



—     quarterly status update and FTE breakout;



—     actual spending relative to budget;



—     description of Subject Inventions and germplasm generated during the period; and



—     copies of slide presentations summarizing research progress.





Page 4 of 45














 




Additional information, if not specifically included in the reports, shall be delivered as
supporting information at the related quarterly meeting, if available:



—    breeding records;



—    copies of field or greenhouse books and records; and



—    copies of raw field trial data.



TAES shall supply samples of germplasm and Lines developed in the course of the Program activities
upon request by CERES. Further, the following procedure will be followed for release of Lines.
“Release Date” means the date that a Line developed, tested and evaluated pursuant to the terms of
this Agreement is ready for release for commercialization, wherein upon such decision, such variety
will be formally released by TAES (if owned by TAES) or CERES and TAES jointly (if jointly owned).
CERES, on advice of the breeder(s) of each Line, shall establish, in its sole discretion, an
appropriate Release Date for such Lines. The Parties agree that the development of new Lines will
not always result in Lines that are commercially acceptable or releasable.




Article 5. Notices



Formal notices provided under this Agreement must be in writing and delivered by (i) certified
mail, return receipt requested; (ii) hand delivered; (iii) facsimile with receipt of a successful
transmission confirmation; (iv) email; or (v) delivery by a reputable overnight courier service (in
the case of delivery by facsimile or email the notice must be followed immediately by a copy of the
notice being delivered by a means provided in (i), (ii), or (v)). The notice will be deemed given
on the day the notice is received. In the case of notice by facsimile or email, the notice is
deemed received at the local time of the receiving machine, and if not received, then the date the
follow-up copy is received. Notices must be delivered to the following addresses or at such other
addresses as may be later designated in writing.




	 	 	 

	TAES:

	 	Diane Gilliland
	 

	 	Agriculture Program Contracts & Grants
	 

	 	2147 TAMU
	 

	 	College Station, TX 77843-2147
	 

	 	d-gilliland@tamu.edu
	 

	 	Phone: (979) 845-4761
	 

	 	Fax: (979) 862-7775
	 
	 	 
	 

	 	Physical Address:
	 

	 	3000 Briarcrest Dr. Suite 101
	 

	 	Bryan, TX 77802
	 
	 	 
	CERES:

	 	Director of Business Development
	 

	 	cc: Legal Department
	 

	 	Ceres, Inc.
	 

	 	1535 Rancho Conejo Blvd.






Page 5 of 45









 






	 	 	 

	 

	 	Thousand Oaks, CA 91320
	 

	 	Phone: (805) 376-6500
	 

	 	Fax: (805) 376-6549






Article 6. Independent Contractor



A. It is expressly understood and agreed that TAES is an independent contractor in the performance
of the research and is not acting as a partner, joint venturer, or agent of CERES under this
Agreement. The employees, researchers, officers, or agents of TAES or TAMUS shall not be considered
or deemed to be employees, researchers, officers, or agents of CERES. TAES shall have exclusive
direction and control over the manner and method of carrying out the tasks for accomplishing the
research to be performed pursuant to this Agreement, CERES being interested only in the completed
performance of the research contemplated.



B. Neither Party is authorized or empowered to act as an agent for the other for any purpose and
shall not on behalf of the other enter into any contract, warranty, or representation as to any
matter. Neither shall be bound by the acts or conduct of the other.




Article 7. Publicity



A. CERES shall not indicate, directly or indirectly, any endorsement by TAMUS, TAES, or any
component institution or agency of TAMUS, of any products or services of CERES for any reason
whatsoever, without obtaining the express, prior written consent of TAMUS. CERES shall not use the
name of TAMUS, TAES, or any component institution or agency of TAMUS, nor the names of any of their
employees or researchers nor any adaptation in any advertising, promotional or sales literature to
be disseminated to the public without prior written consent obtained from TAMUS in each case.



B. Notwithstanding any provision of this Article, either of the Parties can disclose or otherwise
acknowledge, without restriction, the existence of this Agreement as well as the collaborative
relationship between the Parties without the prior consent of the other Party. Notwithstanding the
unilateral disclosure rights provided for in this Article, if the disclosure or acknowledgement
takes the form of a written release by the disclosing Party, the disclosing Party shall provide the
other Party a copy of any such unilateral disclosure prior to its release so as to allow the other
Party to comment and shall take such comments reasonably into account. However, no advance copy
needs to be provided of any releases referred to in Article 7.C. or of any releases which are
identical to previous releases.



C. The Parties may issue joint press releases regarding their collaboration. Any such press release
and any press release by either Party will be subject to the prior written approval of both
Parties; provided however, that (i) CERES shall have the right to otherwise disclose information as
may be required in CERES’ judgment to comply with SEC or IRS regulations or other laws, rules or
regulations governing disclosure of information or to (potential) investors or business partners
and (ii) TAES shall have the






Page 6 of 45









 







right to otherwise disclose information as may be required in TAES’ judgment to comply with laws,
rules or regulations governing disclosure of information. Notwithstanding the unilateral disclosure
rights provided for in this Article, the disclosing Party shall provide the other Party a copy of
any such unilateral disclosure preferably prior to its release.




Article 8. Intellectual Property



A. General



(1) Except for grants of copyright, all grants of intellectual property rights as set forth in this
Article 8 will be made through the instrument of license agreement substantially in the forms
included in the Intellectual Property Rights Agreement (“IPRA”) of even date herewith between TAMUS
and CERES.



(2) All grants of intellectual property rights as set forth in this Article 8 will be subject to
TAES reservation of an irrevocable, nonexclusive, royalty-free right to use or practice the
intellectual property for research and educational purposes only and for the conduct of third party
sponsored research; subject, however, to compliance with the Guidelines for Future Collaborative
Opportunities which both Parties agree to comply with and which are included in the IPRA. This
reservation excludes Lines developed by CERES or other intellectual property rights of CERES. TAES
agrees that such sponsored research will not grant to third party sponsors any rights already
granted to CERES, and that such third party sponsors will be notified of TAES’ use of Subject
Inventions and Lines which are licensed or optioned to CERES. Further, TAES agrees that germplasm
developed using Lines will only be released or made available to third parties for
commercialization or Germplasm Improvement when (i) such germplasm is less than five percent (5%)
identical to any of the Lines under exclusive option or exclusive license to CERES based on DNA
Marker Analysis, (ii) contains no specific Allele(s) optioned or exclusively licensed to CERES to
which a Line’s specific valuable phenotype is attributable and (iii) contains no Subject Inventions
optioned or exclusively licensed to CERES, or other CERES proprietary technology. The foregoing
provisions do not limit and are subject to Article 1.M hereof. “Germplasm Improvement” shall mean
any activities to improve sorghum to produce Biomass/Bioenergy Sorghum, including without
limitation selection, breeding, marker development or marker assisted breeding or transgenic
improvement. “Biomass/Bioenergy Sorghum” shall mean sorghum which has been bred for the purpose of
conversion to fuels or energy, including but not limited, bred to produce higher biomass yields,
higher yields of cellulose, higher yields of sugar , other improved composition, improved
agronomics, improved net energy balance, improved energy density or which has been bred to make its
cellulose or sugars more available to conversion or more efficiently converted. Biomass/Bioenergy
Sorghum shall not include (i) sorghum which has been improved through breeding for increased starch
yields, including but not limited to grain sorghums, even where such sorghum must necessarily
produce increased yields of sugar to achieve increased starch content or (ii) sorghum which has
been improved through breeding for a purpose that does not include conversion to fuels or energy,
including but not limited to the purposes of sugar






Page 7 of 45









 







production, silage, forage, grain or other traditional uses for sorghum. TAES will notify CERES in
advance in writing of any contemplated projects under (i) or (ii) which would result in the grant
of rights by TAES or TAMUS to a for-profit party, and at CERES’ request discuss such project with
CERES, subject to any applicable confidentiality provisions, “DNA Marker Analysis” shall mean a
comparison according to a mutually agreed process based on a mutually agreed set of approximately
one hundred (100) markers. The Management Committee will define DNA Marker Analysis within two (2)
years of the latest signature date of this Agreement.



(3) The Parties shall consult as soon as possible but in any case within twenty (20) days of
receiving an Invention Notice. Such consultation shall concern whether to proceed to obtain
intellectual property protection on disclosed CERES Inventions, TAES Inventions and/or Joint
Inventions or whether to protect the same through other methods. (All such terms are as defined
hereinafter in Article 8 C.(1).)



Each Party shall be responsible for securing intellectual property protection for its own Subject
Inventions. CERES shall have the first option to pursue protection of Joint Inventions, and any
protection of Lines which are jointly owned, in the joint names of both Parties. If CERES so
elects by written notice within sixty (60) days of such initial consultation or with respect to
Lines, at any time but before ninety (90) days after the end of the period set forth in Article 2,
CERES shall be the “Administering Party” for the purposes of this Agreement. If CERES does not so
elect, TAES shall be the Administering Party for the purposes of this Agreement.



TAES may, at its sole discretion, make a written request that CERES be the Administering Party for
certain TAES Inventions or other Subject Inventions for which it is the Administering Party.
Should CERES agree, it shall provide notice of its agreement in writing and shall be the
Administering Party for such Inventions.



The Administering Party shall be responsible for retaining counsel, overseeing the process of
securing intellectual property protection (i.e., the preparation, filing and prosecution of patent
or plant variety rights application(s)) and maintaining intellectual property protection for the
mutual benefit of the Parties, in its best judgment, for that which it had prosecution
responsibility. In addition to other reporting responsibilities provided below, the Administering
Party shall promptly notify the other Party following retention of counsel. The Parties will
provide, and cause their respective employees, researchers and agents to provide, all reasonable
assistance which may be required in connection with the filing and prosecution of such intellectual
property rights, including without limitation the signing of documents.



The Administering Party shall keep the non-administering Party advised as to all developments with
respect to all patent and plant variety rights application(s) and issued patents and plant variety
rights covering TAES owned or jointly owned Subject Inventions or TAES owned or jointly owned
Lines, which includes supplying copies of all papers received and filed in connection with such
applications and patents in sufficient time for the non-administering Party to comment thereon.
Any decision which would




Page 8 of 45









 




result in a change of legal inventorship or ownership of a patent, patent application or plant
variety rights certificate shall not be taken by an Administering Party unless it has first
received authorization in writing from the non-administering Party, provided that the Parties shall
comply with U.S. law on inventorship.



CERES agrees to bear all legal expenses incurred by CERES as an Administering Party in obtaining
and maintaining patents and plant variety rights, U.S. and foreign, covering Subject Inventions and
Lines.



B. Copyright



(1) Title. Title to and the right to determine the disposition of any copyrights or copyrightable
material first produced or composed in the performance of the Program by TAES employees and/or
researchers only shall remain with TAES. Title to and the right to determine the disposition of
any copyrights or copyrightable material first produced or composed in the performance of the
Program by CERES employees only shall remain with CERES. Title to and the right to determine the
disposition of any copyrights or copyrightable material first produced or composed in the
performance of the Program by employees and/or researchers of both TAES and CERES shall remain with
TAES and CERES.



(2) License to Copyrightable Materials (excluding software). TAES grants to CERES an irrevocable,
royalty-free, non-transferable, non-exclusive right and license in TAES’ rights in any
copyrightable materials (technical data, reports, etc.) first developed in the performance of the
Program to use, reproduce, display and perform (to the extent not prohibited by applicable law).
Such grant excludes rights in computer software (including both source and executable code) first
developed under this Agreement, its documentation, and/or information databases (“Software”).



(3) First Right to Negotiate for Commercial License. Additionally, TAES grants to CERES a
time-limited first right to negotiate a non-exclusive or exclusive, at CERES’ election, commercial
license (i) to use, reproduce, display, and perform Software for commercial purposes, and to
distribute and/or sublicense such Software to third parties. CERES shall advise TAES in writing
within ninety (90) days following delivery of such Software to CERES whether or not CERES elects to
negotiate a license agreement to obtain commercial rights to such Software. In the event that
CERES elects to negotiate for a commercial license to such Software, the Parties shall initiate
negotiation of such license agreement, such negotiations not to extend beyond one hundred eighty
(180) days from notice of election without the mutual consent of both Parties. Such license shall
be negotiated in good faith between the Parties, and shall contain reasonable business terms common
to CERES’ field of commercial interest and proposed application. If the Parties fail to reach
agreement within one hundred eighty (180) days after the start of such negotiations which shall be
evidenced by written notice from one Party to the other initiating such negotiations, the terms and
conditions of the license on which no agreement was reached shall be settled in accordance with the
following procedures: the disputed contract terms shall be referred to a mutually agreed impartial
expert whose






Page 9 of 45









 







decision shall be final. Each Party shall submit to the expert within fifteen (15) days of his
appointment its position in writing on the disputed contract terms and conditions. Such expert
shall be limited to choosing one of such two (2) party positions on each of the contract terms and
conditions or related group of contract terms and conditions that the expert considers most
reasonable in the circumstances and shall not make any other determination. Neither Party shall be
bound by any determination by the expert which, in the opinion of Party’s counsel, will result or
be likely to result in that Party violating any applicable law or regulation.



C. Patentable Inventions



(1) Inventorship and Title. Inventorship of inventions, developments, or discoveries first
conceived or actually reduced to practice in the performance of the Program (“Subject Inventions”)
shall be determined in accordance with U.S. Patent Law, whether or not patent applications are
pursued. All rights to Subject Inventions invented solely by employees or researchers of TAES shall
belong solely to TAES (“TAES Inventions”). All rights to Subject Inventions invented solely by
employees of CERES shall belong solely to CERES (“CERES Inventions”). All rights to Subject
Inventions invented jointly by employees or researchers of TAES and employees of CERES (“Joint
Inventions”) shall belong jointly to TAES and CERES. In the event that a Party uses a mapping
population provided by the other Party to discover a marker or Allele, such marker or Allele shall
be a Joint Invention, provided however, that such mapping population is only available to third
parties subject to the same condition that the resulting discoveries of markers or Alleles shall be
jointly owned by TAES and such third party. TAES will notify CERES, in a writing stating expressly
that it is an invention notice under this Agreement (“Invention Notice”), within thirty (30) days
of reduction to practice or knowledge of conception or discovery of a Subject Invention solely
invented by employees and/or researchers of TAES, or of a Joint Invention, and each Invention
Notice will describe the Subject Invention with sufficient specificity to allow assessment by the
other Party.



(2) Option to Obtain a Commercial License. TAES grants to CERES a time-limited option to obtain
an exclusive world-wide commercial license in TAES’ rights in Subject Inventions, with the right to
grant sublicenses, as set forth in the IPRA.



(3) Exercise of Option to a Commercial License. TAES shall promptly disclose to CERES any Subject
Invention pursuant to an Invention Notice. CERES shall hold such disclosure in confidence and shall
not reveal the disclosure to any third party without the written consent of TAES. CERES shall
advise TAES in writing within ninety (90) days of such disclosure to CERES whether or not CERES
elects to obtain exclusive commercial rights to such Subject Invention. In the event that CERES
elects to obtain a commercial license to such Subject Invention, the Parties shall initiate
negotiation of a license agreement in compliance with the IPRA, such negotiations not to extend
beyond one hundred eighty (180) days from notice of election without the mutual consent of both
Parties. Such license shall be negotiated in good faith between the Parties and shall






Page 10 of 45









 







contain reasonable business terms common to CERES’ field of commercial interest and proposed
application.



(4) Joint Inventions. For Joint Inventions conceived in the performance of the Program, TAES and
CERES shall be deemed independent owners under 35 USC 262, in the absence of a written agreement to
the contrary. TAES’ rights in such Joint Inventions shall be subject to the option set forth in
(2) and (3) hereinabove.



D. Germplasm



(1) Definitions:





	 	a.	 	“Hybrid” means a seed or plant that has resulted from genetic crossbreeding between
two or more lines where those lines include one or more (i) Lines or (ii) New Parental
Lines.
	 
	 	b.	 	“TAES Genetic Contribution” means, for any specific Line: (a) the proportion of the
nuclear genes of a Line arisen from Lines licensed by TAES to CERES, based on DNA Marker
Analysis (as defined in Article 8 A. (2)); (b) a contribution to be determined on a
case-by-case basis in each case where a specific valuable phenotype of that Line is
attributable to specific Allele(s) optioned or licensed to CERES by TAES; and (c) Other
Contributions from TAES.
	 
	 	c.	 	“Other Contributions” means intellectual and technical contributions to the
development of Lines or if from CERES, to the development of Lines, New Parental Lines or
Hybrids, such as, without limitation, markers, gene-trait association knowledge or
composition knowledge, that inform the breeding and selection process, or transgenic
traits.
	 
	 	d.	 	“Developed by Breeding” means originated by any form of genetic manipulation
including but not limited to single or multiple hybridization, backcrossing, genetic
transformation or other rearrangement or recombination of genes with or without associated
selection.
	 
	 	e.	 	“New Parental Lines” means new genetic lines or populations which are Developed by
Breeding by CERES and which have one or more of the Lines as progenitors.
	 
	 	f.	 	“Lines” means sorghum lines or populations created in the course of the Program and
new genetic lines or populations developed by CERES through further selection within the
Lines, as distinguished from crossing followed by selection.
	 
	 	g.	 	“Allele” means a particular form of a gene determinant for a valuable characteristic
of a plant (e.g. drought tolerance, specific flowering time), discovered in the Program by
TAES or by TAES and CERES jointly.







Page 11 of 45









 







(2) Ownership. Lines developed by employees of CERES alone will be owned by
CERES. Lines developed by employees and/or researchers of TAES alone will be owned by TAES. CERES
and TAES shall jointly own Lines where the germplasm and Other Contributions of CERES and TAES have
been combined through traditional or artificial means in the Program. When a Party uses jointly
owned Lines or Lines owned by TAES in its own breeding programs outside the Program in compliance
with this Agreement or a license agreement for Lines as referred to in Article 8.D. (4), the
resulting Lines shall be solely owned by that Party. CERES’ use of a jointly owned Line or Line
owned by TAES in its own breeding programs, or any commercial use of such Line(s), shall be subject
to CERES obtaining a license under this Article 8.D and pursuant to the IPRA. In the event that
CERES’ option to license a Line has expired and/or CERES does not license a Line developed under
the Program, TAES shall be able to use such Line for any purpose but subject to the restrictions
set forth in this Agreement, including but not limited to those restrictions set forth in Articles
1.M and 8.A.(2), and the restrictions set forth in the IPRA.



(3) Option to Obtain a Commercial License. TAES grants to CERES a time-limited option to obtain an
exclusive world-wide commercial license to TAES’ rights in Lines, with the right to grant
sublicenses, as set forth in the IPRA.



(4) Exercise of Option to a Commercial License. CERES shall advise TAES in writing at any time,
but before ninety (90) days after the end of the period set forth in Article 2, whether or not
CERES elects to obtain an exclusive world-wide license to maintain and increase seed of Lines;
develop New Parental Lines; develop Hybrids; and sell Hybrids. Such license shall contain royalty
rates customary in the seed industry, taking into consideration (i) TAES Genetic Contribution, (ii)
Other Contributions of CERES, (iii) financial contributions of each Party, and (iv) germplasm
contributed by CERES, if any, all to the development of the Lines and Hybrids. In the event that
CERES elects to obtain a commercial license to one or more or all Line(s), the Parties shall
initiate negotiation of such license agreement in compliance with the IPRA, such negotiations not
to extend beyond one hundred eighty (180) days from notice of election without the mutual consent
of both Parties.




Article 9. Publications



Subject to what is set forth hereinafter with respect to marker-trait associations, TAES shall be
free to publish the results of research performed under this Agreement after providing CERES with a
sixty (60) day period in which to review each publication for patent purposes (enabling
disclosures), and to identify any inadvertent disclosure of CERES’ Confidential Information (as
such term is defined in Article 11). If necessary to permit the preparation and filing of patent
applications, TAES shall agree to an additional delay of publication not to exceed sixty (60) days
to prepare and file necessary applications, and CERES shall agree to reimburse TAES for all
reasonable costs incurred in such filing(s). Any further delay of publication shall require a
separate agreement between TAES and CERES. The Parties agree that neither Party shall publish or
disclose to any third party any information generated in the Program relating to the association of







Page 12 of 56









 







(a) marker(s) with a gene which has been defined in the Program in Appendix A or by
the Management Committee as a cloning target (“Cloning Target”). Such restriction on publication
and disclosure shall cease, and the other provisions on Confidential Information and Publications
of this Agreement shall apply, with respect to each Cloning Target, until the earliest of the
following events: (i) a patent application is filed on the Cloning Target in the U.S.; or (ii) the
Management Committee decides that the Cloning Target is no longer a Cloning Target and such
decision is reflected in a written document; or (iii) at the conclusion of the Program, except if
otherwise agreed by the Parties at that time.




Article 10. Warranty



CONCERNING THE INFORMATION AND DATA PROVIDED UNDER THIS AGREEMENT, TAES MAKES NO REPRESENTATIONS OR
WARRANTIES, EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE OR USE.




Article 11. Confidential Information



A. Any confidential or proprietary information disclosed by CERES to TAES for use in the research
work conducted under this Agreement (“CERES Confidential Information”) shall be designated as
confidential in writing at the time of disclosure to TAES. For the purpose of keeping such
information derived from CERES confidential, TAES shall make all reasonable efforts not to disclose
such information to third parties or release it for publication without the prior written consent
of CERES for a period of five (5) years from the date of this Agreement, but TAES shall not be
liable for unauthorized disclosures of information which occur in spite of such efforts. TAES will
not use CERES Confidential Information for any purpose other than the implementation of the
Program. TAES will only make CERES Confidential Information available to TAES employees or
researchers on a need-to-know basis.



B. TAES shall not be obligated to keep information received from CERES confidential if any such
information; (a) was already in the possession of TAES as evidenced by existing documentation prior
to receipt of information from CERES; (b) appears in issued patents or printed publications; (c) is
now or hereafter becomes generally available to the public on a non-confidential basis through no
fault or action or failure to act on the part of TAES; (d) is disclosed to TAES by third parties
having a bona fide right to make such disclosures; or (e) is ordered produced or disclosed by a
court or administrative body of competent jurisdiction or otherwise required by law, or required to
be disclosed by the Attorney General of The State of Texas, but only to the extent of such required
production or disclosure.



C. Any disclosure by TAES of results of the research performed under this Agreement shall be
subject to compliance with Article 9. Publications.




Page 13 of 45









 





Article 12. Disputes



A. The Parties shall make every possible attempt to resolve in an amicable manner all disputes
between the Parties concerning the interpretation of this Agreement.



B. The Parties must use the dispute resolution process provided in Chapter 2260, Texas Government
Code, and the related rules adopted by the Texas Attorney General to attempt to resolve in the
ordinary course of business. CERES must submit written notice of a claim of breach of contract
under this Chapter to Dr. Mark Hussey, Director, who will examine CERES’ claim and any counterclaim
and negotiate with CERES in an effort to resolve the claim.




Article 13. Governing Law



The validity, interpretation, and enforcement of this Agreement shall be governed and determined by
the laws of the State of Texas, excluding the conflict of laws rules which might require the
application of the laws of another jurisdiction.




Article 14. Termination



A. This Agreement may be terminated for convenience by CERES at any time prior to the full term of
the Agreement period, set forth in Article 2, provided that a written notice is given to TAES
thirty (30) days in advance. However, CERES shall be obligated to pay TAES for all services,
orders, materials, or facilities committed in good faith prior to the effective date of
termination.



B. TAES shall have the right to terminate this Agreement unilaterally with written notice to CERES
in case of failure of CERES to satisfy its material obligations under this Agreement, if CERES
fails to cure such failure(s) within (i) thirty (30) days for failures to remit payment for amounts
due under this Agreement and (ii) ninety (90) days for all other obligations in each case after
receipt of written notice from TAES specifying such failure(s).



C. Promptly upon the delivery of a notice of termination of this Agreement, the Parties will meet
to discuss the Program, and each Party will provide to the other Party any data, information and
germplasm that constitutes Joint Inventions or jointly owned Lines and which has not been provided
prior to the notice of termination.



D. Termination of this Agreement shall not affect the rights and obligations of the Parties accrued
prior to termination hereof nor any license grants then in existence, subject to payment of
remuneration as set forth in any relevant license/commercialization agreements. Further, at or
about the effective date of termination, the Parties will negotiate in good faith to reach
agreement as to the rights to use and commercially exploit Subject Inventions and Lines not covered
by any relevant license/commercialization agreement between the Parties, which rights will be
addressed in one or more written agreements. Such Subject Inventions and Lines shall be deemed







Page 14 of 45









 







subject to the options set forth in this Agreement and to the terms and conditions of the
IPRA.




Article 15. Transfer of Materials



A. “Materials” means plant materials or biological samples owned or otherwise controlled by a Party
(“Originating Party”) and transferred to the other Party under this Agreement.



B. The Party receiving Material(s) (“Receiving Party”) agrees that the Materials will be used
solely for the purpose of the Program, or in the case of CERES, for commercial purposes in
accordance with any applicable license agreement between the Parties.



C. The Receiving Party agrees to use the Material(s) in a safe manner and in compliance with all
applicable state and federal laws and regulations. The Party who makes a delivery of certain
Material(s) will obtain any required permits or proceed to any required notifications prior to the
delivery; the other Party will reasonably cooperate in order to facilitate the issuance of any
required permits.



D. The Receiving Party will only grant access to Material(s) intended for Program activities to its
employees or researchers who need access to such Material(s) for the purpose of the Program.



E. The Receiving Party will exclusively and restrictedly use the Material(s) under suitable
containment conditions, and in accordance with all applicable regulations, and will not use it on
human subjects. The Receiving Party will obtain any authorizations or permits which may be
required for its activities with the Material(s).



F. The Receiving Party agrees that the original Material(s) received from the Originating Party
will not be supplied to other entities, either within or outside of the Receiving Party, without
the prior written approval of the Originating Party. The original Material(s) will not be sold or
transferred for commercial purposes.



G. In the event that Receiving Party desires to utilize the original Material(s) for any uses
beyond the scope of this Agreement, the Parties shall enter into good faith negotiations to
establish the terms and conditions for any such purposes; however, nothing in this Agreement shall
be construed as a representation that the Originating Party may guarantee the grant of such rights.



H. The Receiving Party will keep and maintain written records of all use of the Material(s)
received.



I. All Material provided should be considered experimental and should be handled by the Receiving
Party with appropriate safety precautions. NO REPRESENTATIONS AND NO WARRANTIES OF ANY KIND,
EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY OR







Page 15 of 45









 







FITNESS
FOR A PARTICULAR PURPOSE, ARE PROVIDED HEREIN, NOR ARE
ANY OBLIGATIONS WITH RESPECT TO INFRINGEMENT OF LICENSED PATENTS OR OTHER RIGHTS OF THIRD PARTIES
PROVIDED HEREIN.



J. In the event of termination or expiration of this Agreement, the Receiving Party will return or
destroy, at the sole election of the Originating Party, the Materials no later than thirty (30)
days from such termination or expiration, unless the Originating Party has entered into a written
agreement for the Receiving Party’s continued use of the Materials.



K. Subject to Article 4, the selection of Material(s) for transfer under this Agreement will be at
the sole discretion of the Originating Party. The Originating Party will accompany each transfer
of Material with a transmittal letter that specifies: (i) the roles of each Party involved in the
transfer, e.g., who is the Originating Party, (ii) the experimental designation of the Material(s)
being transferred, and (iii) a statement confirming that the subject Material(s) are being
transferred under the terms of this Agreement.



L. All right and title in Material(s) will remain with the Originating Party in each case. CERES
and TAES shall each retain ownership of their respective contribution in derivatives produced using
Materials where the Materials of CERES and TAES have been combined through traditional or
artificial means. Notwithstanding the foregoing, ownership of derivatives which are Lines shall be
as set forth in Article 8.D.(2).




Article 16. Miscellaneous



A. This Agreement and the IPRA constitutes the entire agreement between the Parties relative to the
subject matter, and may be modified or amended only by a written agreement signed by both Parties.
In this Agreement, the words “includes” and “including” mean “includes” and “including” without
limitation.



B. This Agreement binds and enures to the benefit of the Parties, their successor or assigns, but
may not be assigned by either Party without the prior written consent of the other Party; provided
however, CERES shall have the right to assign its rights and obligations under this Agreement to
any Affiliated Company without such prior consent. CERES shall also have the right to assign its
rights and obligations under this Agreement to a third party in conjunction with the transfer to
such third party of substantially all of the assets of CERES associated with performance under this
Agreement without such prior consent. “Affiliated Company” means any company owned or controlled
by, under common control with or controlling CERES, “control” meaning in this context the direct or
indirect ownership of more than fifty percent (50%) of the voting stock/shares of a company, or the
power to nominate at least half of the directors.



C. The failure of either Party at any time to require performance by the other Party of any
provision of this Agreement shall in no way affect the right to require such performance at any
time thereafter nor shall the waiver by either Party of a breach of any provision be taken or held
to be a waiver of any succeeding breach of such provision or






Page 16 of 45









 







as a waiver of the provision itself.



D. This Agreement, to the greatest extent possible, shall be construed so as to give validity to
all of the provisions hereof. 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.



E. Neither Party shall be liable to the other Party for any incidental, indirect, special, or
consequential damage, however caused, and on any theory of liability, arising out of or related to
the work performed under this Agreement.



F. Each Party must excuse any breach of this Agreement by the other which is proximately caused by
government regulation, war, strike, act of God, or other similar circumstance normally deemed
outside the control of well-managed business.



IN WITNESS WHEREOF, the Parties hereto have caused this Agreement to be executed by their duly
authorized representatives.




	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For The Texas Agricultural
Experiment Station (“TAES”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:
/s/ Peter Mascia

	 	 	 	By: /s/
Mark A. Hussey	 
	 
	 

	 	 	 	 	 

	 	 
	Name: Peter Mascia	 	 	 	Mark A. Hussey	 	 
	Title: Vice President of Product
Development	 	 	 	Director, Texas Agricultural
Experiment Station	 	 
	Date: August 28, 2007

 
	 	 	 	Date: 8-29-2007
 
	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	For Ceres, Inc. (“CERES”)	 	 	 	For The Texas Agricultural
Experiment Station (“TAES”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/
Richard Hamilton	 	 	 	By:	 	/s/
Elsa Murano	 	 
	 

	 	 

	 	 	 	 	 	 

	 	 
	Name: Richard Hamilton	 	 	 	Elsa Murano	 	 
	Title: President & Chief Executive
Officer	 	 	 	Vice Chancellor & Dean of College
of Agriculture and Life Sciences	 	 
	Date: August 29, 2007
 
	 	 	 	Date: 8/29/07
 
	 	 






Page 17 of 45









 








Appendix A




to the Sponsored Research Agreement

between Ceres, Inc. and The Texas Agricultural Experiment Station of The Texas

A&M University System



Program



“Crop Development Using Marker-Assisted Breeding”

Technical Plan for the Development of Bioenergy Sorghum

Texas A&M University System and Ceres



TABLE OF CONTENTS




	 	 	 	 	 
	 	 	Page	 
	I. Executive Summary
	 	 	19	 
	 
	 	 	 	 
	II. Overall Goals
	 	 	19	 
	 
	 	 	 	 
	III. Technical Plan
	 	 	 	 
	 
	 	 	 	 
	A. Sorghum Breeding
	 	 	20	 
	A-1. Sweet sorghum
	 	 	 	 
	A-2. High-biomass cellulosic sorghum
	 	 	 	 
	 
	 	 	 	 
	B. Sorghum Composition/Conversion Testing
	 	 	22	 
	B-1. Biomass composition analysis
	 	 	 	 
	B-2. Biomass conversion testing
	 	 	 	 
	 
	 	 	 	 
	C. Genotyping/Marker-Assisted-Breeding
	 	 	23	 
	 
	 	 	 	 
	D. Technology Development
	 	 	24	 
	 
	 	 	 	 
	E. Sorghum Genome Platform
	 	 	26	 
	 
	 	 	 	 
	F. Bioenergy Traits/Gene Discovery
	 	 	27	 






Page 18 of 45









 





I. Executive Summary:




     Sorghum is one of the most promising biomass feedstocks for the emerging bioenergy/biofuels
industry due to its high yield, drought tolerance, and established production systems. Sorghum is
also an excellent genetic system with relatively simple genetics, a large and diverse germplasm
collection, established genetic/genomic platform and complete genome sequence. Therefore, sorghum
has significant commercial value as a biofuels and bioenergy feedstock, as source of genes and IP,
and as a source of information useful for a wide range of other grass species being developed for
the bioenergy industry (i.e., switchgrass, miscanthus, energy cane).



     The technical plan described in this document is the result of extensive discussion between
CERES and TAES. The scope of work includes; (1) breeding for improved sweet sorghum and high
biomass cellulosic sorghum, (2) analysis of sorghum for biomass composition and conversion
properties, and (3) development of technology for advanced graphical genotyping, enhancement of the
sorghum genome platform, and discovery of QTL and genes for bioenergy traits. The technical plan
integrates germplasm screening, breeding, composition/conversion analysis, and genomics enabled QTL
mapping/gene discovery and marker-assisted breeding (Appendix C, Project Diagram).



     The elements of the technical plan and corresponding budgets are described in sections III and
IV. The background and rationale for each near term budgeted objective/activity is provided in
outline form, followed by a brief description of research objectives and milestones/deliverables.
The technical plan and corresponding budget was designed to identify the most important targets and
milestones based on our current understanding of what needs to be done and to build a technology
platform that would enable accelerated progress over time. A key feature of the proposed agreement
is to establish a sustained investment in the areas of activity described herein for the duration
of the contract assuming reasonable progress towards objectives and milestones. This is essential
because the research and development activities will often involve graduate students who need
support for the duration of their thesis work and because the project requires population and
genotype construction and evaluation that requires many years to come to fruition. However, we
expect that the distribution of funds relative to technical objectives, and the specifics of the
technical plan will change over time as progress occurs, challenges arise, and new opportunities
are identified. Therefore the PIs, in consultation with CERES, expect to modify the specific
research objectives and distribution of funding to projects over the time course of the Agreement
to maximize the impact of investment and overall progress.



II. Overall Goals:



1. Develop bioenergy sorghum inbreds/hybrids that are high yielding, widely adapted, and have
optimum biomass composition for biofuels and bioenergy production systems.



2. Identify and capture IP on key genes/alleles that contribute to bioenergy traits to protect the
value of sorghum bioenergy genotypes co-developed by TAES/CERES.







Page 19 of 45









 







3. Develop sorghum as a model C4 bioenergy grass genetic system for trait assessment and gene
discovery for use in other biomass crops such as switchgrass and energycane.




III. TECHNICAL PLAN DESCRIPTION.




A. SORGHUM BREEDING.



Introduction: Sorghum (Sorghum bicolor) can be used as a feedstock for biofuels production in
several different ways. First, grain sorghum is easily converted to ethanol using the same
methodologies used for the conversion of corn to ethanol and ethanol yields from grain sorghum and
corn are similar. Second, sweet sorghum cultivars that produce high levels of sugar in the stalk
can also be harvested, milled and the juice fermented to ethanol using the same methods that
sugarcane processors use. Third, photoperiod sensitive sorghum hybrids have the capability of
amassing large tonnages for cellulosic production of biofuels while maintaining the highest
water-use efficiency of any crop widely grown in the United States. Moreover, sorghum (all types)
is widely adapted and fits very well into production systems throughout the U.S. and world.
Combined with the water use efficiency, biofuels production from sorghum is feasible in many
regions of the country and the crop will support ecologically sustainable use of the land.




     Grain sorghum hybrids are already available for use in ethanol production. Therefore, over
the past 5 years, TAES researchers have focused on the development of sweet and high biomass
sorghums for biofuels production. Seed supplies of sweet sorghum varieties are limited; their tall
stature and limited seed yields make producing and harvesting seed difficult. Sweet sorghum
hybrids will have two advantages over traditional sweet sorghum cultivars. First, seed production
and processing will use short grain-type female lines that can easily be harvested using technology
already used by the sorghum seed industry. Second, use of hybrids will allow breeders and
producers to capture hybrid vigor; early estimates indicate that hybrids will average 120% the
yield of the high producing parent in the hybrid. Photoperiod sensitive hybrids that produce large
quantities of biomass are commercially available and they are now used for forage production.
However, within the TAES program, we have identified specific genotypes from the world collections
that have even higher yield potential that would likely be superior for biofuels production in a
lignocellulosic conversion system. The manipulation of these lines to develop effective parents
for high biomass sorghum hybrid production has been initiated.


Objectives: This proposal requests funds to accelerate the development of both sweet sorghum and
high biomass cellulosic bioenergy sorghum genotypes. This activity will complement a recently
funded DOE proposal to enhance genomic research into the development of sorghums for biofuels
production. At the completion of both proposals, the sorghum hybrids for energy production will be
developed for commercial use.







Page 20 of 45









 








A-1.
Sweet Sorghum: Complete the development of A/B lines that have high stem sugar content.
Utilize existing varieties as pollinators for hybrid production.



A-2. High-Biomass Cellulosic Sorghum: Develop new pollinators for the production of high biomass
photoperiod sensitive sorghum hybrids. Photoperiod sensitive germplasm with very high biomass
potential has been identified. To utilize these characters, insensitive versions will be generated
that can produce seed in the U.S. allowing these lines to hybridized to existing photoperiod
insensitive A/B lines of the right genotypes to produce photoperiod sensitive high biomass sorghum
bioenergy hybrids.







Technical Plan:





	 	 	A-1. Sweet Sorghum Hybrids






	 	 	20[***]: Offseason Nursery: [***] of next generation [***] of best [***]. Create hybrid seed
for additional evaluation of the best lines in multiple [***] to identify the best hybrids.
Traditional Season: Evaluate selected hybrids in multiple locations, measure agronomic
potential and [***] production potential. If feasible, evaluate [***] potential. Continue completion
of selected [***] lines.






	 	 	20[***]-20[***]: Offseason Nursery:
Increase the best lines for foundation seed increase (both [***] line and
hybrids) to facilitate large scale growouts in the summer of 20[***]. Evaluate sweet
sorghum hybrids; continue [***] to complete [***] lines of most promising [***].
Traditional Season: Evaluate selected hybrids in multiple locations, measure agronomic
potential and [***] potential. If feasible, evaluate [***] potential. Release best [***]
or [***] lines to Foundation seed for [***] and eventual release. Release of [***]lines in fall of
20[***] is expected if all testing proves their worthiness.
Seed of the lines and hybrids should be commercially available in the summer of 20[***].




A detailed breeding plan for sweet sorghum is provided in Appendix D.





	 	 	A-2: High Biomass Photoperiod Sensitive Hybrids






	 	 	20[***] Summer: Grow [***] population, select [***] lines with high biomass potential.






	 	 	20[***]-20[***]: Offseason: Advance
selections to the [***] generation and testcross to [***]line
testers






	 	 	20[***] Summer: Grow [***] generation and evaluate [***]  to identify those that produce
the highest [***].






	 	 	20[***]-20[***] Offseason: Grow [***] generation and create [***]. Further improvement
of additional new lines will be completed through 20[***].






	 	 	20[***] Summer: Multilocation testing and evaluation for selection of best [***]. Further
advancement of the lines and additional [***]






	 	 	20[***] Summer: Multilocation testing and evaluation for selection of best [***]. Selected
lines released to Foundation Seed for Increase and release.






	 	 	20[***] Summer: Seed of the lines and
hybrids should be commercially available.




A detailed breeding plan for high biomass cellulosic sorghum is provided in Appendix D.





	B.	 	SORGHUM BIOMASS COMPOSITION/CONVERSION TESTING.




Background and Rationale: The chemical composition of sorghum biomass will significantly influence
the logistics of harvesting, transport, storage, processing, pretreatment processes, conversion
efficiency and yield of biofuels per dry ton. Therefore, an early objective of this project is to
characterize the range of biomass composition present in sorghum germplasm and to identify biomass
composition traits that need to be selected for during the breeding process. In addition, the
capability to conduct rapid NIR-based composition analysis for sorghum will allow allelic variation
that modulates composition to be mapped and the corresponding genes identified and patented. CERES
is establishing a state-of-the-art biomass composition-testing laboratory in







Page 21 of 45


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California. This laboratory will be able to carry out chemical analysis of biomass required to
establish standard curves for NIR-based analysis. TAES/CERES propose to establish a biomass
composition-testing laboratory at TAES in order to assay several thousand samples generated each
cycle of sorghum breeding and to enable genetic analysis of composition traits. The details of
this activity are described below.




Technical Plan:





	 	 	B-1. Sorghum Biomass Composition Analysis.
	 
	1.1.	 	Establish NIR calibration curves for sorghum biomass samples.





— TAES will sample a range of [***] (diversity of [***])

 — TAES will obtain samples from a range of duration, environments, locations

 — TAES will provide ~[***] samples to CERES for analysis

 — ~[***] gm of dry ([***]% water content)
tissue

 — whole plant biomass sample = silage sample

 — selected lines sampled for [***]/[***]/[***] separately

 — if [***] is present, this needs to be noted or separated out

 — CERES will establish calibration curves for NIR

 — CERES will conduct chemical analysis of selected samples





	1.2.	 	TAES/CERES will establish a biomass composition-testing lab at TAES.




 — laboratory space will be identified for this activity at TAES

 — ovens will be purchased for tissue drying

 — biomass tissue milling instrumentation will be set up (dust/noise issue)

 — NIR instrumentation will be purchased and calibrated





	1.3.	 	Biomass composition testing activity.




 — ~[***] samples will be analyzed by NIR per breeding cycle

 — additional samples of germplasm and from QTL mapping populations

 — selected samples will require chemical analysis
validation

 — TAES may conduct [***]/[***]/[***] analysis of [***]





	 	 	B-2. Biomass Pretreatment/Conversion-Testing Activity.




 — CERES is developing a range of conversion testing capability

 — TAES has developed MixAlco conversion testing capability

 — CERES/TAES will also co-develop third party testing agreements




Milestones:




1.       Establish NIR standard curves for sorghum biomass composition analysis (20[***]).

2.      Establish a biomass composition laboratory at TAES (20[***]).

3.      Establish sorghum biomass conversion testing activity (20[***]).

4.      Characterize biomass composition of breeding lines and germplasm.

5.      Characterize biomass composition
variation associated with QTL.





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	C.	 	GENOTYPING AND MARKER-ASSISTED-BREEDING (MAB).




Background: Genotyping technology is now routinely used to analyze germplasm, select parents for
crossing, accelerate breeding through marker-assisted-selection, and for map-based gene discovery.
Genotyping technology is evolving rapidly from gel-based platform technologies (i.e., AFLP, SSR) to
a wide range of platforms (i.e., TaqMan, MassArray, SNPlex). Recent advances in high throughput
DNA sequencing will also allow sequence-based genotyping using Restriction-Site-Localized
Sequencing on instruments such as the Solexa sequencer. This technology is proposed for
development in Section D.




     We propose to develop TaqMan assays for MAB of selected QTL in the near term. This technology
is being used by CERES and is readily developed for small numbers of loci. In the longer term we
plan to transition to RSL/Solexa-based graphical genotyping as soon as this technology is
developed. Graphical genotyping could replace the need for MAB in most applications and much more
information for selection and genetic mapping experiments.



Technical Plan:





	 	 	C-1. Marker-assisted-breeding (MAB) activity:
	 
	1.1.	 	Taqman assay development for MAB.




 — [***], [***] initial targets

 — sequence ~[***] genes [***] each QTL for
SNP discovery

 — sequence ~[***] [***] lines, [***], [***]-lines

 — optimize SNP-based Taqman assays (ABI7900 platform)

 — add new markers each year ([***], [***], [***], etc.)

 — test BioTrove Taqman platform to explore cost/assay reduction

 — test new methods for DNA extraction, tracking, SNP assays





	1.2	 	MAB assay throughput per year.




 — ~[***] [***] plants X [***] markers ([***]/[***]) in spring 20[***]; fall 20[***]

 — seed from [***] plants will be collected and sent to MAB lab

 — seedlings will be grown out and sampled

 — DNA extraction via Genogrinder

 — [***] breeding cycles requiring MAB per year





	 	 	C-2. Graphical genotyping; MAB and diversity analysis.
	 
	2.1	 	Develop RSL/Solexa graphical genotyping technology (20[***])




 — technology development described in Section D

 — transition to Solexa-based graphical genotyping for MAB (20[***])





	2.2	 	Graphical genotyping applications.





— collect graphical genotypes of all
bioenergy germplasm (diversity)

 — collect graphical genotypes of breeding progeny (MAB)





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— collect graphical genotypes of trait mapping populations
(QTL)




Milestones and deliverables:




1.      [***]/[***] Taqman assay development (20[***]).

2.      ~[***] MAB assays in 20[***].

3.      New Taqman assay development ([***], [***], [***], etc.) (20[***]-20[***]).

4.      Deployment of Solexa-based graphical
genotyping technology (20[***])

5.      Collect graphical genotypes of
bioenergy germplasm (diversity) (20[***]).

6.      Collect graphical genotypes of breeding and trait mapping populations.





	D.	 	TECHNOLOGY DEVELOPMENT.
	 
	 	 	D-1. Graphical genotyping using RSL/Solexa technology.





Background and rationale:



 — sequencing platforms allow sequence-based genotyping

 — sequencing platforms allow digital expression profiling

 — (i.e., Genome Sequencer-20 System, Solexa, ABI-based systems)

 — Sb genome sequence/genetic map alignment allows sequence/SNP mapping

 — haplotypes or graphical genotypes are revealed at sufficient marker density

 — graphical genotypes of germplasm will allow better parent/progeny selection

 — graphical genotyping will accelerate QTL mapping to gene discovery

 — graphical genotyping may replace targeted marker-assisted-breeding

 — TAES has developed a graphical genotyping method called Restriction Site Localized sequencing technology (RSL sequencing technology)

 — TAES has tested RSL-technology on rice/sorghum using 454 technology

 — RSL-sequencing provides a way to sequence genomes at specific sites

 — RSL provides a way to re-sequence the same sub-sample of any genome

 — the number of sites sequenced can be varied depending on need

 — Solexa can collect 1B bp of sequence per run (25-35bp/read) (~$3,000/run)

 — sequence sampling every ~4 kbp (two reads/site) = 10 Mbp of sequence

 — predicted SNP discovery rate = 1 SNP/82kbp (@ 1SNP/1000bp)

 — indexing allows ~100 genotypes per run (~$30/genotype for sequencing)

 — more genotypes can be run at lower sequence/SNP coverage

 — @ $3/~500 marker-genotype this may replace the need for MAB

 — a high quality genome sequence aligned to a genetic map is required




Technical Plan:





	1.1	 	Test RSL-technology on the Solexa sequencing system.





— conduct simulations on rice/sorghum to select restriction enzymes

 — prepare templates from different genotypes of rice, sorghum

 — submit templates to Solexa for sequencing (~$10,000 per test)

 — analyze results; # unique sequences, map location, error rate, etc.

 — SNP frequency, distribution, dependence on restriction enzyme used





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 — streamline DNA extraction, template preparation, sample indexing

 — establish a bioinformatics pipeline for sequence processing

 — test low pass coverage to allow MAB by graphical genotyping





	1.2	 	Applications:





— purchase and set up Solexa sequencers at TAES and CERES

 — transfer technology to the MAB laboratory

 — genotype all relevant germplasm lines being used for bioenergy

 — genotype breeding lines for MAB

 — genotype [***] [***]/[***] populations




Milestones and deliverables:




1.     
Test RSL technology on the Solexa sequencer (20[***])

2.      Refine the technology, test
graphical MAB application (20[***])

3.      Utilize RSL-technology for bioenergy germplasm/breeding analysis (20[***]-20[***])

4.      Utilize RSL-technology for QTL mapping (20[***]-20[***])



D-2. Gene expression platform development: (Solexa/SAGE, qRT-PCR):



Background: A large portion of the phenotypic variation present in germplasm is due to differences
in gene expression. Differences in gene expression can be associated with phenotypic variation by
combining phenotypic QTL analysis and expression QTL analysis in the same population. This type of
eQTL analysis often identifies candidate genes associated with QTL and providing a molecular
understanding of mechanism through analysis of cis- and trans-acting factors that modulate gene
expression. Gene expression profiling also identifies co-regulated genes and regulon structure and
provides diagnostic information about the molecular basis of differences in plant performance. In
recent years, TAES has used microarray studies to characterize expression patterns of ~22,000
genes. A more powerful approach is to acquire [***] from
mRNA using SAGE- or MPSS-technology
combined with a deep sequencing platform. Therefore, we propose to
optimize and utilize SAGE technology in
combination with the Solexa sequencer to obtain [***] of
sorghum germplasm that varies in [***]. This
activity will aid bioenergy pathway gene annotation being done with funding from DOE using
SorghumCyc and accelerate the identification of key genes that modulate bioenergy traits.




Technical Plan:

2.1       Optimize SAGE digital expression profiling technology on the Solexa sequencer.

2.2       Map [***] to genes and genome locations.

2.3       Collect reference profiles of selected treatments/tissues ([***], [***], [***]).

2.4      Utilize Solexa/SAGE for [***]/[***] discovery/[***] screening projects.

2.5       Conduct qRT-PCR-based [***] analysis to further map out [***].




Milestones and deliverables:

2.1      Optimize Solexa/SAGE-based digital
expression profiling technology (20[***]).

2.2       [***] mapped to genes and the genome sequence (20[***])

2.3       Reference [***] profiles collected from selected treatments (20[***]).

2.4      [***] profiles from sorghum bioenergy genotypes/populations (20[***]).





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	E.	 	SORGHUM GENOME PLATFORM.




Background and Rationale: Scientists at TAES have been developed a sorghum genome technology
platform consisting of integrated genetic, cytogenetic and comparative genome maps since 1998. The
TAES sorghum genetic map contains over 3,000 DNA markers based on data collected from 137 RIL lines
derived from BTx623 X IS3620C. A physical map that is aligned to the sorghum genetic map has been
constructed from ~16X deep BAC libraries, HICF fingerprinting, 6D BAC pooling, and ~5,000 EST-STS
linkers. BACs from this map have been end-sequences and sequence scanned providing information for
aligning DOE sequence assemblies to the map. The sorghum genome sequence assemblies produced by
DOE based on 8X shotgun coverage of the genome are large (up to 14 Mbp). Test alignment of DOE
sequence assemblies to SBI03 is promising revealing 6 miss-assemblies in the euchromatic region
(~47Mbp) that were easily corrected.




     Funding is requested to accelerate the next set of sorghum genome map platform improvements
including aligning the DOE sequence scaffolds to the TAES genetic and
physical map followed by [***] and resolution of
issues related to sequence order/quality. In addition,
[***] of the sequence will be done in a targeted
manner (QTL, specific genes/pathways) at different levels depending
on need (automated  [***] prediction and by [***]
analysis, metabolic pathway models, gene expression, etc.). For
example, DOE funding will allow implementation of MetaCyc Annotation
of sorghum genes matching known proteins in metabolic pathways in 20[***] in collaboration with Doreen Ware/Lincoln Stein
(Cold Spring Harbor). We will focus manual annotation efforts on
pathways relevant to [***] with funding from
DOE. We also plan to bring in annotation of gene expression (from
prior microarray, RT-PCR data, plus Solexa/SAGE data
when it becomes available). Comparative genetic maps and the comparative aligned genome sequences
focused on sorghum, rice, maize, and switchgrass will be updated on a regular basis.



     The TAES sorghum genome map platform is a key resource for all future QTL mapping, annotation,
and gene discovery projects done at TAES and those carried out in collaboration with CERES. As
such, the genome map/sequence platform provides our group an advantage in terms of gene
discovery/IP capture. For QTL mapping and gene discovery research it would be ideal if TAES and
CERES were operating with a common genome sequence/genetic map framework. If CERES provides
funding to help TAES to continue development of the TAES genome map/sequence platform, then TAES
will make the genome map/sequence platform available to CERES with regular quality and annotation
updates. CERES will be free to do their own in house annotation of the aligned sorghum genome
map/sequence provided by TAES and to use the information provided by TAES for commercial purposes.



Technical Plan:




1.     
Phase I alignment of DOE sequence assemblies to [***] (20[***]).

2.      Phase II alignment [***], [***] using [***].

3.      Align [***]/[***]/[***]/[***] [***] maps and [***].

4.      Conduct selected [***]and [***].

5.      Identify the location of expression
SAGE/Solexa tags ([***]).

6.      Identify the location of RSL-Solexa
sequence tags on the map (graphical genotypes).

7.      Provide bioinformatics support for
QTL mapping and other projects.




Milestones and deliverables:





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1.      DOE sorghum [***] to [***] (20[***]).

2.      Refined [***] X [***] (20[***]).

3.      Targeted [***] of sorghum
[***], [***], pathways (20[***]).

4.      Improved [***]/[***] [***] ([***], [***], [***], [***]) (20[***]).

5.      [***] onto the [***] (20[***]).

6.      [***] derived from
Solexa/SAGE mapped onto the genome (20[***]).





	F.	 	BIOENERGY TRAITS AND GENE DISCOVERY.
	 
	 	 	F-1.  Flowering time/duration:





Background:



 — duration of growth contributes significantly to biomass yield

 — vegetative growth stops upon initiation of flowering

 — sorghum is a short day plant that responds to photoperiod, thermoperiods

 — dominant forms of maturity (Ma) loci repress time to flowering

 — Ma1-Ma6 modulate time to flowering; additional Ma loci have been identified

 — Ma1 has been mapped (Lin et al., 1995; R. Klein et al., 2007)

 — Ma2 mapping in progress (Mullet/Rooney, 2007/8)

 — Ma3 = PHYB (Childs et al., 1998 — TAES)

 — Ma4 has been mapped, cloning in progress (Mullet/Rooney et al.)

 — Ma5/Ma6 have been mapped, cloning in progress (Mullet et al., 2006-8)

 — CO/FT mapped; mutations in CO modulate [***] ( = [***])

 — [***]+ [***]= [***] when both are [***] ([***] days in College Station)

 — [***]/[***] or [***]/[***] [***] is [***] (~[***] days in College Station)

 — [***]/[***] [***] regardless of
alleles at [***]-[***] ([***] needs checking)

 — most [***] germplasm is [***] ([***]) ([***], [***], [***]) and [***]

 — [***]-high biomass ([***]) lines will be ‘converted’ to [***] using [***]

 — [***] lines will be used as [***] lines
for hybrid seed production

 — [***] [***]-lines X [***]-lines = [***] for testing

 — MAB for [***], [***] during the [***] process will save time, cost

 — modifiers of Ma5 and Ma6 action have been identified (Mullet et al., unpublished)

 — useful for producing hybrids with uniform long duration growth

 — useful for releasing hybrids with flowering times optimized to different regions




Technical Plan:





	1.1.	 	Clone [***] (patent) and map modifiers of [***] action to aid MAB.




 — [***] has been mapped in a large [***] population (~[***] plants)

 — [***] map-based gene discovery is in progress
(~[***] months to candidate gene)

 — a [***] with [***]-like action was detected and is now being mapped





	1.2.	 	Clone [***] (patent) and map modifiers of [***] action to aid MAB.




 — [***] has been mapped in a large [***] population (~[***] plants)

 — a [***] that modifies [***]-action was detected and will be mapped

 — [***] map-based gene discovery will be carried out.






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Milestones and deliverables:




1.1.      DNA markers for [***]/[***] for use in TAES and CERES breeding programs (20[***]).

1.2.     [***] cloning, IP capture (20[***]).

1.3.     [***] cloning, IP capture (20[***]).

1.4.     Map/markers for [***]/[***] [***] (20[***]).





	 	 	F-2. Biomass yield, traits, and composition:





Background:



 — goal is to optimize biomass yield and composition

 — biomass yield is highly heritable in Arabidopsis

 — biomass heterosis is observed in At

 — biomass plant traits to map include lodging, leaf/stem ratio, stem thickness/mass

 — biomass composition traits to map include lignin, cellulose, etc.

 — DOE has provided TAES with partial funding for QTL mapping (2/3 years)




Technical Plan:





	2.1	 	Map QTL for [***] and [***] traits in [***]/[***] populations:





— phase I mapping population; cross [***] lines Dr. Rooney identified in 20[***]

 — phase II mapping population; cross [***] X [***]-line

 — select parents based on [***] and [***] data

 — assay [***] among top [***] lines (in progress)

 — assay diversity of [***] (CERES)/ [***] among [***] lines

 — cross [***] lines (in progress), [***], [***]; assay [***] lines (20[***])

 — select for [***] lines that have fairly [***] ([***])/ [***] for [***]

 — population size of ~[***] is sufficient for initial
QTL mapping

 — assay [***] ([***], etc) and [***] at end of season, replicated

 — College Station; other sites when time, funding permit

 — construct a [***] for QTL mapping (use RSL/Solexa technology)

 — conduct gene expression assays, [***]
(Solexa/qRT-PCR)



Gene
discovery and follow-up:



 — expand sub-populations for [***]

 — identify [***]/[***]/[***] region, [***], generate a large [***] population

 — identify useful [***], phenotype for target trait(s)

 — candidate [***], [***] analysis, and validation

 — capture IP

 — [***] germplasm for [***]

 — translate to other [***]





	2.2.	 	Genetic analysis of [***] for [***].
	 
	 	 	Rationale:




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— biomass production is highly heritable in Arabidopsis (At) ([***]%)

 — six main QTL for biomass were identified in At

 — QTL for biomass could be mapped at the seedling stage (=[***] plants)

 — best parent heterosis was high ([***]%); observed at the seedling stage

 — [***]  not obvious in At; also less well defined in
Sb than Zm

 — heterosis for specific traits has also been identified in different systems

 — sorghum germplasm is diverse; sorghum shows heterosis

 — multiple sources of [***] for biomass traits are likely in sorghum

 — goal is to determine if the genetic basis of [***] can be mapped

 — if so, [***] contributing to [***] from several sources could be pyramided

 — genetic basis of [***] could also be valuable

 — genetic basis of [***] might be too complex, too much [***], etc.

 — high risk, potentially high reward research activity



Proposed research:




— [***] QTL mapping for [***] can be tested using breeding materials

 — ~[***] [***] lines will be derived from each [***]/[***]-[***]

 — [***] lines will contain different portions of the [***]-[***] genome

 — ~[***] [***]-line-[***] sources will be [***] to [***]-lines each year

 — hybrid yield/composition data will be collected to advance the breeding program

 — genotype all [***] lines that are [***] to obtain [***]

 — utilize Solexa-based RSL technology for [***] (see below)

 — test if it is possible to map QTL for [***] of [***]

 — we will be mapping [***] (and [***])
[***] in hybrids

 — QTL for [***] could come from several [***] sources

 — expand to other [***] X [***]-lines if this proves useful

 — [***] from different sources in phase II breeding activity (20[***])




Milestones and deliverables:

2.1       Construct [***],
[***], [***] QTL mapping populations (20[***]).

2.2       [***] data collection on [***] lines (20[***]); [***], (20[***]).

2.3       Gene expression profiling data (parental lines, [***] lines) (20[***]).

2.4       QTL and [***] map construction (20[***]).

2.5       [***], gene discovery, IP capture, [***], etc. (20[***]).

2.6      Obtain graphical genotypes of one [***] population (20[***]).

2.7      Test ability to map genetic basis of variation in [***]/[***] (20[***]).

2.8      If test is positive, analyze other [***]/[***]-line [***] populations (20[***]).





	 	 	F-3. Height (Dw1-4):





Background:



 — variation in plant height is often associated with differences in biomass yield

 — Quinby et al. identified four main loci that modulate height (Dw1-4)

 — Dw2 and Dw3 have been mapped; Dw3 has been cloned

 — map-based cloning of Dw2 is in progress (TAES-ARS collaboration)

 — Dw1, Dw4 require further genetic analysis





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 — most [***] lines will be [***] (but this will vary)

 — [***] = [***] (used for conversion of [***] lines)

 — ‘converted’ [***]-lines need to be at least [***], [***] (and maybe + [***], [***])

 — most [***]-lines will be [***]

 — [***] need to be at least [***], possibly + [***], [***]

 — select [***] lines that are [***] with markers (20[***])




Technical Plan:





	3.1	 	[***] DNA marker development: (budgeted in MAB platform development)





— sequence genes flanking [***] for SNP discovery

 — sequence the alleles corresponding to [***]

 — sequence genes from [***], [***] germplasm used in breeding

 — optimize Taqman assays for MAB

 — assay [***] plants for [***]





	3.2	 	Determine if [***] or [***] have an impact on [***]:




 — utilize [***] populations and [***] populations

 — test association between height and [***] (in [***] backgrounds)

 — variation in [***], [***] and other [***] will be present





	3.3	 	Map [***], [***] and other genes for height if an association with [***] is found.





— map height loci impacting [***] in [***] populations (see below)

 — set up specific populations to map [***], [***] genes

 — [***]: [***] ([***]) X [***] ([***])

 — [***]: [***] ([***]) X Std. [***] ([***])




Milestones and deliverables:

3.1       DNA markers for [***], [***] (20[***]) (included in MAB budget objectives)

3.2       Assessment of [***] or
[***] impact on hybrid yield in [***] backgrounds.

3.3       [***], [***] mapping and DNA markers depending on results and funding.





	 	 	F-4. Other traits:





     The traits listed below were identified as important for the development of superior bioenergy
sorghum hybrids in addition to the traits described above that will be targeted for immediate
funding. Research on the traits listed below will be initiated as soon as new funding becomes
available or as other CERES funded objectives are completed.



4.1      [***] resistance (and other [***], [***] resistance)

4.2       [***] tolerance including [***]

4.3      Response to [***] ([***])

4.4      [***] tolerance (seedling stage emergence)

4.5      [***] efficiency

4.6      [***] ([***], [***])

4.7      [***] tolerance; soil X [***]




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Appendix B




to the Sponsored Research Agreement

between Ceres, Inc. and The Texas Agricultural Experiment Station of The Texas

A&M University System



Budget



A. SORGHUM BREEDING







	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Year	 	 	 	 
	A. SORGHUM BREEDING	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	Year 4	 	 	Year 5	 	 	TOTAL	 
	PI: Bill Rooney
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	To Be Named **
	 	 	32,000	 	 	 	32,960	 	 	 	33,949	 	 	 	34,967	 	 	 	36,016	 	 	 	169,892	 
	Technician
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	To Be Named **
	 	 	18,000	 	 	 	18,540	 	 	 	19,096	 	 	 	19,669	 	 	 	20,259	 	 	 	95,564	 
	Graduate Student
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	50% Time, 12 Cal Mos.
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Student Workers
	 	 	12,000	 	 	 	12,000	 	 	 	12,000	 	 	 	12,000	 	 	 	12,000	 	 	 	60,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Subtotal
	 	 	62,000	 	 	 	63,500	 	 	 	65,045	 	 	 	66,636	 	 	 	68,275	 	 	 	325,457	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe Benefits
	 	 	16,698	 	 	 	16,922	 	 	 	17,154	 	 	 	17,392	 	 	 	17,637	 	 	 	85,803	 
	Total Personnel Costs
	 	 	78,698	 	 	 	80,422	 	 	 	82,199	 	 	 	84,028	 	 	 	85,912	 	 	 	411,260	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials & Supplies
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Breeding
	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	75,000	 
	Agronomic
	 	 	5,000	 	 	 	5,000	 	 	 	10,000	 	 	 	10,000	 	 	 	10,000	 	 	 	40,000	 
	Quality
	 	 	15,000	 	 	 	15,000	 	 	 	10,000	 	 	 	10,000	 	 	 	10,000	 	 	 	60,000	 
	Total Materials & Supplies
	 	 	35,000	 	 	 	35,000	 	 	 	35,000	 	 	 	35,000	 	 	 	35,000	 	 	 	175,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Travel
	 	 	16,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	76,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Other Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	GreenHouse
	 	 	2,000	 	 	 	2,000	 	 	 	2,000	 	 	 	2,000	 	 	 	2,000	 	 	 	10,000	 
	Field Fees
	 	 	8,000	 	 	 	8,000	 	 	 	8,000	 	 	 	8,000	 	 	 	8,000	 	 	 	40,000	 
	Tuition & Fees
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	24 hrs @ $276/hr
	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	33,120	 
	Total Other Costs
	 	 	16,624	 	 	 	16,624	 	 	 	16,624	 	 	 	16,624	 	 	 	16,624	 	 	 	83,120	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Equipment
	 	 	80,000	 	 	 	40,000	 	 	 	0	 	 	 	0	 	 	 	0	 	 	 	120,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Cost — BREEDING
	 	$	226,322	 	 	$	187,046	 	 	$	            148,823	 	 	$	150,652	 	 	$	152,536	 	 	$	            865,380	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 







Page 31 of 45









 







B. COMPOSITION LAB







	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	PI: Bill Rooney	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	Year 4	 	 	Year 5	 	 	TOTAL	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	To Be Named **
	 	 	8,000	 	 	 	8,240	 	 	 	8,487	 	 	 	8,742	 	 	 	9,004	 	 	 	42,473	 
	.25 Technician
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Student Workers
	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	25,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Subtotal
	 	 	13,000	 	 	 	13,240	 	 	 	13,487	 	 	 	13,742	 	 	 	14,004	 	 	 	67,473	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe Benefits
	 	 	3,340	 	 	 	3,382	 	 	 	3,426	 	 	 	3,471	 	 	 	3,518	 	 	 	17,138	 
	Total Personnel Costs
	 	 	16,340	 	 	 	16,622	 	 	 	16,913	 	 	 	17,213	 	 	 	17,522	 	 	 	84,611	 
	 
	 	 
	Materials & Supplies
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	NIR
	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	20,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Materials & Supplies
	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	20,000	 
	Travel
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	0	 
	Other Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Wet Chemistry
	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	75,000	 
	Total Other Costs
	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	75,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Equipment
	 	 	120,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	120,000	 
	(grinder, dryer, NIR)
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Cost — Composition Lab
	 	$	155,340	 	 	$	35,622	 	 	$	            35,913	 	 	$	             36,213 	 	 	$	            36,522	 	 	$	299,611	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 





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C. GENOTYPING/MAB





	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Co-PI: Patricia Klein
	 	Year 1	 	Year 2	 	Year 3	 	Year 4	 	Year 5	 	TOTAL
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Natalie Unruh (0.5-1.0)
	 	 	19,339	 	 	 	19,919	 	 	 	41,033	 	 	 	42,264	 	 	 	43,532	 	 	 	166,089	 
	Student workers
	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	25,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	24,339	 	 	 	24,919	 	 	 	46,033	 	 	 	47,264	 	 	 	48,532	 	 	 	191,089	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe benefits
	 	 	6,766	 	 	 	6,869	 	 	 	13,444	 	 	 	13,662	 	 	 	13,886	 	 	 	54,627	 
	Total Personnel Costs
	 	 	31,105	 	 	 	31,788	 	 	 	59,477	 	 	 	60,926	 	 	 	62,419	 	 	 	245,715	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials and Supplies
	 	 	20,000	 	 	 	20,000	 	 	 	20,000	 	 	 	20,000	 	 	 	20,000	 	 	 	100,000	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Genogrinder, Nanospectrometer
	 	 	20,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	20,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Cost — Genotyping/MAB
	 	$	71,105	 	 	$	51,788	 	 	$	             79,477	 	 	$	             80,926  	 	 	$	           82,419	 	 	$	365,715	 





Page 33 of 45







 






D. TECHNOLOGY/SOLEXA







	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 

	PI: John Mullet
	 	Year 1	 	Year 2	 	Year 3	 	Year 4	 	Year 5	 	TOTAL
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Post-doc (To be named)
	 	 	40,000	 	 	 	41,200	 	 	 	42,436	 	 	 	—	 	 	 	—	 	 	 	123,636	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	40,000	 	 	 	41,200	 	 	 	42,436	 	 	 	 	 	 	 	 	 	 	 	123,636	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe Benefits
	 	 	12,756	 	 	 	12,968	 	 	 	13,187	 	 	 	 	 	 	 	 	 	 	 	38,912	 
	Total Personnel Costs
	 	 	52,756	 	 	 	54,168	 	 	 	55,623	 	 	 	 	 	 	 	 	 	 	 	162,548	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials and Supplies
	 	 	30,000	 	 	 	25,000	 	 	 	20,000	 	 	 	—	 	 	 	—	 	 	 	75,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Nanospectrometer, PCR machines
	 	 	35,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	35,000	 
	Solexa sequencer (TAES)
	 	 	200000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	200,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Cost — Technology/Solexa 
	 	$	317,756	 	 	$	79,168	 	 	$	75,623	 	 	 	 	 	 	 	 	 	 	$	472,548	 










Page 34 of 45






 



E. GENOME PLATFORM




	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 

	Co-PI: Patricia Klein
	 	Year 1	 	Year 2	 	Year 3	 	Year 4	 	Year 5	 	TOTAL
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Natalie Unruh (0.5)
	 	 	19,339	 	 	 	19,919	 	 	 	0	 	 	 	0	 	 	 	0	 	 	 	39,258	 
	Arun Sharma
	 	 	10,012	 	 	 	10,312	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	20,324	 
	CS student (0.5)
*
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	TEES
	 	 	13,000	 	 	 	13,390	 	 	 	13,792	 	 	 	14,205	 	 	 	14,632	 	 	 	69,019	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	42,351	 	 	 	43,621	 	 	 	13,792	 	 	 	14,205	 	 	 	14,632	 	 	 	128,600	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe Benefits
	 	 	13,207	 	 	 	13,402	 	 	 	3,721	 	 	 	3,763	 	 	 	3,806	 	 	 	37,898	 
	Total Personnel Costs
	 	 	55,557	 	 	 	57,023	 	 	 	17,513	 	 	 	17,968	 	 	 	18,437	 	 	 	166,498	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials & Supplies
	 	 	10,000	 	 	 	10,000	 	 	 	2,500	 	 	 	2,500	 	 	 	2,500	 	 	 	27,500	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Other
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Tuition & Fees
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	24 hrs @ $276/hr *
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	TEES
	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	33,120	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Linex computers
	 	 	15,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	15,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Costs — Genome Platform
	 	$	87,181	 	 	$	73,647	 	 	$	             26,637	 	 	$	27,092	 	 	$	27,561	 	 	$	242,118	 





Page 35 of 45






 






F. TRAITS/QTL/GENES




3.1 Duration (Ma5/6)







	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	PI: John Mullet	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	Year 4	 	 	Year 5	 	 	TOTAL	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Graduate student (Bio/Bio)
	 	 	22,000	 	 	 	22,660	 	 	 	23,340	 	 	 	24,040	 	 	 	24,761	 	 	 	116,801	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	22,000	 	 	 	22,660	 	 	 	23,340	 	 	 	24,040	 	 	 	24,761	 	 	 	116,801	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe benefits
	 	 	4,550	 	 	 	4,617	 	 	 	4,685	 	 	 	4,756	 	 	 	4,829	 	 	 	23,437	 
	Total Personnel Costs
	 	 	26,550	 	 	 	27,277	 	 	 	28,025	 	 	 	28,796	 	 	 	29,590	 	 	 	140,238	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials & Supplies
	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	75,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Other
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Tuition & Fees
	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	33,120	 
	Subtotal
	 	 	48,174	 	 	 	48,901	 	 	 	49,649	 	 	 	50,420	 	 	 	51,214	 	 	 	248,358	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	3.2 Biomass traits
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 
	 	 
	PI: John Mullet
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Post-doc
	 	 	40,000	 	 	 	41,200	 	 	 	42,436	 	 	 	43,709	 	 	 	45,020	 	 	 	212,365	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	40,000	 	 	 	41,200	 	 	 	42,436	 	 	 	43,709	 	 	 	45,020	 	 	 	212,365	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe benefits
	 	 	12,756	 	 	 	12,968	 	 	 	13,187	 	 	 	13,413	 	 	 	13,645	 	 	 	65,969	 
	Total Personnel Costs
	 	 	52,756	 	 	 	54,168	 	 	 	55,623	 	 	 	57,122	 	 	 	58,665	 	 	 	278,334	 
	Materials & Supplies
	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	75,000	 
	Subtotal
	 	 	67,756	 	 	 	69,168	 	 	 	70,623	 	 	 	72,122	 	 	 	73,665	 	 	 	353,334	 





Page 36 of 45










 







3.3 Height/anthracnose







	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Co-PI: Patricia Klein	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	Year 4	 	 	Year 5	 	 	TOTAL	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Graduate student (MEPS)
	 	 	20,000	 	 	 	20,600	 	 	 	21,218	 	 	 	21,855	 	 	 	22,510	 	 	 	106,183	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	20,000	 	 	 	20,600	 	 	 	21,218	 	 	 	21,855	 	 	 	22,510	 	 	 	106,183	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe benefits
	 	 	4,348	 	 	 	4,409	 	 	 	4,471	 	 	 	4,535	 	 	 	4,602	 	 	 	22,364	 
	Total Personnel Costs
	 	 	24,348	 	 	 	25,009	 	 	 	25,689	 	 	 	26,390	 	 	 	27,112	 	 	 	128,547	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials and Supplies
	 	 	12,500	 	 	 	12,500	 	 	 	12,500	 	 	 	12,500	 	 	 	12,500	 	 	 	62,500	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Other
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Tuition & Fees
	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	33,120	 
	Subtotal
	 	 	43,472	 	 	 	44,133	 	 	 	44,813	 	 	 	45,514	 	 	 	46,236	 	 	 	224,167	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 






3.4 Other traits







	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	PI: John Mullet	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	Year 4	 	 	Year 5	 	 	TOTAL	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Post-doc (To be named)
	 	 	—	 	 	 	—	 	 	 	—	 	 	 	40,000	 	 	 	41,200	 	 	 	81,200	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	40,000	 	 	 	41,200	 	 	 	81,200	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe Benefits
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	11,948	 	 	 	12,141	 	 	 	24,089	 
	Total Personnel Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	51,948	 	 	 	53,341	 	 	 	105,289	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials and Supplies
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	15,000	 	 	 	15,000	 	 	 	30,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Freeze-mill grinder
	 	 	 	 	 	 	20,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	20,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Subtotal
	 	 	 	 	 	 	20,000	 	 	 	 	 	 	 	66,948	 	 	 	68,341	 	 	 	155,289	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total for Traits/Genes
	 	$	159,402	 	 	$	182,202	 	 	$	165,085	 	 	$	235,003	 	 	$	239,456	 	 	$	981,148	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Operating Summary
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	A. Breeding
	 	 	865,380	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	B. Composition
	 	 	299,611	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	C. Genotyping/MAB
	 	 	365,715	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	D. Technology
	 	 	472,548	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	E. Genome Platform
	 	 	242,118	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	F. Traits/Genes	 	 	981,148	 	 	 	 	 	 	 	 	 	 	TEES Direct Costs	 	 	102,139	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Direct Costs	 	 	3,226,520	 	 	 	 	 	 	 	 	 	 	TEES Indirect Costs	 	 	31,404	 
	Indirect (45.5% MTDC)
	 	 	1,166,638	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	TAES Direct Costs	 	 	3,124,381	 
	Total Request	 	 	4,393,158	 	 	 	 	 	 	 	 	 	 	TAES Indirect Costs	 	 	1,135,235	 









Budget Justification




A. Breeding



Personnel: Funds are budgeted for a 100% FTE research assistant (B.S., Agronomy) to coordinate the
daily activities of the program. Funds for a 50% FTE graduate student are included to address
specific research issues in the project. Student workers will be needed to assist in planting,
harvesting, pollinating, and seed production. Fringe benefits and insurance are charged per Texas
A&M University System policy.



Materials and Supplies: Included all necessary material for managing the breeding program,
including but not limited to pollinating bags, herbicides, sample bags, shipments, grinding costs
for samples, storage and shipping of seed.







Page 37 of 45












 





Travel: Includes expenses associated with travel, lodging and subsistence for working




breeding nurseries, evaluation sites and any promotion and research related presentations.
Other Costs: Greenhouse facilities will be needed to induce flowering in some PS progeny. Field
fees will cover costs of land rental for nursery space in Weslaco and Puerto Rico (as well as
others). Tuition and partial fees for 24 credit hours is budgeted per Texas A&M University System
Policy.



Equipment: Equipment is budgeted to purchase a used experimental plot silage harvester and a pickup
and trailer on which to transport it.




B. Composition



Personnel: Funds are budgeted for a 25% FTE research assistant to coordinate the daily activities
of NIR analysis. Student workers will assist in sample preparation and analysis. Fringe benefits
and insurance have been charged per Texas A&M University System policy.



Materials and Supplies: Includes all necessary material for NIR analysis, including but not limited
to sample bags, grinding and sample vials.




Other Costs: Wet chemistry will be required for a subset of samples.



Equipment: Includes NIR spectrophotometer, grinder and drier for preparing samples.




C. Genotyping/MAB



Personnel: 50% time salary for Natalie Unruh (senior technician) is requested for year one and two
increasing to 100% in years 3-5 reflecting the increasing need for marker-assisted breeding and
graphical genotyping anticipated as the project moves forward. Wages for student workers are
included to help with tissue and DNA preparation. Fringe benefits and insurance are charged per
Texas A&M University System policy.



Materials and Supplies: Includes all reagents for DNA extraction, marker development and
application of Taqman assays and graphical genotyping assays.



Capital costs: A genogrinder is required for tissue disruption and DNA isolation and a
nanospectrometer is required for quantification of DNA.




D. Technology Development/Solexa.



Personnel: Support for a 100% FTE post-doc is requested to carry out the development and testing of
RSL-graphical genotyping and expression profiling technology using the Solexa sequencer. Fringe
Benefits and insurance are charged per Texas A&M University policy.



Materials and Supplies: Funding is requested for the preparation of samples, sequence validation on
capillary platforms, for trial runs on the Solexa sequencer and reagent costs associated with data
collection once a sequencer is installed at TAES. Supplies will also be used for RNA preparation,
qRT-PCR validation and preparation of SAGE samples for digital profiling experiments.



Capital Costs: A nanospectrophotometer and
additional PCR machines are required to quantify and
amplify small amounts of RNA and DNA involved in the proposed studies. Partial support towards the
purchase of a Solexa sequencer is requested in the amount of $200,000.




E. Genome Platform.






Page 38 of 45












 





Personnel: Support for 50% of Natalie Unruh’s time, 27% of Dr. Arun Sharma’s salary,



and 50% of a CS (computer science) graduate student’s time is requested for two years to help with
alignment of the DOE sequence to the TAES genetic and physical map and related genome map
enhancement activity (including support for graphical genotyping, expression tag mapping and QTL
mapping studies). Continued support for the computer science graduate student for bioinformatics
is requested for the duration of the project. Fringe benefits and insurance are charged per Texas
A&M University System policy.



Material and Supplies: Materials such as primers, PCR, gels and other reagents for mapping
sequence contigs onto the genome map is requested for two years. A baseline budget for genome
platform enhancement is requested for years 3-5.



Other: Tuition and partial fees are requested for the graduate student per Texas A&M University
System policy.



Capital Costs: Computers to enhance our ability to handle genome sequence data, genotyping
information and Solexa data are needed to carry out the proposed research.




F. Traits, QTL and Gene Discovery.



Three projects involving genetic mapping and the discovery of genes associated with bioenergy
traits are described, with a fourth project starting in year 4 on a trait target to be named.
Personnel, materials and supplies associated with these projects have been estimated based on past
map-based gene discovery projects. Capital costs are for a freeze-mill grinder needed to isolate
tissue for RNA extraction.




Page 39 of 45









 





Appendix C




to the Sponsored Research Agreement

between Ceres, Inc. and The Texas Agricultural Experiment Station of The Texas

A&M University System



Project Diagram

Process for Developing Sorghum Bioenergy Genotypes 



[***]





Page 40 of 45


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











 








Appendix D




to the Sponsored Research Agreement

between Ceres, Inc. and The Texas Agricultural Experiment Station of The Texas

A&M University System



Breeding Plan



	 	 	 

	Objective

	 	Develop bioenergy sorghum hybrids
	 
	 	 
	Product:

	 	(1) High biomass cellulosic
photoperiod sensitive hybrids and
	 
	 	 
	 

	 	(2) high  sugar sorghum hybrids






	 	 	 
	Year	 	Task
	 
	Objective 1

	 	Sweet Sorghum Line and Hybrid Development ([***]-line, Fig. 1; [***]-line, Fig. 2)
	 
	 	 
	Year 0
	 	 
	 
	 	 
	Summer

	 	Make Breeding Crosses
	 
	 	 
	Winter

	 	Grow out [***] and [***]
	 
	 	 
	Year 1
	 	 
	 
	 	 
	Summer

	 	Grow out [***] populations, crush and select for [***], [***] quantity and agronomic desirability
	 
	 	 
	Winter

	 	For [***]-lines, cross to [***] for [***]
	 
	 	 
	 

	 	For [***]-lines, advance, [***] and select ([***], [***] and agronomic)
	 
	 	 
	Year 2
	 	 
	 
	 	 
	Summer

	 	For [***]-lines, advance in [***]
	 
	 	 
	 

	 	For [***]-lines,
[***] and make testcross hybrid for evaluation
	 
	 	 
	Winter

	 	For [***]-lines, advance in [***]
	 
	 	 
	 

	 	For [***]-lines, make
preliminary evaluation of hybrids, and advance lines with selection
	 
	 	 
	Year 3
	 	 
	 
	 	 
	Summer

	 	For [***]-lines, advance in [***]
	 
	 	 
	 

	 	For [***]-lines, evaluate
testcross hybrids and advance lines to [***] status. Evaluate lines for
[***] and [***], make additional hybrids for further testing and selection
	 
	 	 
	Winter

	 	For [***]-lines, advance
in [***], make testcross hybrids for evaluation







Page 41 of 45


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







 











	 	 	 
	 	 	 
	Year 4
	 	 
	 
	 	 
	Summer

	 	For [***]-lines, advance
in [***] until [***], make additional hybrid [***] for evaluation, and
evaluate hybrids in multiple locations, including evaluations of line
in seed production areas, rating for [***], etc.
	 
	 	 
	 

	 	For [***]-lines, evaluate
testcross hybrids and advance lines to [***] status. Evaluate lines for
[***] and [***], make additional hybrids for further testing and selection
	 
	 	 
	Winter

	 	For [***] lines, use only
if additional [***] or increases are needed.
	 
	 	 
	Year 5
	 	 
	 
	 	 
	Summer

	 	For [***]-lines, use only
if additional [***] or increases are needed, make
additional hybrid [***]
for evaluation, and evaluate hybrids in multiple locations, including
evaluations of line in seed production areas, rating for [***], etc.
	 
	 	 
	 

	 	For [***]-lines, as
conditions merit, release and [***] of foundation seed [***] for new [***]
	 
	 	 
	Winter

	 	Identify the best [***],
increase [***] for eventual [***] to Foundation Seed
	 
	 	 
	Year 6
	 	 
	 
	 	 
	Summer

	 	Release
	 
	 	 
	NOTES

	 	1. The primary need in sweet
sorghum hybrids is for sweet, [***] type [***]-lines for use as
[***] in hybrid seed production. Initial material is [***], but additional material is in the pipeline
which will have enhanced [***], specifically [***] and possibly [***].
	 
	 	 
	 

	 	2. [***] have not been used to date in this process, but they could be useful in several phases.
	 
	 	 
	 

	 	3. Mapping of loci for [***] and [***] is being completed, and these would be candidates for MAB.
	 
	 	 
	 

	 	4. The [***] process was initiated earlier, but takes longer than the [***]-line process. Thus,
the new [***]-lines will be out slightly ahead of [***]-line material. As a [***], we envision
using the [***] sweet sorghum [***].










Figure 1. Flow Diagram for the development of [***] lines for sweet sorghum [***].
The [***] diagram depicts the [***] of the program with the pipeline behind being
filled as well.




	 	 	 	 	 	 	 
	Summer 0

	 	[***]
	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 0

	 	 	 	 	 	S. TX
	 
	 	 	 	 	 	 
	Summer 1

	 	 	 	Select specific genotypes, [***], [***], etc.
	 	Texas
	 
	 	 	 	 	 	 
	Winter 1

	 	 	 	Initiate [***]
	 	S. TX
	 
	 	 	 	 	 	 
	Summer 2

	 	 	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 2

	 	 	 	 	 	S TX
	 
	 	 	 	 	 	 
	Summer 3

	 	 	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 3

	 	 	 	Make [***]
	 	S TX
	 
	 	 	 	 	 	 
	Summer, Winter
4 and 5

	 	 	 	[***] Evaluation
	 	TX, others
	 
	 	 	 	 	 	 
	Summer 6

	 	 	 	[***] Evaluation
	 	TX, others
	 
	 	 	 	 	 	 
	 

	 	Release [***]	 	 	 	 







Page 42 of 45


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










 















Figure 2. Flow Diagram for the development of [***] lines for sweet sorghum [***]. The
[***] diagram depicts the [***] of the program with the pipeline behind being filled
as well. We envision that [***] will be made using [***] sweet [***] as [***]. This
program is designed to [***]-lines.




	 	 	 	 	 	 	 

	Summer 0

	 	[***]
	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 0

	 	 	 	 	 	S. TX
	 
	 	 	 	 	 	 
	Summer 1

	 	 	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 1

	 	 	 	Select specific genotypes, [***], [***], etc.
	 	S. TX
	 
	 	 	 	 	 	 
	Summer 2

	 	 	 	Make Preliminary [***]	 	Texas
	 
	 	 	 	 	 	 
	Winter 2

Summer 3

	 	 	 	[***] Evaluation
	 	S TX
	 
	 	 	 	 	 	 
	Summer 3

	 	Make [***] 	 	 [***] Evaluation
	 	Texas
	 
	 	 	 	 	 	 
	Summer 4, 5

	 	 	 	Advanced [***] Evaluation
	 	Texas, others
	 
	 	 	 	 	 	 
	 	 	Release [***] based line, [***] performance	 	 










	 	 	 
	Year	 	Task
	 
	Objective 2

	 	High Biomass Photoperiod Sensitive
Hybrids (Figure 3)
	 
	 	 
	Year 0
	 	 
	 
	 	 
	Summer

	 	Evaluation of germplasm and identification of best genotypes (select [***] genotypes)
	 
	 	 
	Winter

	 	Increase [***] of Selected Germplasm
	 
	 	 
	 

	 	Testcross selected Germplasm to
Potential [***] and Harvest Testcross Hybrids
	 
	 	 
	 

	 	Make Crosses to introgress the
appropriate [***], [***], and [***]
alleles into [***] germplasm
	 
	 	 
	Year 1
	 	 
	 
	 	 
	Summer

	 	Evaluation of Testcross Hybrids to identify those with [***] (with the goal of selecting the top [***]-[***]
and identifying the [***] of this material).
	 
	 	 
	 

	 	Save [***] sample of
parents and hybrids to assess [***] and [***] potential and to determine [***] of
the traits in hybrids ([***], [***], [***]).
	 
	 	 
	 

	 	Growout and [***] (treat to [***], [***], [***])






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	Winter

	 	Based on [***] in
Testcrosses, growout [***] population of each selected [***]. Plan on growing at least [***]
(possibly more). MAB screening of breeder-selected material to identify the most desirable [***] and
recovery of [***] genotype ([***]).
	 
	 	 
	 

	 	Marker analysis with [***] ([***]/[***]/[***]), [***] ([***]), other selected genes, and ~[***].
	 
	 	 
	 

	 	[***] with
[***], selected [***] alleles and [***]% or greater [***] of the adapted parent
	 
	 	 
	 

	 	Cross selected individuals in each population [***] to the [***] germplasm ([***])
	 
	 	 
	Year 2
	 	 
	 
	 	 
	Summer

	 	Growout selected [***]
progeny (total of [***]), evaluate for [***], and
make testcross hybrids for future
evaluation. Goal
	 
	 	 
	 

	 	Save [***] sample of parents to assess [***]; use as [***] based on information from Summer 1
	 
	 	 
	 

	 	Growout and [***] (treat to [***], [***], [***])
	 
	 	 
	Winter

	 	Growout [***] populations ([***]). MAB screening of breeder-selected material to identify the most
desirable [***] and recovery of [***] genotype ([***] Q: Bill do we still plan to do this?).
	 
	 	 
	 

	 	Marker analysis with [***] ([***]/[***]/[***]), [***] ([***]), other selected genes, and ~[***].
	 
	 	 
	 

	 	[***] with
[***], selected [***] alleles and [***]% (more?) or greater [***] of the adapted parent
	 
	 	 
	 

	 	Advance [***] through [***]
	 
	 	 
	Year 3
	 	 
	 
	 	 
	Summer

	 	Growout [***] lines and [***]populations
	 
	 	 
	 

	 	For [***], grow in
multiple locations: CS for seed production, advance and additional
testcrossing. In SE US, evaluate
for [***] and [***] for adaptation and
[***] to seed production [***]. For the [***], grow in College Station
and testcross.
	 
	 	 
	 

	 	Marker analysis, and allele [***] and cleanup (for [***])
	 
	 	 
	 

	 	Evaluate [***] Testcross
Hybrids in at least [***], replicated, preferably on [***] different testers.
	 
	 	 
	 

	 	Samples for [***] if appropriate
	 
	 	 
	Winter

	 	Selected [***] lines
grown for final [***] increase, expanded hybrid [***] to identify specific [***]
	 
	 	 
	 

	 	Advance [***] lines
	 
	 	 
	Year 4
	 	 
	 
	 	 
	Summer

	 	Single Cross [***] Lines:
Expanded Hybrid Testing and Evaluation, seed production logistics, [***] evaluation, [***], etc.
	 
	 	 
	 

	 	[***] lines; grow in
multiple locations: CS for [***], advance and additional
testcrossing. In SE US, evaluate
for [***] and [***] for adaptation and
[***] to seed production [***].









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	 	Marker analysis, and allele [***] and cleanup
	 
	 	 
	Winter

	 	Selected increases, evaluation as needed
	 
	 	 
	Year 5
	 	 
	 
	 	 
	Summer

	 	Multilocation testing and
evaluation for selection of best [***]. Selected lines
released to Foundation Seed for
Increase and release.
	 
	 	 
	Year 6
	 	 
	 
	 	 
	Summer

	 	Seed of the lines and hybrids commercially available.










Figure 3. Flow Diagram of Breeding Program for the development of [***] for [***] bioenergy
[***].




	 	 	 	 	 	 	 
	Summer 0

	 	[***]
	 	Screen [***] Germplasm
	 	Texas
	 
	 	 	 	 	 	 
	Winter 0

	 	 	 	Make [***] with Selected [***]
	 	Puerto Rico
	 
	 	 	 	 	 	 
	Summer 1

	 	 	 	[***] eval (check [***] status)
	 	Texas
	 
	 	 	 	 	 	 
	Winter 1

	 	 	 	Select
	 	Puerto Rico
	 
	 	 	 	 	 	 
	Summer 2

	 	 	 	Make Preliminary [***]
	 	Texas
	 
	 	 	 	 	 	 
	Winter 2

	 	 	 	 	 	Puerto Rico
	 
	 	 	 	 	 	 
	Summer 3

	 	 	 	[***] Eval.
	 	Texas
	 
	 	 	 	 	 	 
	Winter 3

	 	 	 	select
	 	Texas
	 
	 	 	 	 	 	 
	Summer 4, 5

	 	 	 	[***] Eval.
	 	Texas, others
	 
	 	 	 	 	 	 
	 	 	Release [***] based on [***] 	 	 










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AMENDMENT I



to the Sponsored Research Agreement between Ceres, Inc. (“CERES”) and Texas AgriLife Research
(formerly The Texas Agricultural Experiment Station) of The Texas A&M University System
(“AGRILIFE”) effective as of August 29, 2007 (the “Agreement”).





	 	1.	 	The Parties agree to amend Article 1.A. to read as follows:
	 
	 	 	 	“AGRILIFE agrees to perform the work set forth in Appendix A and Appendix A-I
(jointly the “Program”) entitled respectively “Crop Development Using
Marker-Assisted Breeding” and “Enhancing the Sweet Sorghum Breeding Program”.”
	 
	 	2.	 	The Parties agree to add the “Enhancing the Sweet Sorghum Breeding Program” attached
hereto as Attachment I as Appendix A-I to the Agreement and Attachment II
as Appendix B-I to the Agreement.
	 
	 	3.	 	The Parties agree to add a sentence in Article 3.A. to read as follows:
	 
	 	 	 	“CERES agrees to pay for the direct and indirect cost of work of this Agreement to a
maximum amount of  four million three hundred ninety three thousand one hundred fifty eight dollars ($4,393,158) as described in the budget and attached as
Appendix B... Further, Ceres agrees to pay for the direct and indirect cost of this
Agreement to a maximum amount of  five hundred thousand dollars
($500,000) as described in the budget and
attached as Appendix B-I. AGRILIFE will invoice CERES when the payments become due.”
	 
	 	4.	 	The Parties agree that this Amendment I is effective as of June 18, 2008.
	 
	 	5.	 	For the remainder, the Agreement remains unchanged and this Amendment I shall form an
integral part thereof.





Made in two (2) copies.




	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research (“AGRILIFE”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:
/s/ Richard Flavell

	 	 	By: /s/
Mark A. Hussey
	 

	 

	 	 	 	 	 

	 	 
	Name: Richard Flavell, CBE, FRS	 	 	 	Mark A. Hussey	 	 
	Title: Chief Scientific Officer	 	 	 	Director, Texas AgriLife Research

Interim Vice Chancellor for Agriculture
and Life Sciences

Interim Dean, College of
Agriculture and Life Sciences	 	 







Page 1 of 7













 





	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 
	 
	 	 	 	 
	By:
	 	/s/ Richard Hamilton	 	 
	Name:

	 	 

Richard Hamilton
	 	 
	Title:

	 	President & Chief Executive Officer	 	 






Page 2 of 7









 





Attachment I




Appendix A-I


“Enhancing the Sweet Sorghum Breeding Program”




W.L. Rooney, Sorghum Breeding, Texas A&M University



Summary: Ceres and Texas AgriLife Research have an existing relationship to develop
bioenergy sorghums. Initial efforts have focused on the development of photoperiod-sensitive high
biomass sorghums with secondary emphasis on the development of sweet sorghum. Recent developments
in energy production and regions of production have focused additional importance on sweet sorghum.
Thus, there is a need to enhance and increase the development of sweet sorghum germplasm, parental
lines and hybrids. This describes the enhancement and activities that would be associated with
increased funding for sweet sorghum improvement.



Introduction: The DOE has set a goal of supplying 30% of 2004 transportation fuels consumed
with biofuels by 2030 to curb America’s addiction to oil, but it is clear that starch- and
sucrose-based feedstocks are not sufficient to achieve this goal. As a result, the conversion of
cellulosic feedstocks into ethanol has been recognized as an essential component of the overall
biofuel strategy in the U.S.



Several different plant species, such as (sorghum, switchgrass, energycane) are now being proposed
as lignocellulosic bioenergy crops. There are several different types of sorghum that have
potential as a biofuel crop. Initial interest in sorghum was focused on cellulosic biomass
production, but many regions of the world have realized that production of a sweet sorghum maybe a
better fit for their situation. Sweet sorghums have the potential to produce high total biomass,
sugar, starch and cellulose. A major limitation to the use of sweet sorghums is that paucity of
sweet sorghum hybrids. Current forage hybrids do not work and sweet cultivars are limited in
distribution by seed production problems.



Currently, Agrilife Research has developed a set of sweet A/B pairs that can be used to produce
sweet sorghum hybrids. We envision that first generation hybrids will use existing sweet sorghum
cultivars as pollinators. While this is not optimized, it is the most effective method to produce
hybrids quickly. Significant improvements on both the seed parent and the pollinator will result
in second generation hybrids that have better agronomics, higher yields, and improved quality.
The sorghum program at Agrilife Research has been developing populations to produce lines for the
second generation of sweet sorghum hybrids.



Ceres and Agrilife Research have an existing relationship to develop sorghum as a bioenergy crop.
While sweet sorghum is included in this relationship, it was initially listed as a lower priority
than the development of a cellulosic sorghum biofuel feedstock. Given the increased interest in
the sweet sorghum germplasm, the funding requested in this proposal is designed to increase
research and development activities specifically in the sweet sorghum development.








Page 3 of 7









 









Research Approach:





Research
Approach: For both [***] and [***] line sweet sorghum breeding efforts, a [***]
breeding approach is currently is used (Fig. 1 and 2); this approach is supplemented in the [***]
with a [***] breeding approach to incorporate
[***] to produce the [***]-line from the newly
developed [***]-lines.
The [***] procedure does add time to the process; this modified through the use of [***] to
produce [***]a [***].



In the [***]-line breeding program, the breeding pipeline is composed of germplasm in the [***],
[***] ([***]), [***] ([***]) and [***] ([***]) generations ([***]number in parentheses). The
populations represent [***] of sweet [***]existing [***] with [***]. These lines have been selected for
[***] content (>[***]%), [***] as a [***], and agronomic desirability. As they advance, [***],
[***], and [***] (specifically, [***] and [***]) will be evaluated. Additional populations are
continually being developed and emphasis will be placed on [***].



In the [***]-line breeding program, the breeding pipeline is composed of germplasm in the [***],
[***] ([***]), [***] ([***]) and [***] ([***]) generations ([***] number in parentheses). The
populations represent [***] of sweet [***] existing [***] with [***] as well as sweet [***] as
well. These lines have been selected for [***] content (>[***]%), complementary [***] as a
[***], and agronomic desirability. As they advance, we will evaluate [***] as a [***] and [***],
[***], and [***] (specifically, [***] and [***]) will be evaluated.



As experimental [***] hybrids are developed, Ceres will conduct [***] evaluations in multiple
environments to identify the best [***] and the specific [***] for further testing. Evaluation
shall include, but is not limited to [***] to [***], [***], [***] ([***] and [***]), and [***] and
[***].





The approaches described herein are not unlike those to be used in a traditional breeding program;
current Ceres funding is primarily directed at the high biomass research. If the sweet sorghum
program is continue at a similar pace, the funding requested is required.



Expected Results: This funding will expand the size and scope of the sweet sorghum
breeding program, allowing our cooperative efforts to advance for both the high biomass sorghums
(for cellulosic conversion applications) and the sweet sorghums (for sugar based conversion
applications). From this program, we expect to produce the lines needed for the second generation
of sweet sorghum hybrids. First generation hybrids have emphasized the development of hybrids that
are sweet and produce sugar as primary trait; there has been less attention devoted to improved
quality, enhanced yield, more desirable maturity, and improved disease resistance. The sweet
sorghum breeding program has been engaged in sweet sorghum breeding for over four years, we have a
4 year advantage on other projects that are now being initiated. This funding is critical to
maintain this advantage.




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Attachment II




Appendix B-I




Budget and Timeline for Enhancing the Sweet Sorghum Breeding Program: We propose a four
year program that will match the minimum terms for the existing breeding and genomics proposal.






	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Item	 	Year 1	 	Year 2	 	Year 3	 	Year 4	 	Total
	 
	Labor
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Research Associate
(salary, fringe)
	 	$	61,775	 	 	$	55,675	 	 	$	57,345	 	 	$	59,066	 	 	$	233,861	 
	Undergraduate Labor
	 	$	10,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	$	10,000	 
	Equipment
	 	$	18,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	$	18,000	 
	Expendable Supplies
	 	$	15,457	 	 	$	3,585	 	 	$	3,415	 	 	$	2,565	 	 	$	25,022	 
	Composition Analysis
	 	$	10,000	 	 	$	3,000	 	 	$	2,500	 	 	$	2,000	 	 	$	17,500	 
	Field Expense
	 	$	15,000	 	 	$	3,000	 	 	$	2,500	 	 	$	2,028	 	 	$	22,528	 
	Travel
	 	$	12,000	 	 	$	3,000	 	 	$	2,500	 	 	$	2,601	 	 	$	20,101	 
	 
	Direct Cost
	 	$	142,232	 	 	$	68,260	 	 	$	68,260	 	 	$	68,260	 	 	$	347,012	 
	 
	Indirect Costs
	 	$	57,768	 	 	$	31,740	 	 	$	31,740	 	 	$	31,740	 	 	$	152,988	 
	 
	Total
	 	$	200,000	 	 	$	100,000	 	 	$	100,000	 	 	$	100,000	 	 	$	500,000	 
	 





Budget Justification: A research assistant will be hired and this individual will be
responsible for coordinating and managing the breeding program for sweet sorghum line development
hybrid evaluations. A modest amount of funding for undergraduate labor is included. These
individuals will assist in the day to day activities associated with the program. Capital
equipment is budgeted in this project for a vehicle. Expendable supplies will include bags, tags,
envelopes, fuel and maintenance expenses associated with the project. Composition analysis
includes cost associated with quality analysis of the juice, bagasse or total biomass. It may
include both NIR and HPLC measurements as needed. Field expenses include land preparation, rental,
and fertilization/insecticide applications. Finally, travel funds are requested to offset cost
associated with travel to and from research locations within Texas as well as a winter nursery site
in Puerto Rico. It is expected that in-kind contributions from Ceres in seed production in off
season nurseries and the evaluation of testcross hybrids will be necessary to meet the goals of
this project at its current funding level.



Figure 1. Flow Diagram for the development of A/B lines for sweet sorghum hybrid production. This
scheme is similar to the original plan but modified to reflect the more advanced state of
development.



Page 5 of 7










 










	 	 	 	 	 	 	 

	Summer 0

	 	[***]
	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 0

	 	 	 	 	 	S.TX
	 
	 	 	 	 	 	 
	Summer 1

	 	 	 	 	 	Texas, other locations
	 
	 	 	 	 	 	 
	Winter 1

	 	 	 	Head to row selection
specific genotypes
[***],[***],
agronomics, [***],[***], etc.
	 	S.TX
	Summer 2

	 	 	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 2

	 	 	 	Initiate [***]
	 	S TX
	 
	 	 	 	 	 	 
	Summer 3

	 	 	 	Make [***]
	 	Texas
	 
	 	 	 	 	 	 
	Winter 3

	 	 	 	
	 	S TX
	 
	 	 	 	 	 	 
	Summer, Winter
4 and 5

	 	 	 	[***]
	 	TX, others
	 
	 	 	 	 	 	 
	Summer x

	 	Release [***]
	 	[***]
	 	TX, others






Figure 2. Flow Diagram for the development of R-lines for sweet sorghum hybrid production. We
envision that initial hybrids will be made using currently available sweet varieties as
pollinators. This program is designed to produce future R-lines.






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	Summer 0

	 	[***]
	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 0

	 	 	 	 	 	S. Texas
	 
	 	 	 	 	 	 
	Summer 1

	 	 	 	Head to row selection
specific genotypes [***],[***], agronomics,
[***],[***], etc.
	 	Texas
	Summer 2

	 	 	 	 	 	Texas, Other
	 
	 	 	 	 	 	 
	Winter 2

	 	 	 	 	 	S. Texas
	 
	 	 	 	 	 	 
	Summer 3

	 	 	 	Make Preliminary

[***]
	 	Texas
	 
	 	 	 	 	 	 
	Summer 4

	 	Make [***]
	 	[***]Evaluation	 	Texas, Other
	 
	 	 	 	 	 	 
	Summer 5, 6

	 	Release [***]based on
line and [***] performance
	 	Advanced [***]

Evaluation
	 	Texas, others






Page 7 of 7


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AMENDMENT II



to the Sponsored Research Agreement between Ceres, Inc. (“CERES”) and Texas AgriLife Research
(formally The Texas Agricultural Experiment Station) of The Texas A&M University System
(“AGRILIFE”) effective as of August 29, 2007 (the “Agreement”).





	 	1.	 	The Parties agree to amend Article 1.A. to read as follows:
	 
	 	 	 	“AGRILIFE agrees to perform the work set forth in Appendix A, Appendix A-I and
Appendix A-II (jointly the “Program”) entitled respectively “Crop Development
Using Marker-Assisted Breeding”, “Enhancing the Sweet Sorghum Breeding Program”
and “Management Practices for Efficient Production of High Biomass and Sweet
Sorghums”.”
	 
	 	2.	 	The Parties agree to add the “Management Practices for Efficient Production of High
Biomass and Sweet Sorghums” attached hereto as Attachment I as Appendix A-II to the
Agreement and Attachment II as Appendix B-II to the Agreement.
	 
	 	3.	 	The Parties agree to add a sentence in Article 3.A. to read as follows:
	 
	 	 	 	“CERES agrees to pay for the direct and indirect cost of work of this Agreement to a
maximum amount of four million three hundred ninety three thousand
one hundred fifty eight dollars ($4,393,158) as described in the budget and attached as
Appendix B... Further, Ceres agrees to pay for the direct and indirect cost of this
Agreement to a maximum amount of five hundred thousand dollars
($500,000) as described in the budget and
attached as Appendix B-I. Further, Ceres agrees to pay for the direct and indirect cost
of this Agreement to a maximum amount of one hundred ninety nine
thousand nine hundred seventy six dollars ($199,976) as described in the
budget and attached as Appendix B-II. AGRILIFE will invoice CERES when the payments
become due.”
	 
	 	4.	 	The Parties agree that this Amendment II is effective as of July 15, 2008.
	 
	 	5.	 	For the remainder, the Agreement remains unchanged and this Amendment II shall form an
integral part thereof.




Made in two (2) copies.






Page 1 of 6












 





	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research (“AgriLife”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard Flavell	 	 	 	By:	 	/s/ Mark A. Hussey	 	 
	 

	 	 

	 	 	 	 	 	 

	 	 
	Name: Richard Flavell, CBE, FRS 

Title: Chief Scientific Officer	 	 	 	Mark A. Hussey

Director, Texas AgriLife Research

Interim Vice Chancellor for Agriculture
and Life Sciences

Interim Dean, College of Agriculture and
Life Sciences	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	For Ceres, Inc. (“CERES”)	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:
	 	/s/ Richard Hamilton	 	 	 	 	 	 	 	 
	 

	 	 

	 	 	 	 	 	 	 	 
	Name: Richard Hamilton	 	 	 	 	 	 	 	 
	Title: President & Chief
Executive Officer	 	 	 	 	 	 	 	 






Page 2 of 6









 





Attachment I




Appendix A-II



Proposal to Ceres

Management Practices for Efficient Production of

High Biomass and Sweet Sorghums

J.M. Blumenthal, Sorghum Cropping Systems Specialist


1. Introduction:



Many plant species have the potential to be used as dedicated bioenergy crops and each has unique
ecological and botanical features. For Texas and the Southern and Central U.S. region, sorghum
(Sorghum bicolor L. Moench) is a logical choice due to its high productivity, drought tolerance,
established production systems, and genetic diversity. Sorghum is a versatile feedstock for
conversion to renewable fuels utilizing three crop component approaches. Starch in the sorghum
grain is already utilized since it is easily converted to ethanol with similar efficiency using the
same methodologies as corn. Sweet sorghum stalks, traditionally used to produce sorghum syrup, can
be milled and sugar from extracted juice can be fermented to ethanol using the same methods as in
sugarcane processing. Finally, as cellulosic conversion technologies progress, newly developed
high-biomass sorghum hybrids have the potential to become an ideal lignocellulosic feedstock,
because of their ability to produce high tonnage with a higher water-use efficiency that
conventional forage sorghum(Bean and McCollum, 2006; TCE publication SCS-2006-04).



Management guidelines for producing either sweet or high biomass sorghums in Texas (or anywhere
else) are almost non-existent. While management recommendations for producing hay or silage from
forage sorghums are available, they are of limited relevance for sucrose production in sweet
sorghum stalks or management of high biomass sorghums that have plant heights of 4-6 m and stalk
diameters of 3-6 cm. The most closely related production information may be found in management
guidelines for sugarcane. Therefore, we believe that production information and management
guidelines for these novel sorghums should be developed simultaneously with the breeding effort in
an interdisciplinary approach.



Using this approach, the release of new genotypes will be integrated with deployment of associated
management practices into appropriate agricultural regions of Texas. Adaptation of these new
sorghums will be evaluated across the diverse agroecological zones of Texas and basic production
practices such as optimum seeding rate, planting and harvesting guidelines, and other cropping
components can be assessed. In addition, it is essential that optimum nutrient and water management
guidelines be determined because these inputs are critical to overall profitability and energy
balance associated with biomass cropping systems. Potential disease and insect problems will be
identified and addressed. All crop production factors can be incorporated into appropriate crop
production budgets and modeling efforts. This comprehensive plan will simultaneously promote rapid
adoption of new genotypes and their associated management systems to increase likelihood of
producer success and maximize economic impact.



2. Specific Objectives:




Page 3 of 6









 





1) Examine adaptability of high biomass sorghum and sweet sorghum to the High Plains, Central, and
Coastal areas of Texas.



2) Evaluate the effect of plant population on yield, agronomics, plant composition, sugar
concentration, and profitability of high biomass sorghum and sweet sorghum.



3) Determine nutrient requirement of high biomass sorghum and sweet sorghum under various
environments.



3. Material and Methods:




Objective 1: Hybrid adaptation and evaluation



Experiments will be conducted at Amarillo (irrigated), College Station (rainfed and irrigated),
east Texas (China) (rainfed), and the Rio Grande Valley (Monte Alto) (irrigated). In each
experiment, most advanced materials from the TAMU-Ceres biomass and sweet sorghum program will be
planted in small plots (min. of 4 rows × 15’). Plants will be grown in 30-inch rows (Amarillo,
College Station and China), or 40-inch rows (Monte Alto), respectively. Initially seeding rates for
the different regions will be based on conventional forage sorghum guidelines. The fertilization
requirement will be estimated based on the difference between nutrient measured in deep soil
samples (N: 0’—3’; P, K, Micronutrients: 0-8”) and the plant requirement estimated by yield goal.
Weed control will be atrazine applied preplant or early post emergence. Experiments requiring
irrigation at Amarillo, College Station, and Monte Alto will be furrow irrigated. Insect control
measures will be taken as warranted by pest pressure. At College Station, China, and Monte Alto all
sorghum plants will be harvested for the first time when the head-producing hybrids are in the
soft-dough growth stage. Thereafter a ratoon crop will be grown and all sorghum plants will be
harvested when the head-producing plants reach the soft-dough growth stage for the second time
(dependent on growing conditions and hybrid maturity, a third crop will be harvested at Monte
Alto). At Amarillo, due to is shorter growing season, it is likely that only one harvest will be
performed in late September. Agronomic data (such as plant height, lodging, biomass production, and
plant moisture) and compositional data (analyzed at the TAMU sorghum quality lab for the biomass
hybrids and sucrose yield and concentration for the sweet sorghums and nutrient removal of both the
sweet and biomass sorghums) will be collected at all locations. Experimental design will be a
randomized complete block with 4 replicates. Data will be subjected to ANOVA.




Page 4 of 6









 





Objective 2: Plant populations



Experiments will be conducted at Amarillo (irrigated), College Station (rainfed and irrigated),
China (rainfed), and Monte Alto (irrigated). With the exception of plant populations, agronomic
practices will be as described for objective 1. In this study we will evaluate the effect of
varying plant populations on the two most promising biomass sorghums and the two most promising
sweet sorghums developed by the TAMU-Ceres program. Plant populations tested are 40,000, 60,000,
80,000, 100,000, and 120,000 plants per acre. Agronomic and quality data will be gathered as
described in objective 1. Experimental design will be a randomized complete block with 4
replicates. Data will be subjected to ANOVA and regression analysis.




Objective 3: Nutrient requirement



Experiments will be conducted at Amarillo (rainfed and irrigated), College Station (rainfed and
irrigated), China (rainfed), and Monte Alto (irrigated). With the exception of nitrogen management,
agronomic practices will be as described for objective 1. In this study we will evaluate the effect
of N fertilization on the two most promising biomass sorghums and the two most promising sweet
sorghums developed by the TAMU-Ceres program. Nitrogen rates tested are 0, 60, 120, 180, 240, and
300 lb N per acre. Agronomic and quality data will be gathered as described in objective 1.
Experimental design will be a randomized complete block with 4 replicates. Data will be subjected
to ANOVA and regression analysis.



4. Timeline:




	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Obj. 1	 	Obj. 2	 	Obj. 3
	Year 1
	 	 	X	 	 	 	X	 	 	 	 	 
	Year 2
	 	 	X	 	 	 	X	 	 	 	 	 
	Year 3
	 	 	X	 	 	 	 	 	 	 	X	 
	Year 4
	 	 	X	 	 	 	 	 	 	 	X	 






5. Deliverables:



Annual reports will be submitted to Ceres. Studies will be featured at AgriLife Research and
Extension field days. Extension bulletins will be prepared discussing high biomass sorghum and
sweet sorghum hybrid adaptation and best management practices. Presentations will also be made at
local, regional, and national level to showcase research and to introduce producers and industry to
the potential of high biomass sorghum and sweet sorghum as biofuel crops.




Page 5 of 6









 





Attachment II




Appendix B-II





	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Year 1	 	Year 2	 	Year 3	 	Year 4
	Program specialist (20%)
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salary
	 	$	12,950	 	 	$	12,950	 	 	$	12,950	 	 	$	12,950	 
	Fringe Benefits & Insurance
	 	$	3,410	 	 	$	3,410	 	 	$	3,410	 	 	$	3,410	 
	Salary enhancement program
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Dr. Blumenthal
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salary
	 	$	14,553	 	 	$	14,553	 	 	$	14,553	 	 	$	14,553	 
	Fringe Benefits & Insurance
	 	$	3,447	 	 	$	3,447	 	 	$	3,447	 	 	$	3,447	 
	Total Direct Costs
	 	 	34,360	 	 	 	34,360	 	 	 	34,360	 	 	 	34,360	 
	Institutional overhead (45.5%)
	 	 	15,634	 	 	 	15,634	 	 	 	15,634	 	 	 	15,634	 
	Total costs
	 	 	49,994	 	 	 	49,994	 	 	 	49,994	 	 	 	49,994	 




Page 6 of 6










 




CONFIDENTIAL




AMENDMENT III




to the Sponsored Research Agreement between Ceres, Inc. (“CERES”) and Texas AgriLife Research
(formerly the Texas Agricultural Experiment Station) of The Texas A&M University System
(“AgriLife”) effective as of August 29, 2007, as amended (the “Agreement”).





	 	1.	 	The Parties agree to add a new Article 15.M as follows:
	 
	 	 	 	“M. Notwithstanding anything to the contrary in this Article 15, the Parties
agree that the Materials provided to CERES pursuant to Section B of Appendix A
of the SRA may be supplied to parties with whom CERES has entered into
collaboration or evaluation agreements (“Collaborators”), provided that
Collaborators (i) will only be allowed to use such Materials for the purpose of
the implementation of their agreement or agreements with CERES, and (ii) will be
subject to obligations consistent with Articles 15.C, 15.D, 15.E, 15.F and 15.I.
CERES will provide to AgriLife information with respect to the Materials
feedstock composition generated pursuant to CERES’ agreements with Collaborators
and which CERES has the right to communicate to AgriLife; such information will
be deemed Confidential Information of CERES.
	 
	 	2.	 	The Parties agree that this Amendment III is effective as of October 22, 2008.
	 
	 	3.	 	For the remainder, the Agreement remains unchanged and this Amendment III shall form an
integral part thereof.




Made in two (2) copies.




	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard Flavell
	 	 	 	By:
	 	/s/ Bill Dugas	27/1/09 	 
	 

	 	 

	 	 	 	 	 	 

	 	 
	Name: Richard Flavell, CBE, FRS	 	 	 	Bill Dugas	 	 
	Title: Chief Scientific Officer	 	 	 	Deputy Director, Texas AgriLife Research	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard Hamilton
	 	 	 	By:
	 	/s/ Mark A. Hussey	27/1/09 	 
	 

	 	 

	 	 	 	 	 	 

	 	 
	Name: Richard Hamilton	 	 	 	Mark A. Hussey	 	 
	Title: President & Chief Executive
Officer	 	 	 	Vice Chancellor & Dean of College of
Agriculture and Life Sciences	 	 







Page 1 of 1









 







CONFIDENTIAL




AMENDMENT IV



to the Sponsored Research Agreement between Ceres, Inc. (“CERES”) and Texas AgriLife Research
(formerly the Texas Agricultural Experiment Station) of The Texas A&M University System (“TAES”)
effective as of August 29, 2007, as amended (the “Agreement”).





	 	1.	 	The Parties agree to add a new Article 15.N as follows:
	 
	 	 	 	“N. Notwithstanding anything to the contrary in this Agreement, the Parties
agree that any Materials provided by TAES to CERES pursuant to this Agreement
which are germplasm or Lines may be used by CERES for the following purposes:
(a) creating hybrids using Materials and/or other germplasm or lines and (b)
research activities with, and trialing and evaluating of (i) the Materials and
any hybrids made using Materials and (ii) any plant material or seed derived
from such Materials or hybrids. Further, such Materials and any hybrids derived
therefrom and any plant material or seed of any of the foregoing may be supplied
by CERES to parties with whom CERES has entered into collaboration, evaluation,
material transfer or field evaluation agreements (“Collaborators”) or to any
subcontractors of Ceres (“Subcontractors”), provided that Collaborators and
Subcontractors (i) will only be allowed to use such Materials for the purpose of
the implementation of their agreement or agreements with CERES, (ii) will be
subject to obligations consistent with Articles 15.C, 15.D, 15.E, 15.F and 15.I
and (iii) will only perform activities as referred to in (a) or (b) hereinabove.
Any commercialization by CERES of Material or hybrids therefrom will be
governed by the relevant clauses of this Agreement, the IPRA and/or license
agreements which may be entered into by the Parties.”
	 
	 	2.	 	The Parties agree that this Amendment IV is effective as of the start of the Program
Term.
	 
	 	3.	 	For the remainder, the Agreement remains unchanged and this Amendment IV shall form an
integral part thereof.




Made in two (2) copies.




	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research (“AgriLife”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard Flavell	 	 	 	By:	 	/s/ Bill Dugas	7/4/09	 
	 

	 	 

	 	 	 	 	 	 

	 
	Name: Richard Flavell, CBE, FRS	 	 	 	Bill Dugas	 	 
	Title: Chief Scientific Officer	 	 	 	Interim Director, Texas Agricultural
Experiment Station	 	 






Page 1 of 2









 






	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research (“AgriLife”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/
Richard Hamilton	 	 	 	By:	 	/s/
Mark A. Hussey	 	 
	 

	 	 

	 	 	 	 	 	 

	 	 
	Name: Richard Hamilton	 	 	 	Mark A. Hussey	 	 
	Title: President & Chief Executive
Officer	 	 	 	Vice Chancellor & Dean, Agriculture and
Life Sciences	 	 







Page 2 of 2