Seed Institute Overview

The Seed Institute

I.    Goals
II.   Origins of the Seed Institute
III.  Novel Aspects of the Seed Institute/Ceres Partnership
IV.  Five Years of Collaborative Efforts Between the Seed Institute and Ceres
V.  References

Goals (Back to Top)

The Seed Institute was established in order to carry out basic research in seed biology with the objective of uncovering the genes and processes required to "make a seed."  The long-range goal of the Seed Institute, in partnership with Ceres, is to use new insights obtained on the mechanisms that control seed formation to improve seeds in major crop plants.  

Origins of The Seed Institute (Back to Top)

The Seed Institute has its origins in the Embryo 21st Century Project that was initiated in 1990 to identify the genes required for embryo development.  The rationale was that a large team effort involving several laboratories could be very effective in solving a "big problem" of plant biology -- for example, what are all the genes and processes required "to make a seed."  In 1990, we initiated a project, designated as the Embryo 21st Century Project, to dissect the mechanisms controlling seed and embryo development using a combination of genetics and molecular biology, focusing primarily on the Arabidopsis plant as a model system  This project linked together faculty, postdocs, and students at several UC campuses including UCLA (my lab), UC Davis (John Harada's lab ), UC Santa Cruz (lab of Jack Okamuro and Diane Jofuku), and UC Berkeley (Bob Fischer's lab ). ( Gary Drews' lab )became part of the Embryo 21st Century Project after he became a faculty member at the University of Utah (1992).  The idea was that (1) all of the labs would participate collectively in generating the ideas and approaches, (2) all the labs would collectively carry out the experiments, and (3) all of the labs would collectively share in the "rewards" (publications, patents, slides for talks).  The Embryo 21st Century Project created a "laboratory without walls" to dissect the processes controlling seed and embryo development.  It pre-staged the multi-campus research efforts that have now become "the norm" for large genome projects and it demonstrated how a "virtual lab" can be created in which all of the faculty, students, postdocs, and staff work collectively towards a common goal.  In fact, it has provided an alternative to the classical "lab by lab" model for doing research in an academic setting. 

Research on seed biology being carried out at the present time in the Seed Institute (and Ceres) can be traced back to several screens for Arabidopsis mutants carried out both collectively (1-3) and individually (4-6) by Embryo 21st Century laboratories in the early 1990s.  These screens uncovered the importance of the AP2 gene (4) , LEC1 gene (3) , FIE gene (5) , and MEDEA gene (7) in seed development and eventually lead to their isolation, sequencing, and characterization (4, 7-10) .  Other screens lead to the identification of genes that play an important role in the development of the female gametophyte prior to fertilization (6) .  

During this same period, Embryo 21st Century Project experiments using molecular approaches and embryo-specific marker genes (11) determined that early, undifferentiated plant embryos are divided into domains or territories in which distinct transcriptional events occur (2) .  These territories establish a pre-pattern for the morphogenetic events that occur in these territories later in embryo development (e.g., axis formation).  Regions of promoters required to program transcription in different embryonic territories and regions were identified, indicating that "embryo-specific" promoters are composites of distinct, region-specific regulatory modules (2, 12, 13) . These observations lead directly to the decision by Embryo 21st Century Project investigators to utilize the "giant" embryos of the Scarlet Runner Bean, Phaseolus coccineus, as a model system to investigate the earliest, post-fertilization events in embryo development and to use genomics in order to identify the genes and factors that control the establishment of embryonic territories with distinct developmental fates (14)

By 1996, laboratories of the Embryo 21st Century Project had (1) established an active collaborative effort, (2) identified several genes that play a major role in seed development, (3) adopted several different genetic and molecular approaches to investigate the earliest steps in seed development, and (4) began to generate ideas and patents on how to use several genes in order to improve seed production -- for example, big seeds using AP2 and apomixis using FIE . This effort provided the framework for the establishment of the Seed Institute and an initial vision, set of technologies, and scientific network that helped launch Ceres after it was founded in March of 1996.  It is fair to say that both the Seed Institute and Ceres trace their lineages back directly to the Embryo 21st Century Project. 

Novel Aspects of the Seed Institute/Ceres Partnership (Back to Top)

The long-range goal of the collaboration between the Seed Institute and Ceres is to generate new knowledge on the basic processes required for seed development and to use this information to generate improved varieties of seeds in important crop plants with novel "breakthrough" traits.  The "birth" of the Seed Institute and Ceres occurred "simultaneously" in January, 1996 with the goal of creating a close partnership between (1) a university-based institute carrying out basic research on the processes that control seed development and (2) a company that could form an integrated platform of genomic technologies to uncover the tens of thousands of genes required to "make a plant."   The knowledge, ideas, and technologies generated in the institute would be licensed to the company in order to develop and "take to the market" novel new seed varieties.  On the other hand, Institute investigators would have access to high throughput technologies, genes, and databases generated in the company in order to speed up the pace of on-going research efforts and provide new leads into the processes that govern seed formation.  Our original vision was that a novel synergy would be created between the institute and company to form a powerful collaborative effort that would eventually lead to new, "breakthrough" agricultural technologies (e.g., apomictic hybrid crops, crops with bigger seeds that increase yield). 

The formal creation of the Seed Institute/Ceres Partnership provided a new "model" for interactions between university and industry and lead to many "firsts" for the University of California.  Among these include:

All of these "firsts" required a considerable amount of time and effort by the founders of Ceres, its first management team, and by University-wide and campus-specific administrators.  There were many debates and much "give and take."  However, not only did this effort have the practical effect of creating a novel and successful research partnership, it also  generated of a large amount of "good-will" between Ceres and the University in order to forge a new path in university/industry collaborations.  Good-will that continues to this day. 

Five Years of Collaborative Efforts Between the Seed Institute and Ceres (Back to Top)

Over the past five years much of the original vision used to create the Seed Institute and Ceres has been realized.  Ceres has evolved into the premier plant genomics company.  The Seed Institute has carried out a cutting-edge research that has provided new insights into the genes and processes of seed development.  Exchanges between Seed Institute PIs and Ceres scientists occur on a daily basis and involve the use of different techniques, computer programs, equipment, gene annotations, and approaches.  Collaborative efforts have led to new ideas (and joint patents) on how to improve seeds and have lead to novel joint projects to identify genes that play a role in seed development.  Genes studied in the Seed Institute that have been shown to play important roles in seed development have been shared with Ceres scientists (e.g., LEC1, FIE, AP2; DMT) and have provided the basis of new traits and approaches for the improvement of seeds.  Arabidopsis knock-out mutants generated at Ceres have been provided to the Seed Institute in order to obtain insights into the role that corresponding wild-type genes play in seed formation.  Joint meetings and retreats have been held between Ceres scientists and Seed Institute PIs, postdocs, and students in order to discuss latest research results and lay the foundation for future collaborative research efforts in seed biology.  Clearly,  a unique research partnership has been created between the Seed Institute and Ceres.

No partnership, no matter how strong, can afford to remain static.  There is much to learn about the genes and processes that control seed formation and that govern the "every day" functioning of seeds.  We have only begun to understand how thousands of genes act to "make a seed."  Only a few genes have been identified that play major roles programming seed development and how these genes are organized into networks that regulate seed formation is not understood.  In order to identify genes and processes that can provide the basis for novel, "breakthrough" seed traits will require closer collaborative efforts.  For example, Ceres has generated information on thousands of plant genes.  Allowing Seed Institute laboratories access to this information, as originally envisioned when the Seed Institute/Ceres partnership was established, could help generate new ideas (and results) about the role that many of these genes play in seed development.  On the other hand, the Seed Institute has the ability to generate tissues (and RNAs) from stages of seed development that are very difficult to harvest (e.g., embryo sacs, suspensors, early embryonic stages).  These RNAs could be analyzed using Ceres' unique high throughput expression and bioinformatics capabilities to identify novel gene sets that are active in unique seed regions and stages of seed development.  Candidate genes identified by these experiments could be investigated in more detail in Seed Institute laboratories to illuminate their roles in seed formation.

Finally, the Seed Institute and Ceres are in a unique position to make major breakthroughs in seed biology.  Ceres provides a unique perspective on what the "breakthrough" traits are for generating novel seed varieties.  The Seed Institute provides a unique perspective on the biology of seeds and the processes that occur during seed development.  Ceres has the ability to provide an overview of thousands of genes that function during seed development and what their roles might be.  The Seed Institute has the ability to investigate, in depth, the role that several of the most important candidate genes play in seed formation.  By working more closely to generate ideas, share information, generate novel approaches, and carry out collaborative efforts the Seed Institute/Ceres Partnership should be able make major progress in understanding "how to make a seed" in the not-to-distant future.

References (Back to Top)

1.         Yadegari, R., De Paiva, G. R., Laux, T., Koltunow, A. M., Apuya, N., Zimmerman, J. L., Fischer, R. L., Harada, J. J. & Goldberg, R. B. (1994) Plant Cell 6, 1713-1729. [Download pdf file]

2.         Goldberg, R. B., De Paiva, G. & Yadegari, R. (1994) Science 266, 605-614. [Download pdf file]

3.         West, M. A. L., Yee, K. M., Danao, J., Zimmerman, J. L., Fischer, R. L., Goldberg, R. B. & Harada, J. J. (1994) Plant Cell 6, 1731-1745.  [Download pdf file]

4.         Jofuku, K. D., DenBoer, B. G. W., Van Montagu, M. & Okamuro, J. K. (1994) Plant Cell 6, 1211-1225.  [Download pdf file]

5.         Ohad, N., Margossian, L., Hsu, Y. C., Williams, C., Repetti, P. & Fischer, R. L. (1996) Proceedings of the National Academy of Sciences of the United States of America 93, 5319-5324.  [Download pdf file]

6.         Christensen, C. A., King, E. J., Jordan, J. R. & Drews, G. N. (1997) Sexual Plant Reproduction 10, 49-64. [Download pdf file]

7.         Kiyosue, T., Ohad, N., Yadegari, R., Hannon, M., Dinneny, J., Wells, D., Katz, A., Margossian, L., Harada, J. J., Goldberg, R. B. & Fischer, R. L. (1999) Proceedings of the National Academy of Sciences of the United States of America 96, 4186-91. [Download pdf file]

8.         Okamuro, J. K., Caster, B., Villarroel, R., Van Montagu, M. & Jofuku, K. D. (1997) Proceedings of the National Academy of Sciences of the United States of America 94, 7076-7081. [Download pdf file]

9.         Lotan, T., Ohto, M., Yee, K. M., West, M. A., Lo, R., Kwong, R. W., Yamagishi, K., Fischer, R. L., Goldberg, R. B. & Harada, J. J. (1998) Cell 93, 1195-205. [Download pdf file]

10.       Ohad, N., Yadegari, R., Margossian, L., Hannon, M., Michaeli, D., Harada, J. J., Goldberg, R. B. & Fischer, R. L. (1999) Plant Cell 11, 407-16. [Download pdf file]

11.       Perez-Grau, L. & Goldberg, R. B. (1989) Plant Cell 1, 1095-1109.  [Download pdf file]

12.       De Paiva, G. (1994) in Department of Molecular, Cell, and Developmental Biology (University of California, Los Angeles, Los Angeles), pp. 513.

13.       Yadegari, R. (1996) in Department of Molecular, Cell, and Developmental Biology (University of California, Los Angeles, Los Angeles), pp. 221.

14.       Weterings, K., Apuya, N. R., Bi, Y., Fischer, R. L., Harada, J. J. & Goldberg, R. B. (2001) Plant Cell 13, 2409-2425. [Download pdf file]

15.      Stone, S. L., Kwong, L. W., Yee, K. M., Pelletier, J., Lepiniec, L., Fischer, R. L., Goldberg, R. B. & Harada, J. J. (2001) Proc. Natl. Acad. Sci. USA, 98, 11806-11811. [Download pdf file]

16.      Kinoshita, T., Yadegari, R., Harada, J. J., Goldberg, R. B. & Fischer, R. L. (1999) Plant Cell 11, 1945-52. [Download pdf file]

17.      Yadegari, R., Kinoshita, T., Lotan, O., Cohen, G., Katz, A., Choi, Y., Nakashima, K., Harada, J. J., Goldberg, R. B., Fischer, R. L. & Ohad, N. (2000) Plant Cell 12, 2367-2381. [Download pdf file]

18.      Drews, G. N., Lee, D. & Christensen, G. A. (1998) Plant Cell 10, 5-17.  [Download pdf file]

19.      Christensen, C. A., Subramanian, S. & Drews, G. N. (1998) Developmental Biology 202, 136-151.   [Download pdf file]


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