Diane Jofuku Okamuro IOS Division Of Integrative Organismal Sys
BIO Direct For Biological Sciences
November 1, 2012
October 31, 2016 (Estimated)
Awarded Amount to Date:
Zachary Lippman email@example.com (Principal Investigator)
Joyce Van Eck (Co-Principal Investigator) Michael Schatz (Co-Principal Investigator)
Cold Spring Harbor Laboratory
1 BUNGTOWN ROAD
COLD SPRING HARBOR, NY
PLANT GENOME RESEARCH PROJECT
Program Reference Code(s):
7577, 9109, 9178, 9179, BIOT, 9251
Program Element Code(s):
PI: Zachary B. Lippman (Cold Spring Harbor Laboratory)
Co-PIs: Michael C. Schatz (Cold Spring Harbor Laboratory) and Joyce Van Eck (Boyce Thompson Institute for Plant Research)
Key Collaborators: Molly Hammell and Jesse Gillis (Cold Spring Harbor Laboratory)
Plants show remarkable variation in the number of flowers they produce during their lifetime. This widespread variation traces back to differences in how, when, and where plants switch from making leaves to making flowers - the flowering transition. Although vitally important to crop yields, the transition to flowering and the subsequent effects on shoot growth and flower production remain poorly understood in many types of plants. For example, it is still not known why one plant will form just a single flower each time there is a flowering transition, as in pepper, and yet another plant will grow dozens of branches bearing hundreds of flowers, as in some types of tomato. To address this fundamental question in plant biology, this project is uniting a unique set of genetic, genomic, and natural variation tools in tomato and related Solanaceae plants, such as pepper, potato, and petunia, to reveal the genes and networks controlling how, when, and where plants undergo flowering transitions throughout development to continuously generate new branches and flowers. By analyzing a wide range of tomato mutants and wild Solanaceae species reflecting a wide range of flower production, this research will identify and characterize the differences in gene expression and DNA sequences that underlie variation in flowering transitions and flower production. This multi-dimensional project will provide the most detailed information yet on the key genetic regulators that drive the initiation and production of flowers in both agricultural and wild plants, which will enable the application of novel strategies to improve crop yields. The Solanaceae comprise the most valuable family for vegetable crop production, and we will deliver to both the public and scientific community broad genetic and genomic data in tomato, pepper, and edible wild Solanaceae species that have the potential to become agriculturally important crops.
This project will train high school and college students in interdisciplinary plant research, and a unique outreach program has been developed with an elementary school in Queens, New York to excite young students about plant biology and to explain the importance of integrating multiple research disciplines to create the knowledge and tools that will ensure food security. Students will meet scientists, experience plant genetic research in their own school, experiment in a "Virtual Greenhouse" with kid-friendly genetics games, and practice science writing. Each year, several students will be awarded a daylong visit to CSHL to experience firsthand, modern plant biology research. All data from this project, including gene expression, genetic mapping, network analyses, and computational tools for analyzing DNA sequences will be made publically available immediately after passing quality control. All DNA sequence data will be deposited in Genbank (http://www.ncbi.nlm.nih.gov/Genbank/), the SOL Genomics Network (SGN) website (http://www.sgn.cornell.edu/), and a project web site that will be developed.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
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Brooks, C., Nekrasov, V., Lippman, Z.B., and Van Eck, J. "Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system," Plant Physiology, 2014, p. pii: pp.1.
Parks, S.J., Eshed, Y., Lippman, Z.B.. "Meristem maturation and inflorescence architecture-lessons from Solanaceae," Current Opinion in Plant Biology, v.17, 2014, p. 70.
Parks, S.J., Jiang, K., Tal, Y., Gar,O., Zamir, D., Eshed, Y., Lippman, Z.B.. "Optimization of crop productivity in tomato using induced mutations in the florigen pathway," Nature Genetics, v.46, 2014, p. 1337.
Park, S.J., Eshed, Y., and Lippman, Z.B.. "Meristem maturation and inflorescence architecture ? lessons from the Solanaceae.," Current Opinion in Plant Biology, v.17, 2014, p. 70.
Brooks, C., Nekrasov, V., Lippman, Z.B., and Van Eck, J.. "Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system.," Plant Physiology, v.166, 2014, p. 1292.
Xu, C., Liberatore, K.L., MacAlister, C.A., Huang, Z., Chu, Y.H., Jiang, K., Brooks, C., Ogawa-Ohnishi, M., Xiong, G., Pauly, M., Van Eck, J., Matsubayashi, Y., van der Knaap, E., Lippman, Z.B.. "A cascade of arabinosyltransferases controls shoot meristem size in tomato.," Nature Genetics, v.47, 2015.
Wences, A.H., and Schatz, M.C.. "Metassembler: Merging and optimizing de novo genome assemblies.," Genome Biology, 2015.