An international project led by Cornell and the Boyce Thompson Institute for Plant Research (BTI) at Cornell has received $1.8 million from the National Science Foundation (NSF) to continue sequencing the tomato genome and to create a database of genomic sequences and information on the tomato and related plants.
The grant for the International Tomato Sequencing Project, a collaboration with researchers from nine other countries, will enable U.S. researchers to continue their work. In 2004 the NSF provided $4 million for the U.S. part of the research.
Sequencing the tomato genome is the first step in creating the comprehensive International Solanaceae Genomics Project (SOL) Genomics Network database. This will tie together genetic maps and genomes of all plants in the Solanaceae family, also called nightshades, which includes the potato, eggplant, pepper and petunia and is closely related to coffee from the Rubiaceae family.
The public database will help researchers ask fundamental questions: Have changes from a common ancestor brought about the attributes of crop species? What are the functions of specific genes? How has domestication changed genes? Which plants might be good candidates for genetically engineered improvements for growing crops?
Cornell researchers are close to completing a toolkit of resources about tomato and solanaceae species (some currently available in the database) to make the sequencing possible. These resources include genetic maps, DNA libraries, individual gene sequences, DNA markers and associated information, comparative mapping data to go from one species to another as sequences are added, and tools to query and search this information.
"The intention is to create an entirely public database," said the project's principal investigator, James Giovannoni, a plant microbiologist with the U.S. Department of Agriculture's Agriculture Research Station and BTI, both based at Cornell, and an adjunct professor in Cornell's Department of Plant Biology. As information is released, it is put online, he said.
In sequencing the 12 chromosomes that comprise the tomato's genome, researchers from each of the nine other countries in the project (China, France, India, Italy, Japan, Korea, Spain, Netherlands and the United Kingdom) will sequence one chromosome, with U.S. researchers sequencing three. As sequences are completed, they will be analyzed by researchers in the laboratory of Steven Tanksley, co-principal investigator and Cornell's Liberty Hyde Bailey Professor of Plant Breeding. The database is housed in Tanksley's lab.
Because it is difficult and expensive to sequences all of a species' genome, the researchers will just focus on gene-rich areas at the end of each chromosome, where 80 to 90 percent of the genes reside.
Lukas Mueller, a senior research associate in plant breeding and genetics at Cornell, and Joyce Van Eck, a senior research associate at BTI, are co-principal investigators on the project.