Understanding the Global Virus Distribution in Tomato and Development of Translational Genomic Tools to Accelerate Breeding for Resistance
Location: Vegetable Research
Project Number: 6659-22000-025-06
General Cooperative Agreement
Start Date: Sep 01, 2012
End Date: Jul 31, 2013
Specific objectives are to 1) Develop a global tomato virome and virus distribution map through extensive virus survey and next generation sequencing of small RNAs. 2) Develop tomato translational genomic tools through transcriptome analysis to identify genes that are associated with virus resistance.
Dr. Fei’s lab recently received a National Science Foundation (NSF) grant (2011-2013) entitled “BREAD: Determining the Pan-African crop virome: understanding virus diversity, distribution and evolution and their impacts on crop production in Africa” and the bioinformatics tools developed under that grant will have a direct application to the current project. Fei’s group has also developed a Tomato Functional Genomics Database, which includes a set of interfaces and tools that allow users to mine, analyze, and integrate large-scale tomato gene expression, metabolite profile, and small RNA datasets. A web-based package, Plant MetGenMAP, which can identify significantly changed pathways and biological processes based on user-given gene expression and/or metabolite profile datasets, was also developed. Fei’s group developed a de novo transcriptome assembly package, iAssembler, which can assemble ESTs generated using Sanger and/or 454 pyrosequencing technologies with much higher accuracy. Together with Dr. Giovannoni’s group, Fei’s group developed a high-throughput strand-specific Illumina RNA-Seq library preparation protocol and a small RNA library preparation protocol, which can be directly used for the current project. Dr. Fei’s group has been extensively involved in analyzing tomato genome sequences. The number of proteins with typical R-gene domains in tomato, potato, Arabidopsis, grape and rice genomes have been identified, which will serve as a backbone of R-gene candidates to be used in the current project. Specifically, Dr. Fei will serve as a contact person in performing small RNA deep sequencing and RNA-seq using an Illumina HiSeq 2000 system at the Cornell University core sequencing facility, provide bioinformatics support in sequence analysis and virus and viroid identification, assist in generating a global tomato virus distribution map, and identify SNPs and candidate R-genes, and molecular marker development.