Genomics, Bioinformatics and Database Development for Crop Improvement and Biofuel Research
Genomics and Gene Discovery
Project Number: 5325-21000-021-02
Specific Cooperative Agreement
Start Date: Apr 01, 2013
End Date: Jan 31, 2015
Genomics research is posed to play an important role in future crop improvement for sustainable food, alternative energy, and environmentally friendly green bioproducts. The program research and development efforts are to be accomplished within a framework of coordination and collaboration between Western Regional Research Center, United States Department of Agricultural, Agriculture Research Service and University of California, Davis to meet high priority agricultural research needs. There are three broad objectives for this USDA-ARS Specific Cooperative Agreement. 1) Develop bioinformatics resources through software development, and data collection and collation for entry into public databases such as GrainGenes. 2) To use genomics and bioinformatics to develop knowledge and public resources by analyzing sequence data and displaying results for public view and access to the genomics resources generated in this project. 3) To develop genomic resources using cost-effective and high-throughput next generation sequencing technology and high-efficient reverse genetic approaches. The resources generated can be directly apply to develop molecular markers for genotyping and marker-assisted breeding program, and isolate genes and regulatory sequences controlling agronomically important traits and metabolic pathways for potential biotechnological improvement of crop production.
1) Collaborate in development of software tools for processing and storage of data and website to make the data accessible to public. 2) Data collation and curation for inclusion in the GrainGenes database. 3) Develop a large T-DNA insertional mutant population for Brachypodium distachyon, a Triticeae and template grass model for functional characterization of genes controlling agronomically traits important for food improvement, bioenergy, and bio-product research. 4) Apply state-of-art Roche 454 and Illumina MiSeq sequencing technologies to generate genomic sequences for genome assembly, gene annotation and molecular marker development for guayule, a target species for alternative natural rubber production, and generate genome-wide transcriptome sequences for functional analyses of gene expressions associated with important traits for Ae. tauschii, the diploid D genome donor of wheat.