Location: Plant, Soil and Nutrition Research
Project Number: 8062-21000-041-000-D
Project Type: In-House Appropriated
Start Date: Apr 4, 2013
End Date: Apr 3, 2018
1: Apply computational, genomic, genetic and/or systems biology approaches to develop new models for plant genome structure and organization that advance our understanding of plant evolution and diversity. 1.1: Establish an integrated reference genome resource for plant genomes. 1.2: Analysis and visualization of genotypic, epigenomic, and functionally phenotypic diversity. 1.3: Comparative genomics: analysis of plant genomes (stewardship of reference resource) and visualization informed by evolutionary histories. 2: Analyze and develop genome level regulatory network models that focus on and integrate the processes underlying plant development and responses to environmental change. 2.1: Develop genome-wide functional networks for the model plant genome Arabidopsis. 2.2: Crop GRNs to support functional prediction for agriculturally relevant phenotypes. 3: Collaborate, develop and implement new standards for the management and analysis of plant genomic, genetic and phenotypic information to facilitate integration and interoperability between biological databases. 4: Facilitate the use of genomic and genetic data, information, and tools for germplasm improvement, thus empowering ARS scientists and partners to use a new generation of computational tools and resources. 5: Accelerate sorghum trait analysis, germplasm analysis, genetic studies, and breeding by acquiring, integrating, and providing open access to sorghum genome sequences and annotations, germplasm diversity information, trait mapping information, and phenotype information in a sorghum crop genome database system, with an initial emphasis on sugarcane aphid resistance.
We propose to leverage emerging and standard computational and experimental approaches, building on existing and newly developed resources to support stewardship of plant genome reference sequences, genome annotations and gene networks. This will support development of a common standard platform for comparative genomic analysis and visualization. The enriched genome annotations will include controlled vocabularies to describe metadata and primary data associated with comparative phylogenomics, epigenetics, and population-based phenotypes. The proposed research in gene networks is directed at the development and validation of gene regulatory networks (GRN). The network view of the underlying molecular processes will enhance the fundamental biological understanding of development and abiotic stress responses and its relationship to agronomic traits. The computationally predicted and experimentally verified sub-networks combined with the prioritized regulatory gene targets will provide focal points for further research at gene-by-gene level. They will be integrated with the suite of genetic resources obtained from Objective 1, including SNPs and orthology mapping, and thus will be a resource for breeders and researchers engaged in molecular breeding approaches and segregation analysis. Genome-wide network reconstructions will be quite useful in quantifying and characterizing the genotype-to-phenotype relationships. We propose to leverage and build upon existing infrastructure to manage and analyze plant genomic, genetic, and phenotypic data. The resources will focus on the delivery of anticipated products from Objectives 1 and 2 with a focus on plant datasets, but much of the software will be species-agnostic, making the resources developed from the project usable to a broader audience including animals, insects, and fish relevant to agriculture, human health, and a sustainable environment.