Location: Genomics and Bioinformatics Research
Project Number: 6066-21310-006-000-D
Project Type: In-House Appropriated
Start Date: May 20, 2023
End Date: May 19, 2028
1. Advance and accelerate translational research for ARS and its collaborators that address the agricultural needs of the Southeast region and ARS, through data generation, data integration and analysis, with an emphasis on ‘omics and machine learning approaches in crops, animals, insects, and microbiomes; support germplasm analysis for breeding and for trait genetic and molecular analyses; and support gene expression analysis and gene discovery. 1.A. Supplying bridge services in genomics and bioinformatics. 1.B. Translating standard genomic tools to outlier and non-model genetic systems. 2. Accelerate the integration of bioinformatics and advanced technologies in research, for the Southeast region and ARS, through direct project collaboration; develop and evaluate new tools, workflows, and systems that enable ARS and its collaborators to more efficiently manage, integrate, analyze, and share diverse streams of biological data and knowledge, including high throughput genotyping and phenotyping, thereby enhancing crop and animal genetic improvement, health, and nutrition. 2.A. Developing bioinformatic capacity that supports universal resource utility. 2.B. Pangenomic and phenomic data integration.
Genomic technologies are powerful tools for germplasm improvement using marker assisted selection (MAS), biotechnology, or synthetic biology, and for analyzing associated biological processes (genetics, physiology, cell and molecular biology, biochemistry, and evolutionary biology). Thus, many ARS scientists, e.g., crop and animal breeders, have a direct need for genomic tools in their research. Others, e.g., soil scientists, can enhance their research dramatically using genomic tools to analyze the microbiome, if the technologies and appropriate expertise are available. The Genomics and Bioinformatics Research Unit’s (GBRU) primary function is conducting research in the areas of bioinformatics and genomics on a wide array of species and topics. GBRU also provides collaborative assistance with various ARS project that are constrained by routine genomics or bioinformatics hurdles. Not all ARS locations have sufficient resources to support core genomic technologies. Thus, some specific roles of GBRU are to: (1) coordinate, facilitate, collaborate and conduct genomics and bioinformatics research emphasizing the Southeast region; (2) serve as a research and training resource for genomic technologies and bioinformatic analyses in support of ARS scientists and their collaborations; and (3) serve as a technical resource for ARS research programs that have not typically utilized these technologies, and aid in their development of genomic resources. Within the GBRU, this research project will conduct and collaborate on genome sequencing, sequence assembly and analysis, diversity analysis, marker development, haplotyping, physical and genetic map production, and transcription profiling research. To provide sequencing and analysis for polyploids, clonally-propagated cultivars, historically resource limited systems, and other edge cases for which standard bioinformatic protocols are problematic. In part this will be possible through exploring and advocating universal and reproducible bioinformatic approaches for researchers engaged in genome-wide or high-throughput experiments, and by connecting phenotypic information with genotypic and genomic data in a coherent way that supports germplasm utilization and gene discovery. Thus, essential product development includes new and improved reference genomes for plants, animals, insects, fish, and microbes that enable genomics assisted breeding; new physical and genetic maps; improved cultivars, germplasm, or breeding lines; and new information on key agricultural problems such as disease resistance and drought tolerance.