Location: Animal Genomics and Improvement Laboratory
Project Number: 8042-31000-112-020-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2024
End Date: Aug 31, 2025
Objective:
The proposed research is expected to generate new data on Galectin gene variation in relation to autophagy by utilization of pangenome resources and approaches. The findings of this research will add to our knowledge and generate new training materials about discovering ruminant genetic variation through pangenomes. This project will broadly contribute to use and application of comparative genomics efforts to make livestock production safer and more sustainable. Specific objectives are:
Objective 1: Conduct experiental research: Cooperator will learn the latest genomics workflows and resources in Host's lab at the USDA ARS. She will learn assembly and annotation workflows and the use of USDA’s High Performance Computing resources. She will contribute to Bovine Pangenome Consortium working groups. She will learn about available resources, technologies, databases and how to use advances in pangenome assembly to study polymorphisms and structural variants to uncover candidate functional variations associated with Galectins and autophagy.
Objective 2: Develop training materials: Cooperator will develop training materials to introduce students to research methods used for cataloging gene variation, ruminant genetic diversity and for comparative genomic studies across ruminant species. She will also incorporate knowledge gained to develop a learning module on a component of the pangenome project that can be used by researchers and students. A module that provides a framework for animal pangenome projects, addressing experimental design, sampling; collaboration policy and ethics, data storage, and data sharing considerations is proposed. The module would include information flows, key expertise, and planning requirements associated with pangenome sequencing and assembly.
Objective 3: Expand research and training in animal genomics: Cooperator will consult with Host and collaborators to learn about training needs and opportunities to strengthen research collaboration and design student training in animal genomics at NCAT.
Approach:
Objective 1: Cooperator will study the (i) location of galectin encoding genes (LGALS) in the cattle, sheep, and goat genomes; (ii) exon-intron organization of galectin encoding genes; and (iii) conduct sequence comparison of carbohydrate recognition domains (CRDs) of cattle, sheep, and goat galectins. In human galectins, tryptophan residues are associated with ligand recognition. Polymorphism in this region may impact structural and ligand binding and function. We will screen databases for galectin protein and nucleic acid sequences. Comparative sequence analysis and amino acid sequence alignments will be done using ClustalW. Maximum-likelihood distances will be computed using Tree-Puzzle. She will apply lessons learned and include pangenome assemblies, approaches and resources.
Objective 2: Cooperator will determine what modules are needed and develop a module development plan including core activities. Input will be sought from colleagues and stakeholders. Cooperator will create a content outline and host will provide feedback and needed changes. Key topics, concepts, resources, and a list of core activities for each step will be included. To write the content for the framework module Cooperator will extract and assemble material relevant to core activities identified. She will search PubMed, other databases, National Agricultural Library resources and the web. A list of funding, databases, and other resources on relevant topics will compiled. Products will be created using the Articulate Rise 360 e-learning software.
Objective 3: Cooperator will seek input on course content and learn about research approaches and skills needed. She will use this information to expand and update Course based undergraduate research (CURE) modules. She will visit facilities, and learn about research infrastructure needs and capacity. She will attend animal genomics related seminars and workshops at USDA and at collaborating agencies. She will hold discussions with the pangenome consortium committees and visit global partners to discuss training needs and opportunities for student and researcher engagement. We will develop recommendations on student engagement opportunities. We will compile undergraduate research education and extension resources in animal genomics. This will aid in sustained collaboration in research education and extension between USDA and NCAT in animal genomics. We will disseminate the outcomes and training materials to 1890 colleagues and to the animal genomics community through a joint report and presentations at conferences such as the Plant and Animal Genome, NRSP-8 and the International Society for Animal Genomics. All materials and outcomes will be shared with researchers and students in courses to catalyze engagement in animal genomics to diverse audiences including producers.
