Recipient Organization
IOWA STATE UNIVERSITY
2229 Lincoln Way
AMES,IA 50011
Performing Department
ANIMAL SCIENCE - CALS/AES
Non Technical Summary
The individual cell is the fundamental unit of life, and biological function - including genetic control of all traits - begins with the individual cells in each tissue and organ. All organs are made up of distinct cell types which provide unique aspects of organ function. Specific traits such as growth or disease resistance result from the combined output of these cells, yet currently all economic traits are measured at the tissue, organ, or organismal level even though genetics acts through genes that function within each cell type. Multiple groups have demonstrated genetic control of molecular traits (phenotypes) such as gene expression in many tissues in humans, animals and plants. Such traits can explain the relationships between genetic variants and disease and other complex but economically important traits; this is called the "genotype to phenotype" question, or "how does genetic differences lead to individual differences in important traits?" However, such molecular phenotypes are based on a mixture of signals from different cell types in multicellular tissues; thus, the gene expression levels made from these mixtures could be misleading or less sensitive to important signals from lowly abundant cell types. Further, cell composition is entirely missed in such analysis of tissues which is an important deficit since variation in the cellular composition of tissues has substantial genetic control- good evidence that we can improve these traits through breeding if we could better measure them.To address this gap in understanding of specific molecular phenotypes of different cell types, many groups have measured traits like gene expression in individual single cells (SC) and created multi-tissue cell expression atlases. These extensive cross-tissue atlases, almost exclusively reported for human and biomedical model species, have demonstrated not only the value of single cell analysis in understanding cell type function and genetic control of cell function within tissues and but also the enormous value in community-wide joint analyses of their data. The agricultural research community does not currently have the resources or tools to apply SC technology to genetic improvement of studying biology at the SC level.In this proposal, we will develop and educate a sustainable community of agricultural researchers and resource developers who can connect the application of SC technologies to understanding genome-to-phenome in agricultural systems. We will accomplish this using a mixture of activities including on-line training and discussion, as well as convene a face-to-face conference with the purpose to organize resources for application of SC technologies for improved plant and animal traits. We will summary our results and outcomes in a white paper to be published for the community.
Animal Health Component
20%
Research Effort Categories
Basic
70%
Applied
20%
Developmental
10%
Goals / Objectives
Our overall goal is to develop a robust and sustainable network of researchers who are interested in developing SC genomics techniques and best practices to apply to agricultural systems. We will achieve this goal via the following specific aims:Aim 1. Create a community of researchers interested in applying SC genomics to elucidate genotype to phenotype in agricultural systems.Aim 2. Determine community needs and potential resources for applying SC genomics techniques to agricultural systems.Aim 3. Organize and convene a conference on discussion and development of SC resources required for agriculture.Aim 4. Broadly disseminate conference findings and develop resources for community infrastructure
Project Methods
Aim 1. Create a community of researchers interested in applying Single cell (SC) genomics to elucidate genotype to phenotype in agricultural systems. This aim will be initiated prior to the conference and will address the need for a common understanding of the application of SC techniques, its benefits and its current limitations in agricultural systems. Briefly, we will achieve this aim by a series of online, informational sessions about SC methods and modalities, with a focus on transcriptomics. Conference attendees will have access to session recordings and summaries to maximize progress at the conference (Aim 3). These recordings will also be made available to the public as we have done with prior AG2PI activities.Aim 2. Determine community needs and potential resources for applying SC genomics techniques to agricultural systems. This aim will be initiated prior to the conference and will address the need to assess existing SC resources (e.g., sequencing portals, data repositories and expertise in curating SC data) as well as identifying the current needs for the agricultural community (e.g., metadata capture, data deposition and marker annotation). Briefly, we will achieve this aim by reviewing resources and surveying the agricultural community interested in applying SC techniques. The results of this review and the survey will be presented at the conference to provide sufficient preparation for discussion and planning.Aim 3. Organize and convene a conference on discussion and development of SC resources required for agriculture. This aim addresses the need for the community to develop the reflexive mindset and relationships needed for best practices in successful multidisciplinary consortia, standardized processes and infrastructure to support analysis, and interpretation and sharing of SC data. We will do this via a SC conference adjoining the AGBT-Ag meeting, where the community will have the opportunity to develop such relationships, hear from experts working with medical and agricultural SC data and to discuss how to document and address the community's needs.Aim 4. Broadly disseminate conference findings and develop resources for community infrastructure. To ensure that the findings from the conference are broadly disseminated, we will develop a white paper reporting them to the community and AG2PI leadership. We will also develop funding proposals to support the development of community resources using teams and funding opportunities identified during the conference. We anticipate that the most important opportunity would be a research proposal to AG2PI itself, but additional relevant agencies would be genomics-interested sections of USDA-AFRI, NSF, DOE and NIH.