DEVELOPING CRISPR-BASED IN VITRO FUNCTIONAL GENOMIC SCREENING RESOURCES IN CHICKENS

A better understanding of the relationship between the genotype and the phenotype is critical for improving productivity and animal well-being, optimizing economic return and sustainability for producers, and increasing the quality of poultry products for consumers. Because most (>90%) of the genetic markers used in genomic selection are found in non-coding regions of the genome, linking these variants to relevant genes or pathways is not trivial. The goal of this proposal is to develop and validate user-friendly CRISPR (clustered, regularly interspaced, short palindromic repeat)-based in vitro screening resources for chickens, including cell lines, DNA vectors, protocols, data, and training, and share these resources with the research community. We will achieve this through establishing and optimizing in vitro CRISPR-based transcription activation (CRISPRa) and CRISPR-based transcription repression (CRISPRi) systems in different lineages of chicken cell lines, followed by high-throughput single-cell-based CRISPR functional screening. Outcomes of this proposal will include a more approachable in vitro platform for testing the function of genes and regulatory elements of interest in a high-throughput manner. This will contribute to broadening the scope of poultry genomics research from association-based findings to mechanistic principles of gene regulation, bringing us one step closer to connecting genome to phenome.