A CHICKEN PAN-GENOME REFERENCE PANEL AND SINGLE CELL ATLAS TO BROADLY STUDY ENVIRONMENTAL CHALLENGES

The international nutritional security that relies on poultry protein resources requires our attentive study of their genetic health. The scope of gene biomarkers that define cell-type and our cell-specific knowledge of the chicken immune system is very limited. The chicken genome reference sequence that is required to advance our understanding of the segregating variation associated with multiple traits of economic importance, especially relevant for immune genic focused studies and in this proposal utilized to etstablish an immune cell atlas is in need of further improvements. To ensure a detailed knowledge of immune cell types in the chicken and the expanded use of this critical resource in the context of future studies of environmental challenges, we have three main goals: a more complete and accurate chicken genome assembly, in particular immune gene families that is a first for representative layer and broiler genetic lines, a single-cell atlas enriched for immune cell types that catalog cell markers for the chicken's major immune organ systems and an multifaceted genome browser to simplify access and queries of all data generated. The fruition of all these efforts promises to provide the poultry industry and the scientific community the most accurate and complete set of chicken genome resources to date.