A pangenome of worldwide chicken diversity to discover structural variants impacting health, sustainability, breeding, and domestication

• Applicant: Dr. Edward Ricemeyer, Ph.D.
• Subject Area: Animal Breeding, Animal Nutrition, Animal Husbandry
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 563353940

The domestic chicken is a major source of protein in human diets worldwide. Modern breeding practices incorporating genetics have increased growth rate and meat and egg production dramatically in the past 50 years, but the specific genetic variants responsible for these and other phenotypes are for the most part unknown. Moreover, genomic research in chickens has been primarily limited to short and easy-to-genotype variants such as single nucleotide variants and short insertions and deletions, although larger structural variants (SVs) are responsible for more of the total sequence variation present in chickens. Now, with new genome-sequencing technologies and algorithms for assembly and alignment, it is possible to cheaply assemble whole genomes for many individuals of a species and use these genome assemblies to find the structural variants present in a population with high accuracy and recall. We previously published a demonstration as a proof of concept that creating a pangenome from long-range assemblies of chicken genomes allows finding more SVs and also provides an alignment reference that can be used to reduce reference bias and genotype known SVs using only short reads. However, to gain the full advantage of this method, it will be necessary to sequence and assemble many more chickens from diverse populations. Therefore, we propose building a pangenome of the domestic chicken made up of 90 chickens with diverse geographic and breeding backgrounds, including a diversity panel of 50 chickens from both modern and heritage breeds from around the world and a selection panel of 40 chickens from a single highly-selected commercial line. We will then use this pangenome to genotype SVs and other variants from an existing set of almost 5,000 chickens sequenced with short read data, to which we have access as members of the Chicken Genetic Diversity Consortium, led by Prof. Dr. Frantz. With this pangenome, we and other researchers will be able to assess how domestication and breeding have affected the genome of the modern chicken in greater detail than was previously possible with existing resources. The publication of this pangenome will provide a valuable resource to the chicken genomics community, which currently only has access to a linear genome reference for the chicken genome. Moreover, the genotypes we generate by combining the pangenome with existing short-read data will allow us to study the role of SVs in both the initial domestication of chickens from their wild outgroup, the red jungle fowl, as well as how they have shaped the recent advances in commercial breeding.

• DFG Programme: Research Grants
• Co-Investigator: Professor Laurent Frantz, Ph.D.