Interpretive Summary: Genotyping complex structural variants using a Chicken Pangenome reference

By: Derek M. Bickhart¹, Edward S. Rice^2,3, Laurent A. F. Frantz³, Wesley C. Warren⁴

(¹Hendrix Genetics, Boxmeer, The Netherlands, ² Bond Life Sciences Center, University of Missouri, ³ Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany, ⁴ Department of Animal Sciences, University of Missouri)

Genomic Structural Variants (SVs) are large genetic duplications and deletions that are known to contribute to animal production and fertility. Unfortunately, SVs are quite difficult to accurately and efficiently detect in livestock populations as they have false discovery rates that range from 15-30%. New assembly graphs that incorporate known SV locations into a Pangenome resource promise to reduce this error rate by improving classification of known SV rates. Using a recently constructed Pangenome graph for chicken, we identified over 10,000 additional SVs over conventional methods, owing mostly to improved read mapping rates.