A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Edward S. Rice, Antton Alberdi, James Alfieri, Giridhar Athrey, Jennifer R. Balacco, Philippe Bardou, Heath Blackmon, Mathieu Charles, Hans H. Cheng, Olivier Fedrigo, Steven R. Fiddaman, Giulio Formenti, Laurent A. F. Frantz, M. Thomas P. Gilbert, Cari J. Hearn, Erich D. Jarvis, Christophe Klopp, Sofia Marcos, Andrew S. Mason, Deborah Velez-IrizarryLuohao Xu, Wesley C. Warren*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

3 Citations (Scopus)
14 Downloads (Pure)

Abstract

Background: The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. Methods: We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. Results: We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference. Conclusions: We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.

Original languageEnglish
Article number267
JournalBMC Biology
Volume21
Number of pages17
ISSN1741-7007
DOIs
Publication statusPublished - 2023

Bibliographical note

Publisher Copyright:
© 2023, The Author(s).

Keywords

  • ev21
  • Gallus gallus
  • IGLL1
  • K locus

Cite this