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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Endemic Poultry Viral Diseases Research » Research » Publications at this Location » Publication #399997

Research Project: Enhancing Genetic Resistance and Vaccinal Response to Control Marek's Disease, Infectious Laryngotracheitis, and Infectious Bursal Disease in Chicken

Location: Endemic Poultry Viral Diseases Research

Title: Multiple chicken (Gallus gallus) genome references to advance genetic variation studies

item WARREN, WESLEY - University Of Missouri
item FEDRIGO, OLIVIER - Rockefeller University
item TRACEY, ALLEN - Wellcome Trust Sanger Institute
item MASON, ANDREW - York University
item FORMENTI, GIULOLIO - Rockefeller Foundation
item PERINI, FRANCESCO - University Of Perugia
item WU, ZHOU - University Of Edinburgh
item MURPHY, TERRANCE - National Institutes Of Health (NIH)
item SCHNEIDER, VALERIE - National Institutes Of Health (NIH)
item STIERS, KYLE - University Of Missouri
item RICE, EDWARD - University Of Missouri
item COGHILL, LYNDON - University Of Missouri
item ANTHONY, NICK - Cobb-Vantress, Inc
item OKIMOTO, RON - Cobb-Vantress, Inc
item CARROLL, RACHEL - University Of Missouri
item MOUNTECASTLE, JACQUELYN - Rockefeller University
item BALACCO, JENNIFER - Rockefeller University
item HAASE, BETTINA - Rockefeller University
item YANG, CHENTAO - Bgi Shenzhen
item ZHANG, GUOJIE - Zhejiang University
item SMITH, JACQUELYN - University Of Edinburgh
item DRESCHLER, YVONNE - Western University Of Health Sciences
item Cheng, Hans
item HOWE, KERSTIN - Wellcome Trust Sanger Institute
item JARVIS, ERICH - Rockefeller University

Submitted to: Cytogenetics and Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/22/2023
Publication Date: 6/26/2023
Citation: Warren, W.C., Fedrigo, O., Tracey, A., Mason, A.S., Formenti, G., Perini, F., Wu, Z., Murphy, T., Schneider, V., Stiers, K., Rice, E.S., Coghill, L., Anthony, N., Okimoto, R., Carroll, R., Mountecastle, J., Balacco, J., Haase, B., Yang, C., Zhang, G., Smith, J., Dreschler, Y., Cheng, H.H., Howe, K., Jarvis, E. 2023. Multiple chicken (Gallus gallus) genome references to advance genetic variation studies. Cytogenetics and Genome Research. 3-12.

Interpretive Summary: In the modern era of biology, high quality genome assemblies of your organism of interest are essential especially for understanding complex traits like growth, reproduction, and disease resistance. In 2004, chicken was the first farm animal to generate a draft genome assembly, which was based Red Jungle Fowl, the ancestor of domestic chickens. Since then, a number of improvements have been made. In this publication, two new reference genomes were assembled that were based on a commercial broiler (meat-type bird) and commercial layer (egg-type bird). These references are more complete and likely more suitable for studies in commercial birds. These references should enable more precise studies especially those involving genetic improvement, which will ultimately aid poultry producers and consumers.

Technical Abstract: We present two phased chromosome-scale assemblies of chicken, a layer (GRCg7w) and broiler (GRCg7b), that better meet research demands to characterize important for traits of interest in commercial birds. Annotation with existing long- and short-read RNAseq data improved contiguity, accuracy, and protein-coding and non-coding gene counts, when compared to the existing Red Jungle Fowl reference, GRCg6a. Most striking were the improvements in placed telomeres, corrections for erroneous microchromosome fusions, and gap reduction in these phased assemblies. We add six putative microchromosomes that were previously missing in GRCg6a. Using a pairwise genome comparison of the parental genomes, and two independent cohorts of sequenced chickens, we show small discernable differences in mapping rates of whole genome sequence (WGS) and RNAseq data, gene annotation, and called single nucleotide variants (SNVs) or indels. Structurally, some regional differences suggest future assembly curation will further improve variant ascertainment. These Gallus references also enabled a new genome-wide review of endogenous Avian Leukosis Virus (ALVE) integrations, exemplifying the improved representation of chicken genomic diversity by these phased genomes. Our genome references will collectively improve our computational outcomes when testing multiple variant hypotheses that are at the core of our understanding of avian biology.