Y and mitochondrial chromosomes in the heterogeneous stock rat population
Genome-wide association studies typically evaluate the autosomes and sometimes the X Chromosome, but seldom consider the Y or mitochondrial (MT) Chromosomes. We genotyped the Y and MT Chromosomes in heterogeneous stock (HS) rats (Rattus norvegicus), an outbred population created from 8 inbred strains. We identified 8 distinct Y and 4 distinct MT Chromosomes among the 8 founders. However, only 2 types of each nonrecombinant chromosome were observed in our modern HS rat population (generations 81-97). Despite the relatively large sample size, there were virtually no significant associations for behavioral, physiological, metabolome, or microbiome traits after correcting for multiple comparisons. However, both Y and MT Chromosomes were strongly associated with the expression of a few genes located on those chromosomes, which provided a positive control. Our results suggest that within modern HS rats there are no Y and MT Chromosomes differences that strongly influence behavioral or physiological traits. These results do not address other ancestral Y and MT Chromosomes that do not appear in modern HS rats, nor do they address effects that may exist in other rat populations, or in other species.
Authors
- Leah C. Solberg Woods (ORCID: https://orcid.org/0000-0002-7943-798X)
- Thiago Missfeldt Sanches (ORCID: https://orcid.org/0000-0001-6962-9569)
- Oksana Polesskaya (ORCID: https://orcid.org/0000-0003-3024-114X)
- Maya Eid (ORCID: https://orcid.org/0000-0001-5906-8825)
- Christopher P. King (ORCID: https://orcid.org/0000-0002-6641-237X)
- Giordano de Guglielmo (ORCID: https://orcid.org/0000-0002-4782-7430)
- Marsida Kallupi (ORCID: https://orcid.org/0000-0002-8688-709X)
- Amelie Baud (ORCID: https://orcid.org/0000-0003-2448-0283)
- Angela Beeson (ORCID: https://orcid.org/0000-0002-4388-5983)
- Angel Garcia Martinez
- Keita Ishiwari (ORCID: https://orcid.org/0000-0002-6190-2249)
- Abraham A. Palmer (ORCID: https://orcid.org/0000-0003-3634-0747)
- Hannah Bimschleger (ORCID: https://orcid.org/0000-0001-6578-7201)
- Jordan A. Tripi
- Rob Knight (ORCID: https://orcid.org/0000-0002-0975-9019)
- Wenyan Han (ORCID: https://orcid.org/0000-0003-0886-1430)
- Brittany N. Kuhn (ORCID: https://orcid.org/0000-0002-6240-5826)
- Alexander Lamparelli (ORCID: https://orcid.org/0000-0003-1908-9562)
- Tyler Jackson (ORCID: https://orcid.org/0000-0003-2988-4340)
- Lieselot L. G. Carrette (ORCID: https://orcid.org/0000-0002-5217-2774)
- Paul Meyer (ORCID: https://orcid.org/0000-0001-5665-2292)
- Olivier George (ORCID: https://orcid.org/0000-0002-3700-5003)
- Apurva S. Chitre (ORCID: https://orcid.org/0000-0003-1709-9214)
- Daniel Munro (ORCID: https://orcid.org/0000-0002-0724-218X)
- Alesa H. Netzley (ORCID: https://orcid.org/0000-0003-0171-3363)
- Monica M. Jablonski (ORCID: https://orcid.org/0000-0002-4021-3559)
- Denghui Chen (ORCID: https://orcid.org/0000-0002-6541-3418)
- Allegra T. Aron (ORCID: https://orcid.org/0000-0002-9596-021X)
- Khai‐Minh Nguyen (ORCID: https://orcid.org/0000-0003-3939-7773)
- Thomas C. Jhou (ORCID: https://orcid.org/0000-0001-8811-0156)
- Douglas J. Adams (ORCID: https://orcid.org/0000-0002-6090-0516)
- Hao Chen (ORCID: https://orcid.org/0000-0002-2680-6921)
- Pieter C. Dorrestein (ORCID: https://orcid.org/0000-0002-3003-1030)
- Benjamin B. Johnson (ORCID: https://orcid.org/0000-0001-7269-5145)
- Beverly Peng (ORCID: https://orcid.org/0009-0001-1511-3089)
- Faith Okamoto (ORCID: https://orcid.org/0009-0007-4163-6928)
- Kendra S Ziegler (ORCID: https://orcid.org/0009-0005-6006-2996)
- Katie Holl (ORCID: https://orcid.org/0009-0007-9166-7423)
- Tengfei Wang
Institutions
- University of Maryland, Baltimore (US)
- University of Denver (US)
- Medical University of South Carolina (US)
- University of Tennessee Health Science Center (US)
- University of California, Los Angeles (US)
- Universitat Pompeu Fabra (ES)
- Medical College of Wisconsin (US)
- University of Michigan (US)
- University of California San Diego (US)
- Centre for Genomic Regulation (ES)
- Wake Forest University (US)
- University of Colorado Anschutz Medical Campus (US)
- University at Buffalo, State University of New York (US)
- University of Montana (US)
- Icahn School of Medicine at Mount Sinai (US)
Publication Details
- Journal
- G3 Genes Genomes Genetics
- Published
- 2024-09-05
- DOI
- https://doi.org/10.1093/g3journal/jkae213
- Citations
- 3
- Primary Topic
- Genetic Mapping and Diversity in Plants and Animals
- Type
- article
- Field-Weighted Citation Impact
- 1.65
Funders
- National Institute of Development Administration
- National Institute of Arthritis and Musculoskeletal and Skin Diseases