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Okamoto F, Chitre AS, Missfeldt Sanches T, Chen D, Munro D, Aron AT, Beeson A, Bimschleger HV, Eid M, Garcia Martinez AG, Han W, Holl K, Jackson T, Johnson BB, King CP, Kuhn BN, Lamparelli AC, Netzley AH, Nguyen KMH, Peng BF, Tripi JA, Wang T, Ziegler KS, Adams DJ, Baud A, Carrette LLG, Chen H, de Guglielmo G, Dorrestein P, George O, Ishiwari K, Jablonski MM, Jhou TC, Kallupi M, Knight R, Meyer PJ, Solberg Woods LC, Polesskaya O, Palmer AA. Y and mitochondrial chromosomes in the heterogeneous stock rat population. G3 (BETHESDA, MD.) 2024; 14:jkae213. [PMID: 39250761 PMCID: PMC11540319 DOI: 10.1093/g3journal/jkae213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 07/18/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024]
Abstract
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.
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Affiliation(s)
- Faith Okamoto
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Apurva S Chitre
- Bioinformatics and System Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Denghui Chen
- Bioinformatics and System Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208, USA
| | - Angela Beeson
- Department of Internal Medicine, Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Hannah V Bimschleger
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Maya Eid
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angel G Garcia Martinez
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Wenyan Han
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Katie Holl
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Tyler Jackson
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Benjamin B Johnson
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Brittany N Kuhn
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Alexander C Lamparelli
- Department of Psychology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Alesa H Netzley
- Department of Emergency Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Khai-Minh H Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Beverly F Peng
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Jordan A Tripi
- Department of Psychology, University at Buffalo, Buffalo, NY 14260, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Kendra S Ziegler
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Douglas J Adams
- Department of Orthopedics, University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Amelie Baud
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Lieselot L G Carrette
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Giordano de Guglielmo
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Pieter Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
| | - Olivier George
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Keita Ishiwari
- Department of Pharmacology and Toxicology, University at Buffalo, Buffalo, NY 14203, USA
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA
| | - Monica M Jablonski
- Department of Ophthalmology and Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Thomas C Jhou
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Marsida Kallupi
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Paul J Meyer
- Department of Psychology, University at Buffalo, Buffalo, NY 14260, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
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Okamoto F, Chitre AS, Missfeldt Sanches T, Chen D, Munro D, Polesskaya O, Palmer AA. Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.566473. [PMID: 38076923 PMCID: PMC10705385 DOI: 10.1101/2023.11.29.566473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Genome-wide association studies typically evaluate the autosomes and sometimes the X Chromosome, but seldom consider the Y or mitochondrial Chromosomes. We genotyped the Y and mitochondrial chromosomes in heterogeneous stock rats (Rattus norvegicus), which were created in 1984 by intercrossing eight inbred strains and have subsequently been maintained as an outbred population for 100 generations. As the Y and mitochondrial Chromosomes do not recombine, we determined which founder had contributed these chromosomes for each rat, and then performed association analysis for all complex traits (n=12,055; intersection of 12,116 phenotyped and 15,042 haplotyped rats). We found the eight founders had 8 distinct Y and 4 distinct mitochondrial Chromosomes, however only two of each were observed in our modern heterogeneous stock rat population (Generations 81-97). Despite the unusually large sample size, the p-value distribution did not deviate from expectations; there were no significant associations for behavioral, physiological, metabolome, or microbiome traits after correcting for multiple comparisons. However, both Y and mitochondrial Chromosomes were strongly associated with expression of a few genes located on those chromosomes, which provided a positive control. Our results suggest that within modern heterogeneous stock rats there are no Y and mitochondrial Chromosomes differences that strongly influence behavioral or physiological traits. These results do not address other ancestral Y and mitochondrial Chromosomes that do not appear in modern heterogeneous stock rats, nor do they address effects that may exist in other rat populations, or in other species.
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Affiliation(s)
- Faith Okamoto
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Apurva S Chitre
- Bioinformatics and System Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Thiago Missfeldt Sanches
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Denghui Chen
- Bioinformatics and System Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | | | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
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