Y and mitochondrial chromosomes in the heterogeneous stock rat population

Faith Okamoto; Apurva S. Chitre; Thiago Missfeldt Sanches; Denghui Chen; Daniel Munro; Allegra T. Aron; Angela Beeson; Hannah V. Bimschleger; Maya Eid; Angel G. Garcia Martinez; Wenyan Han; Katie Holl; Tyler Jackson; Benjamin B. Johnson; Christopher P. King; Brittany N. Kuhn; Alexander C. Lamparelli; Alesa H. Netzley; Khai Minh H. Nguyen; Beverly F. Peng; Jordan A. Tripi; Tengfei Wang; Kendra S. Ziegler; Douglas J. Adams; Amelie Baud; Lieselot L.G. Carrette; Hao Chen; Giordano de Guglielmo; Pieter Dorrestein; Olivier George; Keita Ishiwari; Monica M. Jablonski; Thomas C. Jhou; Marsida Kallupi; Rob Knight; Paul J. Meyer; Leah C. Solberg Woods; Oksana Polesskaya; Abraham A. Palmer

doi:10.1093/g3journal/jkae213

Y and mitochondrial chromosomes in the heterogeneous stock rat population

Faith Okamoto
, Apurva S. Chitre
, Thiago Missfeldt Sanches
, Denghui Chen
, Daniel Munro
, Allegra T. Aron
, Angela Beeson
, Hannah V. Bimschleger
, Maya Eid
, Angel G. Garcia Martinez
, Wenyan Han
, Katie Holl
, Tyler Jackson
, Benjamin B. Johnson
, Christopher P. King
, Brittany N. Kuhn
, Alexander C. Lamparelli
, Alesa H. Netzley
, Khai Minh H. Nguyen
, Beverly F. Peng

Jordan A. Tripi, Tengfei Wang, Kendra S. Ziegler, Douglas J. Adams, Amelie Baud, Lieselot L.G. Carrette, Hao Chen, Giordano de Guglielmo, Pieter Dorrestein, Olivier George, Keita Ishiwari, Monica M. Jablonski, Thomas C. Jhou, Marsida Kallupi, Rob Knight, Paul J. Meyer, Leah C. Solberg Woods, Oksana Polesskaya, Abraham A. Palmer

University of California at San Diego
University of Denver
Wake Forest University
Icahn School of Medicine at Mount Sinai
University of Tennessee Health Science Center
Medical College of Wisconsin
University of Maryland, Baltimore
SUNY Buffalo
Medical University of South Carolina
University of California at Los Angeles
University of Michigan, Ann Arbor
University of Colorado Anschutz Medical Campus
Barcelona Biomedical Research Park
Pompeu Fabra University

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

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.

Original language	English
Article number	jkae213
Journal	G3: Genes, Genomes, Genetics
Volume	14
Issue number	11
DOIs	https://doi.org/10.1093/g3journal/jkae213
State	Published - Nov 2024

Keywords

PheWAS
RNA-seq
Y Chromosome
haplotype
heterogeneous stock
low-coverage
mitochondria
rat

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10.1093/g3journal/jkae213

Cite this

Okamoto, F., Chitre, A. S., Sanches, T. M., Chen, D., Munro, D., Aron, A. T., Beeson, A., Bimschleger, H. V., Eid, M., Garcia Martinez, A. G., Han, W., Holl, K., Jackson, T., Johnson, B. B., King, C. P., Kuhn, B. N., Lamparelli, A. C., Netzley, A. H., Nguyen, K. M. H., ... Palmer, A. A. (2024). Y and mitochondrial chromosomes in the heterogeneous stock rat population. G3: Genes, Genomes, Genetics, 14(11), Article jkae213. https://doi.org/10.1093/g3journal/jkae213

@article{4f89172e756941ebbd9b9a22518b5ea0,

title = "Y and mitochondrial chromosomes in the heterogeneous stock rat population",

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.",

keywords = "PheWAS, RNA-seq, Y Chromosome, haplotype, heterogeneous stock, low-coverage, mitochondria, rat",

author = "Faith Okamoto and Chitre, \{Apurva S.\} and Sanches, \{Thiago Missfeldt\} and Denghui Chen and Daniel Munro and Aron, \{Allegra T.\} and Angela Beeson and Bimschleger, \{Hannah V.\} and Maya Eid and \{Garcia Martinez\}, \{Angel G.\} and Wenyan Han and Katie Holl and Tyler Jackson and Johnson, \{Benjamin B.\} and King, \{Christopher P.\} and Kuhn, \{Brittany N.\} and Lamparelli, \{Alexander C.\} and Netzley, \{Alesa H.\} and Nguyen, \{Khai Minh H.\} and Peng, \{Beverly F.\} and Tripi, \{Jordan A.\} and Tengfei Wang and Ziegler, \{Kendra S.\} and Adams, \{Douglas J.\} and Amelie Baud and Carrette, \{Lieselot L.G.\} and Hao Chen and \{de Guglielmo\}, Giordano and Pieter Dorrestein and Olivier George and Keita Ishiwari and Jablonski, \{Monica M.\} and Jhou, \{Thomas C.\} and Marsida Kallupi and Rob Knight and Meyer, \{Paul J.\} and \{Solberg Woods\}, \{Leah C.\} and Oksana Polesskaya and Palmer, \{Abraham A.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2024",

month = nov,

doi = "10.1093/g3journal/jkae213",

language = "English",

volume = "14",

journal = "G3: Genes, Genomes, Genetics",

issn = "2160-1836",

publisher = "Genetics Society of America",

number = "11",

}

Okamoto, F, Chitre, AS, Sanches, TM, 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 2024, 'Y and mitochondrial chromosomes in the heterogeneous stock rat population', G3: Genes, Genomes, Genetics, vol. 14, no. 11, jkae213. https://doi.org/10.1093/g3journal/jkae213

TY - JOUR

T1 - Y and mitochondrial chromosomes in the heterogeneous stock rat population

AU - Okamoto, Faith

AU - Chitre, Apurva S.

AU - Sanches, Thiago Missfeldt

AU - Chen, Denghui

AU - Munro, Daniel

AU - Aron, Allegra T.

AU - Beeson, Angela

AU - Bimschleger, Hannah V.

AU - Eid, Maya

AU - Garcia Martinez, Angel G.

AU - Han, Wenyan

AU - Holl, Katie

AU - Jackson, Tyler

AU - Johnson, Benjamin B.

AU - King, Christopher P.

AU - Kuhn, Brittany N.

AU - Lamparelli, Alexander C.

AU - Netzley, Alesa H.

AU - Nguyen, Khai Minh H.

AU - Peng, Beverly F.

AU - Tripi, Jordan A.

AU - Wang, Tengfei

AU - Ziegler, Kendra S.

AU - Adams, Douglas J.

AU - Baud, Amelie

AU - Carrette, Lieselot L.G.

AU - Chen, Hao

AU - de Guglielmo, Giordano

AU - Dorrestein, Pieter

AU - George, Olivier

AU - Ishiwari, Keita

AU - Jablonski, Monica M.

AU - Jhou, Thomas C.

AU - Kallupi, Marsida

AU - Knight, Rob

AU - Meyer, Paul J.

AU - Solberg Woods, Leah C.

AU - Polesskaya, Oksana

AU - Palmer, Abraham A.

PY - 2024/11

Y1 - 2024/11

N2 - 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.

AB - 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.

KW - PheWAS

KW - RNA-seq

KW - Y Chromosome

KW - haplotype

KW - heterogeneous stock

KW - low-coverage

KW - mitochondria

KW - rat

UR - https://www.scopus.com/pages/publications/85208772371

U2 - 10.1093/g3journal/jkae213

DO - 10.1093/g3journal/jkae213

M3 - Article

C2 - 39250761

AN - SCOPUS:85208772371

SN - 2160-1836

VL - 14

JO - G3: Genes, Genomes, Genetics

JF - G3: Genes, Genomes, Genetics

IS - 11

M1 - jkae213

ER -

Y and mitochondrial chromosomes in the heterogeneous stock rat population

Abstract

Keywords

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