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 inbr...

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Published in:	G3 : genes - genomes - genetics Vol. 14; no. 11
Main Authors:	Okamoto, Faith, Chitre, Apurva S, Missfeldt Sanches, Thiago, Chen, Denghui, Munro, Daniel, Aron, Allegra T, Beeson, Angela, Bimschleger, Hannah V, Eid, Maya, Garcia Martinez, Angel G, Han, Wenyan, Holl, Katie, Jackson, Tyler, Johnson, Benjamin B, King, Christopher P, Kuhn, Brittany N, Lamparelli, Alexander C, Netzley, Alesa H, Nguyen, Khai-Minh H, Peng, Beverly F, Tripi, Jordan A, Wang, Tengfei, Ziegler, Kendra S, Adams, Douglas J, Baud, Amelie, Carrette, Lieselot L G, Chen, Hao, de Guglielmo, Giordano, Dorrestein, Pieter, George, Olivier, Ishiwari, Keita, Jablonski, Monica M, Jhou, Thomas C, Kallupi, Marsida, Knight, Rob, Meyer, Paul J, Solberg Woods, Leah C, Polesskaya, Oksana, Palmer, Abraham A
Format:	Journal Article
Language:	English
Published:	US Oxford University Press 06-11-2024
Subjects:	Investigation PheWAS haplotype rat RNA-seq Y Chromosome mitochondria heterogeneous stock low-coverage Heterogeneous stock Mitochondria Rat Low-coverage Haplotype
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Conflicts of interest RK is a scientific advisory board member, and consultant for BiomeSense, Inc., has equity and receives income. He is a scientific advisory board member and has equity in GenCirq. He is a consultant for DayTwo, and receives income. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity. He is a cofounder of Micronoma, and has equity and is a scientific advisory board member. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies.
ISSN:	2160-1836 2160-1836
DOI:	10.1093/g3journal/jkae213