Okamoto, FaithBaud, AmeliePalmer, Abraham A.Okamoto, Faith; Baud, Amelie; Palmer, Abraham A.2025-01-222025-01-222024Okamoto F, Chitre AS, Missfeldt Sanches T, Chen D, Munro D, Aron AT, et al. Y and mitochondrial chromosomes in the heterogeneous stock rat population. G3 (Bethesda). 2024 Nov 6;14(11):jkae213. DOI: 10.1093/g3journal/jkae2132160-1836http://hdl.handle.net/10230/69231Genome-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.application/pdfeng© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.info:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/g3journal/jkae213PheWASRNA-seqY ChromosomeHaplotypeHeterogeneous stockLow-coverageMitochondriaRatinfo:eu-repo/semantics/openAccess