biostudies-literatureOkamoto FNIAMSNIDA NIH HHSNIAMS NIH HHSNIDAjkae213https://www.ebi.ac.uk/biostudies/studies/S-EPMC11540319biostudies-literatureUnknown14(11)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 loG3 (Bethesda, Md.)Y and mitochondrial chromosomes in the heterogeneous stock rat population.PMC11540319P50 DA037844R01AR070879R01 AR070879P50DA037844Ishiwari KGeorge OHan WCarrette LLGJablonski MMBeeson AAdams DJKallupi MWang TKuhn BNde Guglielmo GJhou TCBimschleger HVPeng BFSolberg Woods LCMeyer PJBaud ADorrestein POkamoto FJohnson BBTripi JAGarcia Martinez AGJackson TPolesskaya OZiegler KSKing CPChen HMunro DChen DAron ATEid MKnight RMissfeldt Sanches TNetzley AHChitre ASPalmer AAHoll KLamparelli ACNguyen KHfalseY 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 lo2024-01-01T00:00:00Z2024 Nov2026-07-09T11:59:13.8Z2025-04-22T09:41:21.767ZS-EPMC115403193925076110.1093/g3journal/jkae213