Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides

摘要: The laboratory mouse is the most commonly used model for studying variation in complex traits relevant to human disease. Here we present whole-genome sequences of two inbred strains, LG/J and SM/J, which are frequently study as diverse aging, bone-growth, adiposity, maternal behavior, methamphetamine sensitivity. We identified small nucleotide variants (SNVs) structural (SVs) SM/J strains relative reference genome discovered novel these by comparing their other genomes. find that 39% genomes identical-by-descent (IBD). characterized amino-acid changing mutations using three algorithms: LRT, PolyPhen-2 SIFT. also polymorphisms between fall regulatory regions highly informative transcription factor binding sites (TFBS). intersected functional predictions with quantitative trait loci (QTL) mapped advanced intercrosses strains. QTL both over-represented non-IBD enriched predicted have a impact. Variants associated metabolic (231 an F16 generation) developmental (41 F34 were interrogated highlight candidate genes (QTG) nucleotides (QTN) on chr13 basal glucose levels chr6 tibia length. show how integrating genomic sequence reduces search space helps researchers prioritize experimental follow-up. Additionally, given phylogenetic context among data contribute important information landscape mouse.