In this study, we exploited 18 diverse array datasets derived from different mouse crosses to systematically dissect the expression QTLs in Qrr1. The strong trans effects are consistently detected in CNS tissues of C57BL/6J (B6)×DBA/2J (D2) and B6×C3H/HeJ (C3H) crosses, but are largely absent in ILS/Ibg (ILS)×ISS/Ibg (ISS) and C57BL/6By (B6y)×BALB/cBy (BALB), and in all non-neural tissues we have examined. We applied high-resolution mapping and haplotype analysis of Qrr1 using a large panel of BXD recombinant inbred (RI) strains that included highly recombinant advanced intercross RI lines. Our analyses revealed multiple distinct loci in Qrr1 that regulate gene expression specifically in the CNS. The distal part of Qrr1 (Qrr1d) has a strong effect on the expression of numerous genes involved in RNA metabolism and protein synthesis, including more than half of all aminoacyl-tRNA synthetases. Fmn2 and Rgs7, and a cluster of tRNAs are the strongest candidates in Qrr1d.
