QTL Hotspot on Mouse Distal Chromosome 1 LOD$3 LOD$4 transb cisb % transc % cisd % transc % cisd 197 79 439 345 279 156 97 94 700 9 8 0 10 516 15 63 56 7 56 30 44 54 39 43 31 25 20 33 6 28 51 33 46 34 12 8 1 9 7 5 2 1 2 0.3 0.2 0 0.4 14 0.3 0.7 0.5 0.08 5 2 2 1 1 1 1 1 1 1 1 3 1 3 2 3 3 2 18 5 27 22 13 2 2 6 0 0 1 0.5 0.7 23 0.3 0.6 0.4 0.1 5 2 2 1 1 1 1 1 1 1 1 3 1 2 2 3 3 2 Cross B6D2F2 B6D2F2 BXD BXD BXD BXD BXD BXD BXD BXD BXD BXD LXS B6C3F2 B6C3F2 B6C3F2 B6C3F2 CXB Na 58 56 45 69 39 64 54 29 63 40 53 30 75 238 306 298 282 13 Dataset & Normalization OHSU/VA (Sep05) PDNN OHSU/VA mRNA (Aug05) PDNN SJUT (Mar05) PDNN INIA (Jan06) PDNN Hamilton Eye Institute (Sep06) RMA HQF (Nov 07) RankInv HBP/Rosen(Apr05) PDNN UMUTAffy RMA (Mar08) UNC (Jan06) BothSexes LOWESS Kidney Consortium (Aug06) PDNN GNF (Mar03) MAS5 NIAAA INIA (May07) RankInv UCLA BHHBF2 (2005) mlratio UCLA BHHBF2 (2005) mlratio UCLA BHHBF2 (2005) mlratio UCLA BHHBF2 (2005) mlratio Tissue Striatum Whole brain Cerebellum Forebrain Eye Striatum Striatum Liver Kidney Brain Muscle Liver Adipose Array Affymetrix M430v2 Affymetrix M430 Affymetrix M430 Affymetrix M430v2 Affymetrix M430 Affymetrix M430v2 Illumina M6.1 Affymetrix M430v2 Agilent G4121A Affymetrix M430v2 Agilent Agilent Agilent Agilent Hippocampus Affymetrix Exon 1.0 ST 302 0.4 Hematopoietic Cells Affymetrix U74Av2 Hippocampus Illumina M6.1 Table 2. Expression QTLs in Qrr1 in different crosses and tissues. Hippocampus Consortium (Dec05) PDNN Hippocampus Hippocampus Consortium (Dec05) PDNN Hippocampus Affymetrix M430v2 aNumber of RI strains or F2 mice. bNumber of cis- and trans-QTLs in Qrr1 at minimum LOD of 3; complete list of these transcripts can be retrieved from www.genenetwork .org using search key ‘‘LRS = (15 500 Chr1 172 178)’’. cPercent of trans-QTLs in Qrr1 = [(number of trans-QTLs in Qrr1)/(total number of trans-QTLs in the whole genome)6100]. dPercent of cis-QTLs in Qrr1 = [(number of cis-QTLs in Qrr1)/(total number of cis-QTLs in the whole genome)6100]. doi:10.1371/journal.pgen.1000260.t002 crosses. We also scanned Qrr1 for variation in copy number [54,55]. Graubert et al. [55] reported segmental duplication in Qrr1 with a copy number gain in D2 compared to B6 near the intelectin 1 (Itlna) gene at 173.352 Mb. We failed to detect any expression signatures of a copy number variation around Itlna in any of the GeneNetwork datasets. However, we did identify an apparent 150 kb deletion across the Ifi200 gene cluster (175.584– 175.733 Mb). Affymetrix probe sets 1426906_at, 1452231_x_at, Figure 1. Highly replicable trans-QTLs in Qrr1. The charts illustrate the total number of trans-QTLs (LOD$4) in Qrr1 (shaded) and in other regions of the genome (non-shaded) in three datasets—BXD cerebellum, BXD hippocampus, and B6C3H F2 brain. The smaller charts represent the trans-QTLs in BXD hippocampus that are also detected in BXD cerebellum, and B6C3HF2 brain datasets. Out of the 101 trans-QTLs common to both BXD hippocampus and cerebellum, 64 are in Qrr1 and the remaining 37 are located in other regions of the genome. The BXD hippocampus and B6C3HF2 brain datasets have 54 common trans-QTLs, and almost all (52 out of 54) are in Qrr1. doi:10.1371/journal.pgen.1000260.g001 PLoS Genetics | www.plosgenetics.org 4 November 2008 | Volume 4 | Issue 11 | e1000260