QTL Hotspot on Mouse Distal Chromosome 1 Table 4. Validation of cis-QTLs by measuring allele specific expression difference. Gene Ndufs2 Adamts4 Ufc1 Nit1 Pfdn2 Usf1 Copa Atp1a2 Kcnj9 Kcnj10 Dfy Igsf4b Fmn2 ProbeSet ID 1451096_at 1455965_at 1416327_at 1417468_at 1421950_at 1426164_a_at 1415706_at 1455136_at 1450712_at 1419601_at 1432273_a_at 1418921_at 1450063_at SNP ID rs8245216 rs31537832 rs13470410 rs31552469 rs31549998 rs31542370 rs13461812 rs31570902 rs31569118 rs30789204 rs31616337 rs31613626 rs33800912 Cis-LOD Add. effect (QTL)a High allele (ASE) 12 25 21 15 5 5 9 49 19 28 24 7 17 0.172 20.376 20.262 20.154 0.174 20.166 20.148 1.186 0.511 0.349 20.337 0.171 20.286 D D B D B B D D D B B P-value 2.461025 0.2 0.02 0.01 4.161027 0.004 3.961025 0.02 0.01 0.003 0.006 0.3 5.561026 aAdditive effect is computed as [(mean expression in DD homozygote)2(mean expression in BB homozygote)]/2 on a log2 scale. Positive value means D high expression, and negative value means B high expression. doi:10.1371/journal.pgen.1000260.t004 based on the location of peak LOD score markers (figure 4). This method of resolving trans-QTLs effectively grouped subsets of transcripts into functionally related cohorts. For instance, all the QTLs for the aminoacyl-tRNA synthetases (ARS) have peak LOD scores only within the distal three segments of Qrr1 (figure 5). This consistency in QTL peaks for transcripts of the same gene family is itself a good indicator of mapping precision. In addition to the ARS, numerous other genes involved in amino acid metabolism and translation map to the distal part of Qrr1 (e.g., Atf4, Asns, Eif4g2, and Pum2). We divided the trans-QTLs into two broad subgroups—those with peak QTLs on markers in the proximal part of Qrr1 (Qrr1p; 172–174.5 Mb or segments 1, 2, 3 in figure 2), and those with peak QTLs on markers in the distal part of Qrr1 (Qrr1d; 174.5– 177.5 Mb or segments 4, 5, and 6 in figure 2). While Qrr1p is relatively gene-rich, only 35% of the trans-QTLs (129 out of 365 probe sets) have peak LOD scores in this region. The majority of trans-QTLs—about 65% (236 out of 365 probe sets)—have peak QTLs in the relatively gene-sparse Qrr1d. The two subsets of transcripts—those with trans-QTLs in Qrr1p and those with trans-QTLs in Qrr1d—were analyzed for overrep- resented gene functions using the DAVID functional annotation tool (http://david.abcc.ncifcrf.gov/). This revealed distinct gene ontology (GO) categories enriched in the two subsets (dataset S2). Enriched GOs among the transcripts modulated by Qrr1p include GTPase-mediate signal transduction (modified Fisher’s exact test Figure 2. Haplotype maps of Qrr1 recombinant BXD strains. BXD8, BXD29, BXD62, BXD64, BXD68, and BXD84 have recombinations in Qrr1. B haplotype is assigned blue (2), D haplotype is assigned pink (+), and recombination regions are shown in grey. The Qrr1 interval (in Mb scale) is shown above and approximate positions of recombination are highlighted (red). The recombinant strains collectively divide Qrr1 into six segments (labeled 1–6), and provide six sets of informative markers. Markers are shown below and approximate positions of candidate genes (yellow bars) and tRNA clusters (orange triangles) are indicated. doi:10.1371/journal.pgen.1000260.g002 PLoS Genetics | www.plosgenetics.org 6 November 2008 | Volume 4 | Issue 11 | e1000260