Experiment
QTL analysis on 101 phenotypic traits was performed on 1,904 heterogeneous stock mice using 13,459 single nucleotide polymorphisms (SNPs) spanning the genome. Results yielded 843 mostly small effect QTLs linked to 97 traits with an average 95% confidenceinterval of 2 Mb. QTLs with the largest effects are assigned nomenclature by MGI and reported below. The entire data set may be viewed at http://gscan.well.ox.ac.uk.
On mouse Chromosome 1, linkage to serum HDL mapped to 171.5 Mb - 172 Mb (logP=54.34).The Apoa2 gene at 173 Mb (92.6 cM) was identified as the gene responsible for this locus. Total cholesterol is also linked to this interval (logP=47.25). Mean cellular hemoglobin concentration (logP=15.25, 3.3% of variance) and red cell mean cellular volume (logP=17.73, 4.09% of variance) mapped to 129 Mb - 132 Mb. This locus is named Blct1 (blood cell traits 1). Mean platelet volume mapped to 171 - 173.5 Mb (logP=36.9; 10.49% of variance) and hematocrit (logP=9.21, 3.41% of variance) mapped to 188 Mb -189.8 Mb. This locus is collectively called Blct2 (blood cell traits 2).
On mouse Chromosome 2, body mass index mapped to an interval at 126 Mb - 130 Mb with logP=10.7. This locus accounts for 3.34% of the variance and is designated Bdym1 (body mass 1).
On mouse Chromosome 4, linkage to alkaline phosphatase mapped to an interval at 136 Mb - 138 Mb with logP=82.7. This locus accounts for 14.23% of the variance and the underlying gene was identified as Akp2 at 137 Mb (70.2 cM).
On mouse Chromosome 5, linkage to anxiety traits mapped to an interval at 48.8 Mb - 52 Mb. Latency to enter elevated plus maze (EPM) open arms reached logP=12.39 and open field arena center time reached logP=12.82. This locus accounts for 3.37% of the variance and is named Anyt1 (anxiety traits 1).
On mouse Chromosome 6, linkage to basophils mapped to 79.8 Mb - 82.7 Mb with logP=8.35. This locus explains 3.54% of the variance and is named Imct1 (immune cell traits 1).
On mouse Chromosome 7, linkage to wound healing (ear punch hole area) mapped to 75.8 Mb - 77.6 Mb with logP=25.28. This locus explains 5% of the variance and is named Erph1 (ear punch hole 1). Linkage to body weight at 6 weeks of age mapped to an interval at 51.4 Mb - 54.8 Mb with logP=17.02. This locus explains 3.34%of the variance and is named W6bw1 (week 6 body weight 1). Red cell distribution width mapped to an interval at 98.2 Mb - 101.1 Mb with logP=18.6. This locus explains 3.98% of the variance and is named Blct3 (blood cell traits 3).
On mouse Chromosome 9,linkage to mean cellular hemoglobin (logP=17.17, 3.36% of variance), mean cellular hemoglobin concentration (logP=14.5, 3.69% of variance), and red cell distribution width (logP=12.69, 2.6% of variance) mapped to an interval at 107.8 Mb - 11.9 Mb. Thislocusis named Blct4 (blood cell traits 4).
On mouse Chromosome 11, linkage to mean cellular hemoglobin mapped to 4.9 Mb - 5.9 Mb with logP=12.7. This locus explains 12.3% of the variance and is named Blct5 (blood cell traits 5). Linkage to aspartate transaminase mapped to an interval at 56.1 Mb - 59.6 Mb (logP=9.22) and explains 3.28% of the phenotypic variance. This locus is named Aspt1 (aspartate transaminase trait 1). Linkage to startle response mapped to 118.2 Mb - 120.3 Mb with logP=13.1. This locusis named Sttr1 (startle response 1) and accounts for 3.15% of the variance. Body length mapped to 79.3 Mb - 83.1 Mb (logP=10.85) and explains 3.14% of the variance. This locus is named Byln1 (body length 1).
Blct6 (blood cell traits 6) mapped to 64.7Mb - 66.1 Mb on mouse Chromosome 14 with logP=20 for mean cellular hemoglobin (4% of variance) and logP=17.4 for red cell mean cellular volume (3.7% of variance).
Startle response (logP=24.5) and time freezing during cue (logP=28) mapped to 91.4 Mb - 92.2 Mb on mouse Chromosome 15. This locus is named Sttr2 (startle response 2) and explains 5.7% of the startle response phenotype variance and 10.1% of the freezing time variance.
Imct2 (immune cell traits 2) mapped to an interval at 30.8 Mb - 43.2 Mb onmouse Chromosome 17. This locus is associated with CD4+/CD8+ ratio (logP=65.8, 11.9% of variance), percentage CD4+/CD3+ cells (logP=54, 11.2% of variance), and percentage CD8+ cells (logP=48.6, 8% of variance).
Analysis Tools