Genome-wide linkage scan. (A) Linkage analysis on 20 murine chromosomes. Genotyping assays were performed on 34 Gp6^−/− SHORT and 44 Gp6^−/− LONG mice. The results were analyzed by MAPMANAGER QTX, generating a linkage statistic that was converted to a LOD score. The chromosome number is indicated to the top left of each panel, wherein the LOD score (ordinate) is plotted against the SNP position (abscissa) on that chromosome. Congenic segments are represented by the absence of a plotted line in any of the panels. A horizontal bar in each panel indicates a LOD score of 2.0, and the top of each panel represents a LOD score of 4.5. The LOD score obtained for each SNP tested as a function of position (Mb) on each chromosome is plotted. The SNP with the highest LOD score of 4.2 (P < .001) is located at position chr4: 63 714 000 (marker = rs13477745). For the remaining 18 mouse autosomes and the X chromosome, none of the SNPs generated LOD scores more than 2.5, and 97% were less than 2.0 and 84% were less than 1.0. (B) Haplotype diagram of chromosome 4. This diagram schematically depicts the haplotypes for the 44 Gp6^−/− LONG (LEFT).and 34 Gp6^−/− SHORT (RIGHT) mice used in the initial genome wide linkage scan (see A). Each column represents the results for a single mouse. Each row depicts the typing results at a particular SNP, and the position of a selected number of key SNPs is indicated on the ordinate as the position from the 5′ end (TOP) in Mb. White boxes indicate the 129 × 1/SvJ allele; black boxes, the C57BL/6J allele; and gray boxes, heterozygosity. (C) Fine mapping on chromosome 4. Additional fine mapping of chromosome 4 using 76 SNPs conducted with 129 mice. Linkage to markers encompassing the locus from chr4:48 163 000 to chr4:69 206 000 remained highly significant, and rs13477745 remains the SNP with the highest LOD score of 6.9 (P < .001).