Chromosomal regions of pQTLs with significant genome-wide LRS values determined by single QTL scans and CIM.

<p>Abbreviations and definitions: <b>pQTL (chr):</b> chromosomal position of quantitative trait locus; <b>LRS (max):</b> likelihood ratio statistic, maximum association between genotype and phenotype variation; <b>SNP (max):</b> single nucleotide polymorphism with maximum LRS in QTL region; <b>1.5 LOD support interval (Mb):</b> chromosomal region in Megabases spanning QTL position; <b>Additive allele effect</b>: estimate of a change in the average phenotype by substitution of one parental allele by another at a given marker position; <b>(−)</b> values indicate an increase of phenotype by C57BL/6J allele, <b>(+)</b> values an increase of phenotype by DBA/2J allele; <b>Dataset:</b> dataset in which the QTL was identified; <b>Hyp</b>: hydroxyproline; CIM: composite interval mapping.</p

Phenotypic characterization of parental strains after six weeks of CCl₄ injections.

<p>Liver fibrosis was assessed by morphometric (A) and biochemical (B) measurement of hepatic collagen (Hyp) contents. Hepatic inflammation was measured by serum ALT activities (C). Sirius red staining of hepatic collagen showed circumferential fibrosis in C57BL/6J mice (D) and pronounced fibrosis in DBA/2J mice (E), corresponding to mean F-scores of 2.0±0.1 and 3.9±0.1, respectively.</p

Summary of fibrosis-associated pQTL and eQTL regions.

<p>Abbreviations and definitions: <b>pQTL (chr):</b> position of phenotypic (p) QTL; <b>pQTL Position (Mb)</b>: chromosomal position in Megabases; <b>LRS (max):</b> likelihood ratio statistic, maximum association detected in pQTL analysis; <b>Size of pQTL region (Mb):</b> size of 1.5 LOD support interval of the QTL; <b>Genes in pQTL region</b>: all genes localized in a pQTL region; <b>eQTLs in pQTL region</b>: regulatory genetic markers in pQTL region; <b><i>cis</i></b><b>QTLs in pQTL region</b>: genetic markers in the pQTL region, regulating genes within a 10 Mb distance; <b><i>cis</i></b><b>QTGs in pQTL region</b>: genes in the pQTL region (regulated by markers within a 10 Mb distance) with LRS≥12.0.</p

Phenotypic characterization of the BXD reference panel after six weeks of CCl₄ injections.

<p>(A) Histogram illustrating the distribution of hepatic collagen contents in BXD mice. The mean hepatic collagen concentrations (± SE)are indicated by vertical lines (solid line: BXD recombinant inbred lines, 386.9±5.9 µg Hyp/g liver; dashed line: C57BL/6J (B6) inbred strain, 419.3±22.4 µg/g; dash-dot line: DBA/2J (D2) inbred strain, 570.9±25.9 µg/g). (B) Mean hepatic collagen contents (± SE) stratified according to F-score categories (F1–F4). (C–E) Strain specific mean (± SE) phenotype values compared to the overall means of all mice phenotyped (29–35 BXD lines, strains C57BL/6J and DBA/2J, B6D2 F1 hybrids), which are represented by the horizontal lines. (C) Hepatic collagen areas (mean ± SE: 2.4±0.1%); (D) hepatic collagen (Hyp) contents (386.9±5.9 µg/g); (E) fibrosis stages (F-scores, 2.3±0.1); (F) serum ALT activities (419.4±25.3 U/l). (G)–(K) Representative liver sections of diverse BXD strains after CCl₄ treatment, illustrating increasing F-scores from F0 to F4. (G) F0: no fibrosis; (H) F1: perivenular fibrosis, initially forming collagen bridges; (I) F2: circumferential venular fibrosis with incomplete bridging; (J) F3: centro-central fibrosis with complete bridging; (K) F4: pronounced fibrosis with complete and broadened collagen bridges.</p

QTLs for hepatic fibrosis in the BXD murine reference population.

<p>The heatmaps represent significant interval mapping results on the indicated mouse chromosomes, separately for male and female mice as well as the combined data set (without inclusion of covariates); the QTL plots below illustrate composite interval mapping results (with ‘background’ QTLs as covariates, restricted to significant QTLs or overlapping loci for different phenotypes). Color coding of the heatmaps is as follows: Grey/black regions indicate the absence of genotype to phenotype linkage. Blue to green regions correspond to suggestive and significant linkage, respectively, with C57BL/6J alleles being associated with higher trait values. Red to yellow regions correspond to suggestive and significant linkage, respectively, with an association of DBA/2J alleles with higher values.</p

Fibrosis network graph generated by correlating the hepatic expression levels of the candidate genes.

<p>The graph presents the inter-chromosomal correlations of 51 genes, except for the four candidate genes <i>Adamts17</i>, <i>Gm9860</i>, <i>Klk22 and Ogfr</i> with exclusively intra-chromosomal correlations. Node color and shape illustrate the chromosomal localization of the gene. The size of each node indicates the degree of connectivity, with larger nodes having higher number of correlated genes. The edges show Pearson's correlation coefficients (r) as follows: solid green lines: r>0.5; solid red lines: r<−0.5; dotted green lines r>0.36; dotted red line r<−0.36.</p