Ponsuksili et al. BMC Genomics 2010, 11:572 http://www.biomedcentral.com/1471-2164/11/572 Page 3 of 14 Figure 1 Graphical scheme of eQTL across 18 chromosome obtained by eQTL analysis of 11457 probe-set. Y-axis shows P-values, expressed on the -log10 scale, and X-axis shows position of eQTL in cM though18 chromosome. The genome-wide significant threshold (p ≤ 0.05) is shown with the dot line. composite traits that were generated by principal com- ponent analysis PC2 and PC3 (Tables 3 and 4). In order to unravel the composite traits, the correlation of these 38 and 47 transcripts with each single meat quality trait contributing to the PC was screened and traits with significant correlations with the respective genes are given in tables 3 and 4. Thus the probe-sets represent a subset of probe-sets correlated with individual meat quality traits. As previously shown, analyses of enrich- ment of functional annotation groups as defined in the Table 2 The number of eQTL of probe-sets exhibiting expression levels that are correlated with meat quality traits No. of eQTL with trait correlated express gene Meat quality parameters Traits All eQTL eQTL located on the same chromosome as the corresponding probe-set routine parameters - pH pH1ld 425 35 pH24ld 384 34 pH24sm 271 28 - conductivity LF1h loin 253 16 LF24ld 793 50 LF24ld 1012 64 meat texture DL 298 26 TL 285 28 CL 76 40 technological meat quality parameters QPTO 273 12 SF 439 35 Trait abbreviations: pH1ld pH-value in Mld at 13th/14th rib 45 min post mortem. pH24ld pH-value in Mld at 13th/14th rib 24 h post mortem. pH24sm pH-value in M. semimembranosus (Msm) at 24 h post mortem. LF1ld conductivity in Mld at 13th/14th rib45 min post mortem. LF24ld conductivity in Mld at 13th/14th rib post mortem. LF24sm conductivity in Msm at 24 h post mortem. DL Drip loss: percentage of weight loss after 48 h of Mld samples collected at 24 h post mortem. TL Thaw loss: percentage of weight loss of Mld samples frozen at -20°C. CL Cooking loss: percentage of weight loss of Mld samples incubated in water at 75°C for 50 min. OPTO meat colour 24 h post mortem in M. longissimus dorsi (Mld)at 13th/14th rib; OPTO star. SF Shear force was measured by the Instron-4310 equipment.