Ponsuksili et al. BMC Genomics 2010, 11:572 http://www.biomedcentral.com/1471-2164/11/572 Page 4 of 14 Table 3 Probe-sets with expression levels that are correlated with principal component 2 and information about their eQTL Prob_set_IDs Ssc.25132.3.S1 Ssc.11839.1.S1 Ssc.21636.1.A1 Ssc.21225.1.S1 Ssc.27245.1.S1 Ssc.5869.1.S1 Ssc.11130.2.A1 Ssc.16460.1.S1 Ssc.28435.1.A1 Ssc.6529.1.A1 Ssc.16877.1.S1 Ssc.15224.3.A1 Ssc.1051.1.S1 Ssc.15224.2.S1 Ssc.15224.1.S1 Ssc.24035.1.S1 Ssc.5112.2.S1 Ssc.3935.1.S1 Ssc.26780.1.S1 Ssc.1545.1.A1 Ssc.20488.1.A1 Ssc.14436.1.S1 Ssc.10297.3.S1 Ssc.10297.1.S1 Ssc.21139.2.S1 Ssc.10148.1.S1 Ssc.22107.1.A1 Ssc.16983.1.S1 Ssc.22376.1.A1 Ssc.4217.1.S1 Ssc.20319.1.S1 Ssc.31206.3.S1 Ssc.10429.1.S1 Ssc.10911.1.A1 Ssc.18050.1.S1 Ssc.11397.1.A1 Ssc.6058.1.S1 Ssc.18640.3.S1 Annotation Gene Symbols RAD23B ZNF462 FILIP1 RNASEH2C RTN3 SART1 EGR1 EHD1 AFF4 LOC728816 FOSL2 TGOLN2 FOSL2 FOSL2 EIF2C2 LMNA SLC48A1 BCL2L12 TCF25 RPS9 USP14 CAPZB CAPZB CLIC5 MTHFD1 LOC100131693 TRAPPC4 ITIH4 TMEM115 CGGBP1 ANKRD1 ADRBK2 ZRANB1 MTG1 LOC100129026 UBE2D1 SSC 1 1 1 2 2 2 2 2 2 2 3 3 3 3 3 4 4 5 6 6 6 6 6 6 7 7 8 9 12 13 13 13 14 14 14 14 16 18 eQTL cM 130 138 142 1 18 42 50 52 56 132 0 0 86 86 86 45 67 89 0 0 65 92 95 99 14 81 110 62 63 47 47 52 0 0 87 96 55 34 F 5.11 8.12 5.4 5.2 10.8 8.7 5.4 6.2 8.21 9.3 6.4 5.8 5.9 6.2 6.3 7.4 9.54 5.2 6.9 5.7 8.4 5.4 6.2 6 6 16.1 5.8 7.7 5.5 7.3 5.2 5.9 6 6 5.6 6.7 4.9 4.9 individual trait correlation* traits DL, -pH1ld, LF1ld, LF24sm SF pH24ld LF24sm -LF24sm LF24sm LF24sm -LF24sm CL, -pH24ld, -pH24sm, LF24sm pH24ld, pH24sm, -LF24ld OPTO pH24ld, pH24sm pH24ld -DL, pH24ld, pH24sm -DL, -SF, -TL, pH24ld, pH24sm -DL, -TL pH24ld, pH24sm LF24sm DL, -pH24ld, -pH24sm, LF24sm, LF24sm DL, TL pH24ld DL, CL, TL, -pH24ld, LF24ld, LF24sm CL, LF24sm pH1ld -OPTO, LF1ld pH24ld, LF24sm -OPTO OPTO -DL, pH1ld, -LF24sm LF24sm, -pH24ld, -DL, pH24ld, -LF24sm -CL, pH24ld, -LF24ld -LF24sm LF24sm -DL, -SF, -LF24sm DL, LF24sm “*”the probe-sets listed here represent a subset of probe-sets correlated with individual meat quality traits as indicated in this column naming the traits with which the corresponding probe-sets show correlated expression in addition to the correlated expression with PC2; “-” indicates negative correlation Trait abbreviations are given at table 2. Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, or in the Ingenuity Pathways Analysis library, highlight ubiquitination, phosphorylation, mitochondrion dysfunction, actin-, integrin-, PDGF-, EGF-, VEGF-, and Ca-signalling path- ways [13]. Most of the eQTL related to PC2 were found on chromosomes 2, 3, and 6; for PC3 on chromosomes 1, 3, 7, and 9. Discussion Complex traits are genetically controlled by many loci. The identification of candidate genes for these traits is widely based on the principle of ‘collecting evidences’ in order to prioritize genes for further analysis from the huge lists of functional and positional candidate genes. The detection of eQTL provides information about the positional aspects of gene expression regulation.