Ponsuksili et al. BMC Genomics 2010, 11:572 http://www.biomedcentral.com/1471-2164/11/572 5000 permutations [30]. The 5% chromosome-wide threshold corresponds approximately to the suggestive linkage threshold proposed by Lander & Kruglyak (1995) [10]. Average significance thresholds were 4.92 corresponding to LOD = 2.0 with nominal p ≤ 10-3. Annotations and localization of probe-sets was based on assembly Sscrofa9 (April 2009) [6]. In order to link the genetic map to Ensembl Sscrofa9, all 115 microsatellites sequences, which were used in the linkage map, were BLASTed against the Ensembl porcine BAC sequence (Sscrofa9, April 2009). Only 73 microsatellites sequences could be localized on Sscrofa 9 as shown on Figure 2, 3, 4, 5, 6. Additional material Additional file 1: eQTL detected for probe-sets representing transcripts that are expressed in porcine M. longissimus dorsi. All 9,180 eQTL (at LOD score > 2) estimated for probe-sets of the Affymetrix Porcine Genome Array, their position in cM on linkage groups, corresponding gene names and chromosomal positions according to the current porcine genome sequence assembly (Sscrofa9 assembly, April 2009) [6]. Acknowledgements The authors thank Annette Jugert and Joana Bittner for excellent technical help. This research was supported by German Research Foundation (Deutsche Forschungs-gemeinschaft, DFG; Forschergruppe ‘DRIP’, FOR 753). Author details 1Leibniz Institute for Farm Animal Biology, Research Group Functional Genome Analysis, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany. 2Leibniz Institute for Farm Animal Biology, Research Unit Molecular Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany. 3Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany. Authors’ contributions SP analyzed the microarray data and drafted the manuscript; EM, MS, and KS aided in data analysis and helped in drafting the manuscript; KW conceived and designed the study, contributed to data interpretation and helped in drafting the manuscript. All authors read and approved the final manuscript. Received: 23 May 2010 Accepted: 16 October 2010 Published: 16 October 2010 References 1. Jansen RC, Nap JP: Genetical genomics: the added value from segregation. Trends Genet 2001, 17:388-391. 2. Jansen RC: Studying complex biological systems using multifactorial perturbation. Nat Rev Genet 2003, 4:145-151. 3. Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts SK, Monks S, Reitman M, Zhang C, Lum PY, Leonardson A, Thieringer R, Metzger JM, Yang L, Castle J, Zhu H, Kash SF, Drake TA, Sachs A, Lusis AJ: An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 2005, 37:710-717. 4. Doss S, Schadt EE, Drake TA, Lusis AJ: Cis-acting expression quantitative trait loci in mice. Genome Res 2005, 15:681-691. 5. Ponsuksili S, Jonas E, Murani E, Phatsara C, Srikanchai T, Walz C, Schwerin M, Schellander K, Wimmers K: Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle. BMC Genomics 2008, 9:367. Page 13 of 14 6. Naraballobh W, Chomdej S, Murani E, Wimmers K, Ponsuksili S: Annotation and in silico localization of the Affymetrix GeneChip Porcine Genome Array. Arch Tierz 2010, 53:230-238. 7. Ponsuksili S, Murani E, Phatsara C, Schwerin M, Schellander K, Wimmers K: Expression quantitative trait loci analysis of genes in porcine muscle by quantitative real time RT-PCR compared to microarray data. Heredity 2010. 8. Affymetrix Technical Manual: Affymetrix GeneChip Expression Analysis. Affymetrix, Santa Clara, CA 2001. 9. Affymetrix Technical Note: Guide to Probe Logarithmic Intensity Error (PLIER) Estimation. Affymetrix, Santa Clara, CA 2005. 10. Lander E, Kruglyak L: Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 1995, 11:241-247. 11. Hodgson RR, Belk KE, Savell JW, Cross HR, Williams FL: Development of a quantitative quality grading system for mature cow carcasses. J Anim Sci 1992, 70:1840-1847. 12. Liu G, Jennen DG, Tholen E, Juengst H, Kleinwächter T, Hölker M, et al: A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Anim Genet 2007, 38:241-252. 13. Ponsuksili S, Murani E, Phatsara C, Schwerin M, Schellander K, Wimmers K: Porcine muscle sensory attributes associate with major changes in gene networks involving CAPZB, ANKRD1, and CTBP2. Funct Integr Genomics 2009, 9:455-471. 14. Brem RB, Yvert G, Clinton R, Kruglyak L: Genetic dissection of transcriptional regulation in budding yeast. Science 2002, 296:752-755. 15. Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, et al: Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 2003, 35:57-64. 16. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, et al: Genetic analysis of genome-wide variation in human gene expression. Nature 2004, 430:743-747. 17. Göring HH, Curran JE, Johnson MP, Dyer TD, Charlesworth J, Cole SA, et al: Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet 2007, 39:1208-1216. 18. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH: Genetics of gene expression surveyed in maize, mouse and man. Nature 2003, 422:297-301. 19. Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, Mueller M, Hummel O, Monti J, Zidek V, Musilova A, Kren V, Causton H, Game L, Born G, Schmidt S, Müller A, Cook SA, Kurtz TW, Whittaker J, Pravenec M, Aitman TJ: Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet 2005, 37:243-253. 20. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, et al: Uncovering regulatory pathways that affect hematopoietic stem cell function using ‘genetical genomics’. Nat Genet 2005, 37:225-232. 21. Mehrabian M, Allayee H, Stockton J, Lum PY, Drake TA, Castellani LW, Suh M, Armour C, Edwards S, Lamb J, Lusis AJ, Schadt EE: Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat Genet 2005, 37:1224-1233. 22. Liu G, Kim JJ, Jonas E, Wimmers K, Ponsuksili S, Murani E, Phatsara C, Tholen E, Jüngst H, Tesfaye D, Chen JL, Schellander K: Combined line-cross and half-sib QTL analysis in Duroc-Pietrain population. Mamm Genome 2008, 6:429-438. 23. Wimmers K, Murani E, Ponsuksili S: Functional genomics and genetical genomics approaches towards elucidating networks of genes affecting meat performance in pigs. Brief Funct Genomics 2010, 9:251-258. 24. Verdugo A, Farber CR, Warden CH, Medrano JF: Serious limitations of the QTL/microarray approach for QTL gene discovery. BMC Biology 2010, 8:96. 25. ZDS, Zentral Verband der Deutschen Schweineproduktion e. V: Richtlinie fuer die Stationspruefung auf Mastleistung, Schlachtkoerperwert und Fleischbeschaffenheit beim Schwein. Bonn, Germany 2003. 26. Honikel KO: Wasserbindungsvermögen von Fleisch. Mitteilungsblatt der BAFF 1986, 6:7150-7154. 27. Kauffman RG, Eikelenboom G, Wal van der PG, Merkus G, Zaar M: The use of filter paper to estimate drip loss of porcine musculature. Meat Sci 1986, 18:191-200. 28. Gene Expression Omnibus. [http://www.ncbi.nlm.nih.gov/geo/].