{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T07:26:42Z","timestamp":1789198002029,"version":"build-2803163510"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2014,3,1]],"date-time":"2014-03-01T00:00:00Z","timestamp":1393632000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Genetical genomics has been suggested as a powerful approach to study the genotype\u2013phenotype gap. However, the relatively low power of these experiments (usually related to the high cost) has hindered fulfillment of its promise, especially for loci (QTL) of moderate effects.One strategy with which to overcome the issue is to use a targeted approach. It has two clear advantages: (i) it reduces the problem to a simple comparison between different genotypic groups at the QTL and (ii) it is a good starting point from which to investigate downstream effects of the QTL. In this study, from 698 F2 birds used for QTL mapping, gene expression profiles of 24 birds with divergent homozygous QTL genotypes were investigated. The targeted QTL was on chromosome 1 and affected initial pH of breast muscle. The biological mechanisms controlling this trait can be similar to those affecting malignant hyperthermia or muscle fatigue in humans. The gene expression study identified 10 strong local signals that were markedly more significant compared to any genes on the rest of the genome. The differentially expressed genes all mapped to a region &amp;lt;1 Mb, suggesting a remarkable reduction of the QTL interval. These results, combined with analysis of downstream effect of the QTL using gene network analysis, suggest that the QTL is controlling pH by governing oxidative stress. The results were reproducible with use of as few as four microarrays on pooled samples (with lower significance level). The results demonstrate that this cost-effective approach is promising for characterization of QTL.<\/jats:p>","DOI":"10.1534\/genetics.113.160440","type":"journal-article","created":{"date-parts":[[2014,1,4]],"date-time":"2014-01-04T03:20:31Z","timestamp":1388805631000},"page":"867-874","source":"Crossref","is-referenced-by-count":9,"title":["An Expression QTL of Closely Linked Candidate Genes Affects pH of Meat in Chickens"],"prefix":"10.1093","volume":"196","author":[{"given":"Javad","family":"Nadaf","sequence":"first","affiliation":[{"name":"Institut National de la Recherche Agronomique, Recherches Avicoles, Nouzilly 37380, France"},{"name":"The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cecile","family":"Berri","sequence":"additional","affiliation":[{"name":"Institut National de la Recherche Agronomique, Recherches Avicoles, Nouzilly 37380, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian","family":"Dunn","sequence":"additional","affiliation":[{"name":"The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Estelle","family":"Godet","sequence":"additional","affiliation":[{"name":"Institut National de la Recherche Agronomique, Recherches Avicoles, Nouzilly 37380, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"Le Bihan-Duval","sequence":"additional","affiliation":[{"name":"Institut National de la Recherche Agronomique, Recherches Avicoles, Nouzilly 37380, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dirk Jan","family":"De Koning","sequence":"additional","affiliation":[{"name":"The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom"},{"name":"Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,3,1]]},"reference":[{"key":"2022011219430260400_bib1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing.","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. B"},{"key":"2022011219430260400_bib2","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1080\/00071660500303099","article-title":"Variations in chicken breast meat quality: implications of struggle and muscle glycogen content at death.","volume":"46","author":"Berri","year":"2005","journal-title":"Br. Poult. Sci."},{"key":"2022011219430260400_bib3","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1111\/j.1365-2052.2011.02223.x","article-title":"Complex traits analysis of chicken growth using targeted genetical genomics.","volume":"43","author":"Cabrera","year":"2012","journal-title":"Anim. Genet."},{"key":"2022011219430260400_bib4","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.bcp.2008.09.029","article-title":"Catalase and glutathione peroxidase mimics.","volume":"77","author":"Day","year":"2009","journal-title":"Biochem. Pharmacol."},{"key":"2022011219430260400_bib5","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/j.tig.2005.05.004","article-title":"Genetical genomics in humans and model organisms.","volume":"21","author":"De Koning","year":"2005","journal-title":"Trends Genet."},{"key":"2022011219430260400_bib6","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1093\/ps\/86.7.1501","article-title":"Genetical genomics: combining gene expression with marker genotypes in poultry.","volume":"86","author":"De Koning","year":"2007","journal-title":"Poult. Sci."},{"key":"2022011219430260400_bib7","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1080\/00071660500303032","article-title":"Behavioural and physiological responses of three chicken breeds to pre-slaughter shackling and acute heat stress.","volume":"46","author":"Debut","year":"2005","journal-title":"Br. Poult. Sci."},{"key":"2022011219430260400_bib8","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1152\/japplphysiol.00953.2007","article-title":"Muscle-derived ROS and thiol regulation in muscle fatigue.","volume":"104","author":"Ferreira","year":"2008","journal-title":"J. Appl. Physiol."},{"key":"2022011219430260400_bib9","doi-asserted-by":"crossref","first-page":"D48","DOI":"10.1093\/nar\/gks1236","article-title":"Ensembl 2013.","volume":"41","author":"Flicek","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2022011219430260400_bib10","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1126\/science.1862346","article-title":"Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia.","volume":"253","author":"Fujii","year":"1991","journal-title":"Science"},{"key":"2022011219430260400_bib34","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1038\/ng.141","article-title":"Distribution and Functional Impact of DNA Copy Number Variation in the Rat.","volume":"40","author":"Guryev","year":"2008","journal-title":"Nat Genet."},{"key":"2022011219430260400_bib11","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1093\/genetics\/136.3.1195","article-title":"Mapping quantitative trait loci in crosses between outbred lines using least squares.","volume":"136","author":"Haley","year":"1994","journal-title":"Genetics"},{"key":"2022011219430260400_bib12","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. Protoc."},{"key":"2022011219430260400_bib13","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1038\/86730","article-title":"Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer.","volume":"19","author":"Hughes","year":"2001","journal-title":"Nat. Biotechnol."},{"key":"2022011219430260400_bib14","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/S0168-9525(01)02310-1","article-title":"Genetical genomics: the added value from segregation.","volume":"17","author":"Jansen","year":"2001","journal-title":"Trends Genet."},{"key":"2022011219430260400_bib15","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1016\/S1096-4959(03)00290-2","article-title":"Cloning of bovine peroxiredoxins: gene expression in bovine tissues and amino acid sequence comparison with rat, mouse and primate peroxiredoxins.","volume":"136","author":"Leyens","year":"2003","journal-title":"Comp. Biochem. Physiol. B Biochem. Mol. Biol."},{"key":"2022011219430260400_bib16","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/1471-2164-9-60","article-title":"Characterization of a newly developed chicken 44K Agilent microarray.","volume":"9","author":"Li","year":"2008","journal-title":"BMC Genomics"},{"key":"2022011219430260400_bib17","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/hdy.1997.57","article-title":"Comparison of several confidence intervals for QTL location.","volume":"78","author":"Mangin","year":"1997","journal-title":"Heredity"},{"key":"2022011219430260400_bib18","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/1471-2164-8-155","article-title":"Identification of QTL controlling meat quality traits in an F2 cross between two chicken lines selected for either low or high growth rate.","volume":"8","author":"Nadaf","year":"2007","journal-title":"BMC Genomics"},{"key":"2022011219430260400_bib19","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1152\/physiolgenomics.90384.2008","article-title":"QTL for several metabolic traits map to loci controlling growth and body composition in an F2 intercross between high-and low-growth chicken lines.","volume":"38","author":"Nadaf","year":"2009","journal-title":"Physiol. Genomics"},{"key":"2022011219430260400_bib20","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/S1043-6618(05)80116-1","article-title":"Exogenous glutathione increases endurance to muscle effort in mice.","volume":"23","author":"Novelli","year":"1991","journal-title":"Pharmacol. Res."},{"key":"2022011219430260400_bib21","doi-asserted-by":"crossref","first-page":"e45","DOI":"10.1093\/nar\/29.9.e45","article-title":"A new mathematical model for relative quantification in real-time RT\u2013PCR.","volume":"29","author":"Pfaffl","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2022011219430260400_bib22","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1016\/S0006-291X(02)00268-1","article-title":"Regulation of protein phosphatase 2A by hydrogen peroxide and glutathionylation.","volume":"293","author":"Rao","year":"2002","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2022011219430260400_bib23","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1186\/1471-2105-7-261","article-title":"Empirical array quality weights in the analysis of microarray data.","volume":"7","author":"Ritchie","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2022011219430260400_bib24","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1111\/j.1365-2052.2007.01640.x","article-title":"From QTL to QTN identification in livestock\u2013winning by points rather than knock-out: a review.","volume":"38","author":"Ron","year":"2007","journal-title":"Anim. Genet."},{"key":"2022011219430260400_bib25","volume-title":"SAS\/STAT User\u2019s Guide, version 8","author":"SAS","year":"1999"},{"key":"2022011219430260400_bib26"},{"key":"2022011219430260400_bib27","doi-asserted-by":"crossref","first-page":"2888","DOI":"10.2527\/jas.2008-1062","article-title":"Adenosine monophosphate-activated protein kinase involved in variations of muscle glycogen and breast meat quality between lean and fat chickens.","volume":"86","author":"Sibut","year":"2008","journal-title":"J. Anim. Sci."},{"key":"2022011219430260400_bib28","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1007\/0-387-29362-0_23","article-title":"Limma: linear models for microarray data","volume-title":"Bioinformatics and Computational Biology Solutions Using R and Bioconductor","author":"Smyth","year":"2005"},{"key":"2022011219430260400_bib29","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/S1046-2023(03)00155-5","article-title":"Normalization of cDNA microarray data.","volume":"31","author":"Smyth","year":"2003","journal-title":"Methods"},{"key":"2022011219430260400_bib30","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1111\/j.1745-4514.2003.tb00285.x","article-title":"Phospholipase A2 activity in poultry PSE, pale, soft, exudative, meat.","volume":"27","author":"Soares A. L.","year":"2003","journal-title":"J. Food Biochem."},{"key":"2022011219430260400_bib31"},{"key":"2022011219430260400_bib32","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1038\/nprot.2009.177","article-title":"Network visualization and analysis of gene expression data using BioLayout Express3D.","volume":"4","author":"Theocharidis","year":"2009","journal-title":"Nat. Protoc."},{"key":"2022011219430260400_bib33","first-page":"1","article-title":"A cluster algorithm for graphs. Report","volume":"10","author":"Van Dongen","year":"2000","journal-title":"Inf. Syst."}],"container-title":["Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/genetics\/article-pdf\/196\/3\/867\/42115780\/genetics0867.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/genetics\/article-pdf\/196\/3\/867\/42115780\/genetics0867.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T14:41:51Z","timestamp":1716388911000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/genetics\/article\/196\/3\/867\/5935682"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,3,1]]},"references-count":34,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2014,3,1]]},"published-print":{"date-parts":[[2014,3,1]]}},"URL":"https:\/\/doi.org\/10.1534\/genetics.113.160440","relation":{},"ISSN":["1943-2631"],"issn-type":[{"value":"1943-2631","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2014,3,1]]},"published":{"date-parts":[[2014,3,1]]}}}