{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T12:44:04Z","timestamp":1791549844778,"version":"4.3.4"},"reference-count":58,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2016,2,9]],"date-time":"2016-02-09T00:00:00Z","timestamp":1454976000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0149010","type":"journal-article","created":{"date-parts":[[2016,2,9]],"date-time":"2016-02-09T18:44:57Z","timestamp":1455043497000},"page":"e0149010","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Parallel Evolution of Polydactyly Traits in Chinese and European Chickens"],"prefix":"10.1371","volume":"11","author":[{"given":"Zebin","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changsheng","family":"Nie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaxiong","family":"Jia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Runshen","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haijian","family":"Xia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueze","family":"Lv","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junying","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianyao","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhonghua","family":"Ning","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guiyun","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jilan","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ning","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lujiang","family":"Qu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2016,2,9]]},"reference":[{"issue":"7018","key":"ref1","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/nature03154","article-title":"Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution","volume":"432","author":"W LaDeana","year":"2004","journal-title":"Nature"},{"issue":"8","key":"ref2","doi-asserted-by":"crossref","first-page":"e104652","DOI":"10.1371\/journal.pone.0104652","article-title":"Genome-wide characterization of insertion and deletion variation in chicken using next generation sequencing","volume":"9","author":"Y Yan","year":"2014","journal-title":"PloS One"},{"key":"ref3","first-page":"15","article-title":"Use of chicken models for the analysis of human disease","volume":"15","author":"JB Dodgson","year":"2004","journal-title":"Curr Protoc Hum Genet"},{"issue":"1","key":"ref4","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1006\/geno.2000.6225","article-title":"A novel candidate gene for mouse and human preaxial polydactyly with altered expression in limbs of Hemimelic extra-toes mutant mice","volume":"67","author":"RM Clark","year":"2000","journal-title":"Genomics"},{"issue":"1","key":"ref5","doi-asserted-by":"crossref","first-page":"e54454","DOI":"10.1371\/journal.pone.0054454","article-title":"Sod1 deficiency reduces incubation time in mouse models of prion disease","volume":"8","author":"S Akhtar","year":"2013","journal-title":"PLoS One"},{"issue":"7","key":"ref6","doi-asserted-by":"crossref","first-page":"1401","DOI":"10.1016\/0092-8674(93)90626-2","article-title":"Sonic hedgehog mediates the polarizing activity of the ZPA","volume":"75","author":"RD Riddle","year":"1993","journal-title":"Cell"},{"issue":"5\u20136","key":"ref7","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/j.mod.2008.01.001","article-title":"Polydactyly in the mouse mutant Doublefoot involves altered Gli3 processing and is caused by a large deletion in cis to Indian hedgehog","volume":"125","author":"C Babbs","year":"2008","journal-title":"Mech Develop"},{"key":"ref8","first-page":"117","article-title":"Essential mathematical biology","author":"NF Britton","year":"2003"},{"issue":"3","key":"ref9","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1093\/genetics\/29.3.217","article-title":"Inheritance of polydactylism in the fowl","volume":"29","author":"DC Warren","year":"1944","journal-title":"Genetics"},{"issue":"1","key":"ref10","first-page":"32","article-title":"Clinical and genetic studies on 12 preaxial polydactyly families and refinement of the localisation of the gene responsible to a 1.9 cM region on chromosome 7q36","volume":"36","author":"J Zguricas","year":"1999","journal-title":"J Med Genet"},{"issue":"14","key":"ref11","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.1093\/hmg\/ddg180","article-title":"A long-range <italic>SHH<\/italic> enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly","volume":"12","author":"LA Lettice","year":"2003","journal-title":"Hum Mol Genet"},{"issue":"16","key":"ref12","doi-asserted-by":"crossref","first-page":"3123","DOI":"10.1242\/dev.125.16.3123","article-title":"Evidence that preaxial polydactyly in the Doublefoot mutant is due to ectopic Indian Hedgehog signaling","volume":"125","author":"Y Yang","year":"1998","journal-title":"Development"},{"issue":"3","key":"ref13","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1002\/dvdy.10502","article-title":"Isolation of the chicken <italic>LMBR1<\/italic> coding sequence and characterization of its role during chick limb development","volume":"229","author":"SA Maas","year":"2004","journal-title":"Dev Dyn"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0070-2153(03)53002-2","article-title":"Developmental roles and clinical significance of hedgehog signaling","volume":"53","author":"AP McMahon","year":"2003","journal-title":"Curr Top Dev Biol"},{"issue":"3","key":"ref15","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1093\/jhered\/esp120","article-title":"Genomic regions associated with dermal hyperpigmentation, polydactyly and other morphological traits in the silkie chicken","volume":"101","author":"B Dorshorst","year":"2010","journal-title":"J Hered"},{"issue":"11","key":"ref16","doi-asserted-by":"crossref","first-page":"7548","DOI":"10.1073\/pnas.112212199","article-title":"Disruption of a long-range cis-acting regulator for <italic>SHH<\/italic> causes preaxial polydactyly","volume":"99","author":"LA Lettice","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"ref17","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1101\/gr.142200","article-title":"Active conservation of noncoding sequences revealed by three-way species comparisons","volume":"10","author":"I Dubchak","year":"2000","journal-title":"Genome Res"},{"issue":"11","key":"ref18","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1093\/bioinformatics\/16.11.1046","article-title":"VISTA: visualizing global DNA sequence alignments of arbitrary length","volume":"16","author":"C Mayor","year":"2000","journal-title":"Bioinformatics"},{"issue":"7A","key":"ref19","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1101\/gad.7.7a.1277","article-title":"The regulation of myogenin gene expression during the embryonic development of the mouse","volume":"7","author":"SP Yee","year":"1993","journal-title":"Genes Dev"},{"issue":"4","key":"ref20","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/0168-9525(96)10018-4","article-title":"Small is beautiful: comparative genomics with the pufferfish (<italic>Fugu rubripes<\/italic>)","volume":"12","author":"G Elgar","year":"1996","journal-title":"Trends Genet"},{"issue":"1","key":"ref21","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1002\/ajmg.a.31563","article-title":"Two novel point mutations in the long-range <italic>SHH<\/italic> enhancer in three families with triphalangeal thumb and preaxial polydactyly","volume":"143A","author":"CA Gurnett","year":"2007","journal-title":"Am J Med Genet"},{"issue":"4","key":"ref22","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1111\/cge.12352","article-title":"Microduplications encompassing the Sonic hedgehog limb enhancer ZRS are associated with Haas-type polysyndactyly and Laurin-Sandrow syndrome","volume":"86","author":"S Lohan","year":"2014","journal-title":"Clin Genet"},{"issue":"2","key":"ref23","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.ydbio.2014.05.025","article-title":"Direct functional consequences of ZRS enhancer mutation combine with secondary long range <italic>SHH<\/italic> signalling effects to cause preaxial polydactyly","volume":"392","author":"EJ Johnson","year":"2014","journal-title":"Dev Biol"},{"issue":"8","key":"ref24","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1002\/humu.22581","article-title":"A novel ZRS mutation leads to preaxial polydactyly type 2 in a heterozygous form and Werner Mesomelic Syndrome in a homozygous form","volume":"35","author":"JE VanderMeer","year":"2014","journal-title":"Hum Mutat"},{"issue":"4","key":"ref25","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1002\/ajmg.a.36367","article-title":"A novel mutation (g.106737G &gt; T) in zone of polarizing activity regulatory sequence (ZRS) causes variable limb phenotypes in Werner mesomelia","volume":"164","author":"KM Girisha","year":"2014","journal-title":"Am J Med Genet"},{"issue":"5","key":"ref26","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1002\/dvdy.22623","article-title":"The chicken polydactyly (Po) locus causes allelic imbalance and ectopic expression of <italic>SHH<\/italic> during limb development","volume":"240","author":"IC Dunn","year":"2011","journal-title":"Dev Dynam"},{"issue":"4","key":"ref27","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1111\/j.1399-0004.2010.01465.x","article-title":"Identification of two novel mutations in <italic>SHH<\/italic> long-range regulator associated with familial pre-axial polydactyly","volume":"79","author":"J Albuisson","year":"2011","journal-title":"Clin Genet"},{"issue":"1","key":"ref28","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.ydbio.2009.07.009","article-title":"Aberrant FGF signaling, independent of ectopic hedgehog signaling, initiates preaxial polydactyly in Dorking chickens","volume":"334","author":"CM Bouldin","year":"2009","journal-title":"Dev Biol"},{"issue":"6","key":"ref29","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1534\/g3.114.011338","article-title":"Genome-wide linkage analysis and association study identifies loci for polydactyly in chickens","volume":"4","author":"Y Sun","year":"2014","journal-title":"G3 (Bethesda)"},{"issue":"2","key":"ref30","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.gene.2015.05.049","article-title":"The identification of loci for polydactyly in chickens using a genome-wide association study","volume":"568","author":"X Sheng","year":"2015","journal-title":"Gene"},{"issue":"1","key":"ref31","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1111\/j.1365-2052.2012.02369.x","article-title":"Polydactyly mutation is linked with chromosome 2p region in Beijing fatty chicken","volume":"44","author":"K Yang","year":"2013","journal-title":"Anim Genet"},{"issue":"4","key":"ref32","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1007\/s11427-006-2001-6","article-title":"Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers","volume":"49","author":"L Qu","year":"2006","journal-title":"Sci China C Life Sci"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/1471-2164-14-59","article-title":"Development of a high density 600K SNP genotyping array for chicken","volume":"14","author":"A Kranis","year":"2013","journal-title":"BMC Genomics"},{"issue":"5","key":"ref34","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1007\/s10519-009-9281-0","article-title":"Rank-based inverse normal transformations are increasingly used, but are they merited?","volume":"39","author":"TM Beasley","year":"2009","journal-title":"Behav Genet"},{"issue":"1","key":"ref35","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1002\/gepi.20430","article-title":"Avoiding the high Bonferroni penalty in genome-wide association studies","volume":"34","author":"X Gao","year":"2010","journal-title":"Genet Epidemiol"},{"issue":"7","key":"ref36","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/ng.2310","article-title":"Genome-wide efficient mixed-model analysis for association studies","volume":"44","author":"X Zhou","year":"2012","journal-title":"Nat Genet"},{"key":"ref37","article-title":"Animal genetic resources in China poultry","year":"2010"},{"key":"ref38","year":"1998"},{"issue":"10","key":"ref39","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1242\/dev.032714","article-title":"A cluster of three long-range enhancers directs regional <italic>SHH<\/italic> expression in the epithelial linings","volume":"136","author":"T Sagai","year":"2009","journal-title":"Development"},{"issue":"20","key":"ref40","doi-asserted-by":"crossref","first-page":"3934","DOI":"10.1242\/dev.108480","article-title":"Mapping the <italic>SHH<\/italic> long-range regulatory domain","volume":"141","author":"E Anderson","year":"2014","journal-title":"Development"},{"issue":"1","key":"ref41","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1006\/geno.1995.1104","article-title":"Cloning, expression, and chromosomal location of <italic>SHH<\/italic> and IHH: two human homologues of the Drosophila segment polarity gene hedgehog","volume":"28","author":"V Marigo","year":"1995","journal-title":"Genomics"},{"issue":"12","key":"ref42","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nrg2681","article-title":"Vertebrate limb bud development: moving towards integrative analysis of organogenesis","volume":"10","author":"R Zeller","year":"2009","journal-title":"Nat Rev Genet"},{"issue":"4","key":"ref43","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/j.cell.2004.07.024","article-title":"Evidence for an expansion-based temporal <italic>SHH<\/italic> gradient in specifying vertebrate digit identities","volume":"118","author":"BD Harfe","year":"2004","journal-title":"Cell"},{"issue":"1","key":"ref44","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/S0925-4773(98)00090-2","article-title":"Alteration of limb and brain patterning in early mouse embryos by ultrasound-guided injection of <italic>SHH<\/italic>-expressing cells","volume":"75","author":"A Liu","year":"1998","journal-title":"Mech Develop"},{"issue":"2","key":"ref45","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1016\/j.bbrc.2007.01.129","article-title":"A single C to T transition in intron 5 of <italic>LMBR1<\/italic> gene is associated with triphalangeal thumb-polysyndactyly syndrome in a Chinese family","volume":"355","author":"Z Wang","year":"2007","journal-title":"Biochem Bioph Res Co"},{"issue":"1","key":"ref46","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1086\/316955","article-title":"Acheiropodia is caused by a genomic deletion in C7orf2, the human orthologue of the <italic>LMBR1<\/italic> gene","volume":"68","author":"P Ianakiev","year":"2001","journal-title":"Am J Hum Genet"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.gene.2005.07.047","article-title":"Single nucleotide polymorphisms in the chicken <italic>LMBR1<\/italic> gene are associated with chicken polydactyly","volume":"374","author":"YQ Huang","year":"2006","journal-title":"Gene"},{"issue":"5","key":"ref48","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1038\/ejhg.2008.240","article-title":"Mutation analysis of a large Chinese pedigree with congenital preaxial polydactyly","volume":"17","author":"H Li","year":"2009","journal-title":"Eur J Hum Genet"},{"issue":"2","key":"ref49","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1016\/j.bbrc.2007.01.129","article-title":"A single C to T transition in intron 5 of <italic>LMBR1<\/italic> gene is associated with triphalangeal thumb-polysyndactyly syndrome in a Chinese family","volume":"355","author":"ZQ Wang","year":"2007","journal-title":"Biochem Bioph Res Co"},{"issue":"12","key":"ref50","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1016\/j.ejmg.2013.09.011","article-title":"Novel <italic>MNX1<\/italic> mutations and clinical analysis of familial and sporadic Currarino cases","volume":"56","author":"E Merello","year":"2013","journal-title":"Eur J Med Genet"},{"issue":"1","key":"ref51","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.cmet.2013.11.021","article-title":"Analysis of transcription factors key for mouse pancreatic development establishes NKX2-2 and <italic>MNX1<\/italic> mutations as causes of neonatal diabetes in man","volume":"19","author":"SE Flanagan","year":"2014","journal-title":"Cell Metab"},{"issue":"5","key":"ref52","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1016\/0022-3468(74)90107-9","article-title":"Hereditary presacral teratoma","volume":"9","author":"KW Ashcraft","year":"1974","journal-title":"J Pediatr Surg"},{"issue":"3","key":"ref53","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1055\/s-2007-965121","article-title":"Hereditary sacrococcygeal teratoma\u2014not the same as its sporadic counterpart!","volume":"17","author":"M Gopal","year":"2007","journal-title":"Eur J Pediatr Surg"},{"issue":"1","key":"ref54","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1086\/302723","article-title":"Involvement of the <italic>HLXB9<\/italic> homeobox gene in Currarino syndrome","volume":"66","author":"E Belloni","year":"2000","journal-title":"Am J Hum Genet"},{"issue":"48","key":"ref55","doi-asserted-by":"crossref","first-page":"19529","DOI":"10.1073\/pnas.1217149109","article-title":"Strong signatures of selection in the domestic pig genome","volume":"109","author":"CJ Rubin","year":"2012","journal-title":"Proc Nat Acad Sci USA"},{"issue":"8","key":"ref56","doi-asserted-by":"crossref","first-page":"e71393","DOI":"10.1371\/journal.pone.0071393","article-title":"Endogenous Retrovirus EAV-HP Linked to Blue Egg Phenotype in Mapuche Fowl","volume":"8","author":"D Wragg","year":"2013","journal-title":"PLoS ONE"},{"issue":"1","key":"ref57","doi-asserted-by":"crossref","first-page":"e1003183","DOI":"10.1371\/journal.pgen.1003183","article-title":"An EAV-HP insertion in 5\u2032 flanking region of SLCO1B3 causes blue eggshell in the chicken","volume":"9","author":"Z Wang","year":"2013","journal-title":"PLoS Genet"},{"issue":"1","key":"ref58","doi-asserted-by":"crossref","first-page":"e1000341","DOI":"10.1371\/journal.pgen.1000341","article-title":"Contrasting mode of evolution at a coat color locus in wild and domestic pigs","volume":"5","author":"M Fang","year":"2009","journal-title":"PLoS Genet"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0149010","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,14]],"date-time":"2024-06-14T08:03:18Z","timestamp":1718352198000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0149010"}},"subtitle":[],"editor":[{"given":"Jian-Feng","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,2,9]]},"references-count":58,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2016,2,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0149010","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,2,9]]}}}