{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T00:41:15Z","timestamp":1778805675033,"version":"3.51.4"},"reference-count":63,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2020,8,21]],"date-time":"2020-08-21T00:00:00Z","timestamp":1597968000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"DOI":"10.3389\/fgene.2020.00901","type":"journal-article","created":{"date-parts":[[2020,8,21]],"date-time":"2020-08-21T12:52:17Z","timestamp":1598014337000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":24,"title":["Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus)"],"prefix":"10.3389","volume":"11","author":[{"given":"Jun","family":"Gao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuhua","family":"Lyu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Defu","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kiran Kumar","family":"Reddi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fengping","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianzhong","family":"Yi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengqian","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huijuan","family":"Yao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianjun","family":"Dai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fuyi","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2020,8,21]]},"reference":[{"key":"B1","doi-asserted-by":"crossref","DOI":"10.1186\/s12711-015-0112-x","article-title":"A missense mutation in the agouti signaling protein gene (ASIP) is associated with the no light points coat phenotype in donkeys.","volume":"47","author":"Abitbol","year":"2015","journal-title":"Genet. Select. Evol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1038\/1689","article-title":"A gene related to Caenorhabditis elegans spermatogenesis factor fer-1 is mutated in limb-girdle muscular dystrophy type 2B.","volume":"20","author":"Bashir","year":"1998","journal-title":"Nat. Genet."},{"key":"B3","doi-asserted-by":"publisher","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. Statist. Soc. Ser. B"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2015.00107","article-title":"Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.","volume":"6","author":"Benjelloun","year":"2015","journal-title":"Front. Genet."},{"key":"B5","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/B978-0-12-809841-7.00010-1","article-title":"Skeletal muscle system","author":"Berridge","year":"2018","journal-title":"Fundamentals of Toxicologic Pathology"},{"key":"B6","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1038\/ng.3802","article-title":"Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.","volume":"49","author":"Bickhart","year":"2017","journal-title":"Nat. Genet."},{"key":"B7","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/13770","article-title":"Dysferlin deletion in SJL mice (SJL-Dysf) defines a natural model for limb girdle muscular dystrophy 2B.","volume":"23","author":"Bittner","year":"1999","journal-title":"Nat. Genet."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-3610-0","article-title":"Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers.","volume":"18","author":"Brito","year":"2017","journal-title":"BMC Genom."},{"key":"B9","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1126\/science.1253714","article-title":"Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.","volume":"345","author":"Carneiro","year":"2014","journal-title":"Science"},{"key":"B10","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1038\/nmeth.1363","article-title":"BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.","volume":"6","author":"Chen","year":"2009","journal-title":"Nat. Methods"},{"key":"B11","doi-asserted-by":"publisher","first-page":"4295","DOI":"10.1210\/endo.141.11.7765","article-title":"Estrogen deficiency, obesity, and skeletal abnormalities in follicle-stimulating hormone receptor knockout (FORKO) female mice.","volume":"141","author":"Danilovich","year":"2000","journal-title":"Endocrinology"},{"key":"B12","doi-asserted-by":"publisher","first-page":"5053","DOI":"10.1007\/s11033-014-3371-7","article-title":"Association of the UCP polymorphisms with susceptibility to obesity: case-control study and meta-analysis.","volume":"41","author":"de Almeida Brondani","year":"2014","journal-title":"Mol. Biol. Rep."},{"key":"B13","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1093\/jhered\/est012","article-title":"Identification of a mutation that is associated with the saddle tan and black-and-tan phenotypes in Basset Hounds and Pembroke Welsh Corgis.","volume":"104","author":"Dreger","year":"2013","journal-title":"J. Hered."},{"key":"B14","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1016\/s0960-9822(03)00128-3","article-title":"Molecular genetics and evolution of melanism in the cat family.","volume":"13","author":"Eizirik","year":"2003","journal-title":"Curr. Biol."},{"key":"B15","doi-asserted-by":"crossref","first-page":"D471","DOI":"10.1093\/nar\/gki113","article-title":"The mouse genome database (MGD): from genes to mice\u2014a community resource for mouse biology.","volume":"33","author":"Eppig","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"B16","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.ygeno.2009.11.003","article-title":"Characterization of the rabbit agouti signaling protein (ASIP) gene: transcripts and phylogenetic analyses and identification of the causative mutation of the nonagouti black coat colour.","volume":"95","author":"Fontanesi","year":"2010","journal-title":"Genomics"},{"key":"B17","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1534\/genetics.110.114397","article-title":"The next generation of molecular markers from massively parallel sequencing of pooled DNA samples.","volume":"186","author":"Futschik","year":"2010","journal-title":"Genetics"},{"key":"B18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-28719-w","article-title":"Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds.","volume":"8","author":"Guo","year":"2018","journal-title":"Sci. Rep."},{"key":"B19","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1111\/j.1365-2052.2008.01708.x","article-title":"Characterization of the porcine KIT ligand gene: expression analysis, genomic structure, polymorphism detection and association with coat colour traits.","volume":"39","author":"Hadjiconstantouras","year":"2008","journal-title":"Anim. Genet."},{"key":"B20","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1534\/genetics.118.300900","article-title":"Measuring genetic differentiation from Pool-seq data.","volume":"210","author":"Hivert","year":"2018","journal-title":"Genetics"},{"key":"B21","first-page":"2993","article-title":"A modified goat model of acute spinal cord compression injury from a percutaneous balloon catheter: method feasibility and preliminary observation.","volume":"93","author":"Huang","year":"2013","journal-title":"Zhonghua Yi Xue Za Zhi"},{"key":"B22","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1016\/j.ajhg.2011.04.019","article-title":"Adaptor protein complex 4 deficiency causes severe autosomal-recessive intellectual disability, progressive spastic paraplegia, shy character, and short stature.","volume":"88","author":"Jamra","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"B23","doi-asserted-by":"publisher","first-page":"798","DOI":"10.1007\/s00335-004-2377-1","article-title":"Characterization of the dog Agouti gene and a nonagoutimutation in German Shepherd Dogs.","volume":"15","author":"Kerns","year":"2004","journal-title":"Mammal. Genome"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2015.00699","article-title":"Discovery of genomic characteristics and selection signatures in korean indigenous goats through comparison of 10 goat breeds.","volume":"10","author":"Kim","year":"2019","journal-title":"Front. Genet."},{"key":"B25","doi-asserted-by":"publisher","first-page":"3435","DOI":"10.1093\/bioinformatics\/btr589","article-title":"PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).","volume":"27","author":"Kofler","year":"2011","journal-title":"Bioinformatics"},{"key":"B26","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1016\/j.talanta.2010.01.032","article-title":"Development of a fast and efficient ultrasonic-based strategy for DNA fragmentation.","volume":"81","author":"Larguinho","year":"2010","journal-title":"Talanta"},{"key":"B27","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform.","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B28","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools.","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-3610-863","article-title":"Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions.","volume":"17","author":"Liu","year":"2016","journal-title":"BMC Genom."},{"key":"B30","article-title":"Boer goat production: progress and perspective","author":"Lu","year":"2001","journal-title":"Proceedings of the 2001 International Conference on Boer Goats in China"},{"key":"B31","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/s0921-4488(99)00160-1","article-title":"The improved boer goat.","volume":"36","author":"Malan","year":"2000","journal-title":"Small Ruminant Res."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"B33","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-016-0974-4","article-title":"The ensembl variant effect predictor.","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1016\/j.cell.2007.10.055","article-title":"cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans.","volume":"131","author":"Miller","year":"2007","journal-title":"Cell"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.3390\/d12010020","article-title":"Sustainable utilization of indigenous goats in Southern Africa.","volume":"12","author":"Monau","year":"2020","journal-title":"Diversity"},{"key":"B36","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1136\/jmg.2010.082263","article-title":"Adaptor protein complex-4 (AP-4) deficiency causes a novel autosomal recessive cerebral palsy syndrome with microcephaly and intellectual disability.","volume":"48","author":"Moreno-De-Luca","year":"2011","journal-title":"J. Med. Genet."},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1016\/j.nut.2003.09.024","article-title":"Role of UCP2 and UCP3 in nutrition and obesity.","volume":"20","author":"Nagy","year":"2004","journal-title":"Nutrition"},{"key":"B38","doi-asserted-by":"publisher","first-page":"1282","DOI":"10.1101\/gr.072090.107","article-title":"A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep.","volume":"18","author":"Norris","year":"2008","journal-title":"Genome Res."},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0171845","article-title":"Genomic regions associated with feed efficiency indicator traits in an experimental Nellore cattle population.","volume":"11","author":"Olivieri","year":"2016","journal-title":"PLoS One"},{"key":"B40","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1007\/s40291-016-0218-z","article-title":"Follicle-stimulating hormone receptor (FSHR): a promising tool in oncology?","volume":"20","author":"Papadimitriou","year":"2016","journal-title":"Mol. Diagn. Ther."},{"key":"B41","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1038\/ng.3609","article-title":"Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice.","volume":"48","author":"Parker","year":"2016","journal-title":"Nat. Genet."},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0036346","article-title":"Identification of QTL for UV-protective eye area pigmentation in cattle by progeny phenotyping and genome-wide association analysis.","volume":"7","author":"Pausch","year":"2012","journal-title":"PLoS One"},{"key":"B43","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses.","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"B44","year":"2013","journal-title":"R: A Language And Environment for Statistical Computing."},{"key":"B45","doi-asserted-by":"crossref","first-page":"W191","DOI":"10.1093\/nar\/gkz369","article-title":"g: Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).","volume":"47","author":"Raudvere","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B46","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1007\/s003350020017","article-title":"Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus).","volume":"12","author":"Rieder","year":"2001","journal-title":"Mammal. Genome"},{"key":"B47","doi-asserted-by":"publisher","first-page":"19529","DOI":"10.1073\/pnas.1217149109","article-title":"Strong signatures of selection in the domestic pig genome.","volume":"109","author":"Rubin","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B48","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nature08832","article-title":"Whole-genome resequencing reveals loci under selection during chicken domestication.","volume":"464","author":"Rubin","year":"2010","journal-title":"Nature"},{"key":"B49","doi-asserted-by":"crossref","first-page":"W452","DOI":"10.1093\/nar\/gks539","article-title":"SIFT web server: predicting effects of amino acid substitutions on proteins.","volume":"40","author":"Sim","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B50","article-title":"Goat production in the World: present situation and trends.","volume":"28","author":"Skapetas","year":"2016","journal-title":"Livest Res. Rural Dev."},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-016-2449-0","article-title":"Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus).","volume":"17","author":"Song","year":"2016","journal-title":"BMC Genomics"},{"key":"B52","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1002\/ana.21309","article-title":"Dysferlin-deficient muscular dystrophy features amyloidosis.","volume":"63","author":"Spuler","year":"2008","journal-title":"Ann. Neurol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"1443","DOI":"10.1038\/ng.2007.13","article-title":"Genetic determinants of hair, eye and skin pigmentation in Europeans.","volume":"39","author":"Sulem","year":"2007","journal-title":"Nat. Genet."},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0123380","article-title":"Global developmental gene programing involves a nuclear form of fibroblast growth factor receptor-1 (FGFR1).","volume":"10","author":"Terranova","year":"2015","journal-title":"PLoS One"},{"key":"B55","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1016\/s0307-4412(97)00122-2","article-title":"A fast CTAB method of human DNA isolation for polymerase chain reaction applications.","volume":"25","author":"Thomas","year":"1997","journal-title":"Biochem. Educ."},{"key":"B56","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1034\/j.1600-0749.2002.00039.x","article-title":"Agouti: from mouse to man, from skin to fat.","volume":"15","author":"Voisey","year":"2002","journal-title":"Pigment Cell Res."},{"key":"B57","article-title":"Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits.","volume":"6","author":"Wang","year":"2016","journal-title":"Sci. Rep."},{"key":"B58","doi-asserted-by":"publisher","first-page":"1358","DOI":"10.1111\/j.1558-5646.1984.tb05657.x","article-title":"Estimating F-statistics for the analysis of population structure.","volume":"38","author":"Weir","year":"1984","journal-title":"Evolution"},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2015.00095","article-title":"Melanocortin 1 receptor: structure, function, and regulation.","volume":"7","author":"Wolf Horrell","year":"2016","journal-title":"Front. Genet."},{"key":"B60","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-33078-7","article-title":"Landscape of alternative splicing in Capra_hircus.","volume":"8","author":"Xu","year":"2018","journal-title":"Sci. Rep."},{"key":"B61","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1111\/brv.12265","article-title":"Molecular identification of livestock breeds: a tool for modern conservation biology.","volume":"92","author":"Yaro","year":"2017","journal-title":"Biol. Rev."},{"key":"B62","doi-asserted-by":"publisher","first-page":"1042","DOI":"10.1002\/humu.24001","article-title":"ZMYND11-related syndromic intellectual disability: 16 patients delineating and expanding the phenotypic spectrum.","volume":"41","author":"Yates","year":"2020","journal-title":"Hum. Mutat."},{"key":"B63","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1080\/10495398.2013.790824","article-title":"Comparative messenger RNA expression of FSH\u03b2, LH\u03b2, FSHR, LHR, and ER\u03b2 in high and low prolific goat breeds.","volume":"24","author":"Zi","year":"2013","journal-title":"Anim. Biotechnol."}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2020.00901\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,21]],"date-time":"2020-08-21T12:52:34Z","timestamp":1598014354000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2020.00901\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,8,21]]},"references-count":63,"alternative-id":["10.3389\/fgene.2020.00901"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2020.00901","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,8,21]]},"article-number":"901"}}