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Microsatellite markers with an average spacing of 3 Mb were selected from sequence traces of the cat 1.9\u00d7 whole genome sequence (WGS), including the pseudoautosomal region 1 (PAR1). Extreme variation in recombination rates (centimorgans per megabase) was observed along the X chromosome, ranging from a virtual absence of recombination events in a region estimated to be &amp;gt;30 Mb to recombination frequencies of 15.7 cM\/Mb in a segment estimated to be &amp;lt;0.3 Mb. This detailed linkage map was applied to position the X-linked orange gene, placing this locus on the q arm of the X chromosome, as opposed to a previously reported location on the p arm. Fine mapping placed the locus between markers at positions 106 and 116.8 Mb in the current 1.9\u00d7-coverage sequence assembly of the cat genome. Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level.<\/jats:p>","DOI":"10.1534\/genetics.108.095240","type":"journal-article","created":{"date-parts":[[2009,2,3]],"date-time":"2009-02-03T02:39:23Z","timestamp":1233628763000},"page":"1415-1425","source":"Crossref","is-referenced-by-count":31,"title":["A Domestic cat X Chromosome Linkage Map and the Sex-Linked<i>orange<\/i>Locus: Mapping of<i>orange<\/i>, Multiple Origins and Epistasis Over<i>nonagouti<\/i>"],"prefix":"10.1093","volume":"181","author":[{"given":"Anne","family":"Schmidt-Ku\u0308ntzel","sequence":"first","affiliation":[{"name":"Laboratory of Genomic Diversity , Science Applications International Corporation and"},{"name":"Genetics Department , George Washington University, Washington, DC 20037"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Nelson","sequence":"additional","affiliation":[{"name":"Laboratory of Genomic Diversity , Science Applications International Corporation and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor A","family":"David","sequence":"additional","affiliation":[{"name":"Laboratory of Genomic Diversity , National Cancer Institute, Frederick, Maryland 21702"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro A","family":"Scha\u0308ffer","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information , National Library of Medicine and Department of Health and Human Services, National Institutes of Health, Bethesda, Maryland 20894"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduardo","family":"Eizirik","sequence":"additional","affiliation":[{"name":"Laboratory of Genomic Diversity , National Cancer Institute, Frederick, Maryland 21702"},{"name":"Faculdade de Biocie\u0302ncias , Pontifica Universidade Cato\u0301lica do Rio Grande do Sul, Porto Alegre, RS-900, Brazil"},{"name":"Instituto Pro\u0301-Carnivoros, Atibaia , 12945-010, Brazil, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melody E","family":"Roelke","sequence":"additional","affiliation":[{"name":"Laboratory of Genomic Diversity , Science Applications International Corporation and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James S","family":"Kehler","sequence":"additional","affiliation":[{"name":"Laboratory of Genomic Diversity , National Cancer Institute, Frederick, Maryland 21702"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven S","family":"Hannah","sequence":"additional","affiliation":[{"name":"Nestle\u0301 Purina PetCare , Saint Louis, Missouri 63102"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen J","family":"O'Brien","sequence":"additional","affiliation":[{"name":"Laboratory of Genomic Diversity , National Cancer Institute, Frederick, Maryland 21702"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marilyn","family":"Menotti-Raymond","sequence":"additional","affiliation":[{"name":"Laboratory of Genomic Diversity , National Cancer Institute, Frederick, Maryland 21702"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2009,4,1]]},"reference":[{"key":"2023030705462757700_","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1590\/S0004-27302005000600019","volume":"49","year":"2005","journal-title":"Arq. 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