Genome-wide association mapping and identification of candidate genes for the rumpless and ear-tufted traits of the Araucana chicken
Araucana chickens are known for their rounded, tailless rumps and tufted ears. Inheritance studies have shown that the rumpless (Rp) and ear-tufted (Et) loci each act in an autosomal dominant fashion, segregate independently, and are associated with an increased rate of embryonic mortality. To find...
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| description | Araucana chickens are known for their rounded, tailless rumps and tufted ears. Inheritance studies have shown that the rumpless (Rp) and ear-tufted (Et) loci each act in an autosomal dominant fashion, segregate independently, and are associated with an increased rate of embryonic mortality. To find genomic regions associated with Rp and Et, we generated genome-wide SNP profiles for a diverse population of 60 Araucana chickens using the 60 K chicken SNP BeadChip. Genome-wide association studies using 40 rumpless and 11 tailed birds showed a strong association with rumpless on Gga 2 (P(raw) = 2.45×10(-10), P(genome) = 0.00575), and analysis of genotypes revealed a 2.14 Mb haplotype shared by all rumpless birds. Within this haplotype, a 0.74 Mb critical interval containing two Iroquois homeobox genes, Irx1 and Irx2, was unique to rumpless Araucana chickens. Irx1 and Irx2 are central for developmental prepatterning, but neither gene is known to have a role in mechanisms leading to caudal development. A second genome-wide association analysis using 30 ear-tufted and 28 non-tufted birds revealed an association with tufted on Gga 15 (P(raw) = 6.61×10(-7), P(genome) = 0.0981). We identified a 0.58 Mb haplotype common to tufted birds and harboring 7 genes. Because homozygosity for Et is nearly 100% lethal, we employed a heterozygosity mapping approach to prioritize candidate gene selection. A 60 kb region heterozygous in all Araucana chickens contains the complete coding sequence for TBX1 and partial sequence for GNB1L. TBX1 is an important transcriptional regulator of embryonic development and a key genetic determinant of human DiGeorge syndrome. Herein, we describe localization of Rp and Et and identification of positional candidate genes. |
| doi_str_mv | 10.1371/journal.pone.0040974 |
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Inheritance studies have shown that the rumpless (Rp) and ear-tufted (Et) loci each act in an autosomal dominant fashion, segregate independently, and are associated with an increased rate of embryonic mortality. To find genomic regions associated with Rp and Et, we generated genome-wide SNP profiles for a diverse population of 60 Araucana chickens using the 60 K chicken SNP BeadChip. Genome-wide association studies using 40 rumpless and 11 tailed birds showed a strong association with rumpless on Gga 2 (P(raw) = 2.45×10(-10), P(genome) = 0.00575), and analysis of genotypes revealed a 2.14 Mb haplotype shared by all rumpless birds. Within this haplotype, a 0.74 Mb critical interval containing two Iroquois homeobox genes, Irx1 and Irx2, was unique to rumpless Araucana chickens. Irx1 and Irx2 are central for developmental prepatterning, but neither gene is known to have a role in mechanisms leading to caudal development. A second genome-wide association analysis using 30 ear-tufted and 28 non-tufted birds revealed an association with tufted on Gga 15 (P(raw) = 6.61×10(-7), P(genome) = 0.0981). We identified a 0.58 Mb haplotype common to tufted birds and harboring 7 genes. Because homozygosity for Et is nearly 100% lethal, we employed a heterozygosity mapping approach to prioritize candidate gene selection. A 60 kb region heterozygous in all Araucana chickens contains the complete coding sequence for TBX1 and partial sequence for GNB1L. TBX1 is an important transcriptional regulator of embryonic development and a key genetic determinant of human DiGeorge syndrome. Herein, we describe localization of Rp and Et and identification of positional candidate genes.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0040974</identifier><identifier>PMID: 22844420</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Association analysis ; Base Sequence ; Biochemistry ; Biology ; Birds ; Chickens ; Chickens - anatomy & histology ; Chickens - genetics ; Chromosomes ; Chromosomes - genetics ; Ear ; Ear - anatomy & histology ; Embryogenesis ; Embryonic growth stage ; Gene mapping ; Genes ; Genetic Loci - genetics ; Genetics ; Genome-Wide Association Study ; Genomes ; Genomics ; Genotypes ; Haplotypes ; Heredity ; Heterozygosity ; Homeobox ; Homozygosity ; Iroquois protein ; Localization ; Mapping ; Mental disorders ; Musculoskeletal system ; Mutation ; Native North Americans ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide ; Poultry ; Schizophrenia ; Single-nucleotide polymorphism ; Systems development ; Tbx1 protein ; Thymic hypoplasia ; Transcription ; Transcription (Genetics) ; Vertebra ; Vertebrae</subject><ispartof>PloS one, 2012-07, Vol.7 (7), p.e40974-e40974</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Noorai et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Noorai et al. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-13d84b2ef94cfe2e52535975c8c85f6347a2d996592fde578716cb23af485b653</citedby><cites>FETCH-LOGICAL-c758t-13d84b2ef94cfe2e52535975c8c85f6347a2d996592fde578716cb23af485b653</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402462/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402462/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22844420$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Alsina, Berta</contributor><creatorcontrib>Noorai, Rooksana E</creatorcontrib><creatorcontrib>Freese, Nowlan H</creatorcontrib><creatorcontrib>Wright, Lindsay M</creatorcontrib><creatorcontrib>Chapman, Susan C</creatorcontrib><creatorcontrib>Clark, Leigh Anne</creatorcontrib><title>Genome-wide association mapping and identification of candidate genes for the rumpless and ear-tufted traits of the Araucana chicken</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Araucana chickens are known for their rounded, tailless rumps and tufted ears. Inheritance studies have shown that the rumpless (Rp) and ear-tufted (Et) loci each act in an autosomal dominant fashion, segregate independently, and are associated with an increased rate of embryonic mortality. To find genomic regions associated with Rp and Et, we generated genome-wide SNP profiles for a diverse population of 60 Araucana chickens using the 60 K chicken SNP BeadChip. Genome-wide association studies using 40 rumpless and 11 tailed birds showed a strong association with rumpless on Gga 2 (P(raw) = 2.45×10(-10), P(genome) = 0.00575), and analysis of genotypes revealed a 2.14 Mb haplotype shared by all rumpless birds. Within this haplotype, a 0.74 Mb critical interval containing two Iroquois homeobox genes, Irx1 and Irx2, was unique to rumpless Araucana chickens. Irx1 and Irx2 are central for developmental prepatterning, but neither gene is known to have a role in mechanisms leading to caudal development. A second genome-wide association analysis using 30 ear-tufted and 28 non-tufted birds revealed an association with tufted on Gga 15 (P(raw) = 6.61×10(-7), P(genome) = 0.0981). We identified a 0.58 Mb haplotype common to tufted birds and harboring 7 genes. Because homozygosity for Et is nearly 100% lethal, we employed a heterozygosity mapping approach to prioritize candidate gene selection. A 60 kb region heterozygous in all Araucana chickens contains the complete coding sequence for TBX1 and partial sequence for GNB1L. TBX1 is an important transcriptional regulator of embryonic development and a key genetic determinant of human DiGeorge syndrome. Herein, we describe localization of Rp and Et and identification of positional candidate genes.</description><subject>Animals</subject><subject>Association analysis</subject><subject>Base Sequence</subject><subject>Biochemistry</subject><subject>Biology</subject><subject>Birds</subject><subject>Chickens</subject><subject>Chickens - anatomy & histology</subject><subject>Chickens - genetics</subject><subject>Chromosomes</subject><subject>Chromosomes - genetics</subject><subject>Ear</subject><subject>Ear - anatomy & histology</subject><subject>Embryogenesis</subject><subject>Embryonic growth stage</subject><subject>Gene mapping</subject><subject>Genes</subject><subject>Genetic Loci - genetics</subject><subject>Genetics</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Haplotypes</subject><subject>Heredity</subject><subject>Heterozygosity</subject><subject>Homeobox</subject><subject>Homozygosity</subject><subject>Iroquois protein</subject><subject>Localization</subject><subject>Mapping</subject><subject>Mental disorders</subject><subject>Musculoskeletal system</subject><subject>Mutation</subject><subject>Native North Americans</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Poultry</subject><subject>Schizophrenia</subject><subject>Single-nucleotide polymorphism</subject><subject>Systems development</subject><subject>Tbx1 protein</subject><subject>Thymic hypoplasia</subject><subject>Transcription</subject><subject>Transcription 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Inheritance studies have shown that the rumpless (Rp) and ear-tufted (Et) loci each act in an autosomal dominant fashion, segregate independently, and are associated with an increased rate of embryonic mortality. To find genomic regions associated with Rp and Et, we generated genome-wide SNP profiles for a diverse population of 60 Araucana chickens using the 60 K chicken SNP BeadChip. Genome-wide association studies using 40 rumpless and 11 tailed birds showed a strong association with rumpless on Gga 2 (P(raw) = 2.45×10(-10), P(genome) = 0.00575), and analysis of genotypes revealed a 2.14 Mb haplotype shared by all rumpless birds. Within this haplotype, a 0.74 Mb critical interval containing two Iroquois homeobox genes, Irx1 and Irx2, was unique to rumpless Araucana chickens. Irx1 and Irx2 are central for developmental prepatterning, but neither gene is known to have a role in mechanisms leading to caudal development. A second genome-wide association analysis using 30 ear-tufted and 28 non-tufted birds revealed an association with tufted on Gga 15 (P(raw) = 6.61×10(-7), P(genome) = 0.0981). We identified a 0.58 Mb haplotype common to tufted birds and harboring 7 genes. Because homozygosity for Et is nearly 100% lethal, we employed a heterozygosity mapping approach to prioritize candidate gene selection. A 60 kb region heterozygous in all Araucana chickens contains the complete coding sequence for TBX1 and partial sequence for GNB1L. TBX1 is an important transcriptional regulator of embryonic development and a key genetic determinant of human DiGeorge syndrome. Herein, we describe localization of Rp and Et and identification of positional candidate genes.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22844420</pmid><doi>10.1371/journal.pone.0040974</doi><tpages>e40974</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Animals Association analysis Base Sequence Biochemistry Biology Birds Chickens Chickens - anatomy & histology Chickens - genetics Chromosomes Chromosomes - genetics Ear Ear - anatomy & histology Embryogenesis Embryonic growth stage Gene mapping Genes Genetic Loci - genetics Genetics Genome-Wide Association Study Genomes Genomics Genotypes Haplotypes Heredity Heterozygosity Homeobox Homozygosity Iroquois protein Localization Mapping Mental disorders Musculoskeletal system Mutation Native North Americans Oligonucleotide Array Sequence Analysis Polymorphism, Single Nucleotide Poultry Schizophrenia Single-nucleotide polymorphism Systems development Tbx1 protein Thymic hypoplasia Transcription Transcription (Genetics) Vertebra Vertebrae |
| title | Genome-wide association mapping and identification of candidate genes for the rumpless and ear-tufted traits of the Araucana chicken |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-30T19%3A14%3A14IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome-wide%20association%20mapping%20and%20identification%20of%20candidate%20genes%20for%20the%20rumpless%20and%20ear-tufted%20traits%20of%20the%20Araucana%20chicken&rft.jtitle=PloS%20one&rft.au=Noorai,%20Rooksana%20E&rft.date=2012-07-23&rft.volume=7&rft.issue=7&rft.spage=e40974&rft.epage=e40974&rft.pages=e40974-e40974&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0040974&rft_dat=%3Cgale_plos_%3EA477051299%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1344464309&rft_id=info:pmid/22844420&rft_galeid=A477051299&rft_doaj_id=oai_doaj_org_article_ca76b9eeb8af4df9aa384bcefbcc212e&rfr_iscdi=true |