Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

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dc.contributor.authorWragg, D.
dc.contributor.authorMwacharo, J. M.
dc.contributor.authorAlcalde, J. A.
dc.contributor.authorHocking, P. M.
dc.contributor.authorHanotte, O.
dc.date.accessioned2025-01-20T23:57:56Z
dc.date.available2025-01-20T23:57:56Z
dc.date.issued2012
dc.description.abstractExtensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide single-nucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r(2)>= 0.3) in both traditional and village chickens at pairwise marker distances of similar to 10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling similar to 75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110 K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions. Heredity (2012) 109, 6-18; doi:10.1038/hdy.2012.9; published online 7 March 2012
dc.fuente.origenWOS
dc.identifier.doi10.1038/hdy.2012.9
dc.identifier.eissn1365-2540
dc.identifier.issn0018-067X
dc.identifier.urihttps://doi.org/10.1038/hdy.2012.9
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/95222
dc.identifier.wosidWOS:000305366700003
dc.issue.numero1
dc.language.isoen
dc.pagina.final18
dc.pagina.inicio6
dc.revistaHeredity
dc.rightsacceso restringido
dc.subjecthaplotype blocks
dc.subjectlinkage disequilibrium
dc.subjectassociation mapping
dc.subjectselective sweep
dc.subjectSNP genotyping
dc.subject.ods03 Good Health and Well-being
dc.subject.odspa03 Salud y bienestar
dc.titleAnalysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens
dc.typeartículo
dc.volumen109
sipa.indexWOS
sipa.trazabilidadWOS;2025-01-12
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