title: Genome-wide linkage analysis and association study identifies loci for polydactyly in chickens.
abstract: Polydactyly occurs in some chicken breeds, but the molecular mechanism remains incompletely understood. Combined genome-wide linkage analysis and association study (GWAS) for chicken polydactyly helps identify loci or candidate genes for the trait and potentially provides further mechanistic understanding of this phenotype in chickens and perhaps other species. The linkage analysis and GWAS for polydactyly was conducted using an F2 population derived from Beijing-You chickens and commercial broilers. The results identified two QTLs through linkage analysis and seven single-nucleotide polymorphisms (SNPs) through GWAS, associated with the polydactyly trait. One QTL located at 35 cM on the GGA2 was significant at the 1% genome-wise level and another QTL at the 1% chromosome-wide significance level was detected at 39 cM on GGA19. A total of seven SNPs, four of 5% genome-wide significance (P < 2.98 × 10(-6)) and three of suggestive significance (5.96 × 10(-5)) were identified, including two SNPs (GGaluGA132178 and Gga_rs14135036) in the QTL on GGA2. Of the identified SNPs, the eight nearest genes were sonic hedgehog (SHH), limb region 1 homolog (mouse) (LMBR1), dipeptidyl-peptidase 6, transcript variant 3 (DPP6), thyroid-stimulating hormone, beta (TSHB), sal-like 4 (Drosophila) (SALL4), par-6 partitioning defective 6 homolog beta (Caenorhabditis elegans) (PARD6B), coenzyme Q5 (COQ5), and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, etapolypeptide (YWHAH). The GWAS supports earlier reports of the importance of SHH and LMBR1 as regulating genes for polydactyly in chickens and other species, and identified others, most of which have not previously been associated with limb development. The genes and associated SNPs revealed here provide detailed information for further exploring the molecular and developmental mechanisms underlying polydactyly.
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China College of Life Science, Longyan University, Longyan, Fujian 364012, P. R. China Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Longyan, Fujian 364012, P. R. China.
authors.forename: Yanfa
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China State Key Laboratory of Animal Nutrition, Beijing 100193, P. R. China.
authors.forename: Ranran
authors.initials: R
authors.lastname: Liu
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China State Key Laboratory of Animal Nutrition, Beijing 100193, P. R. China.
authors.forename: Guiping
authors.initials: G
authors.lastname: Zhao
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China State Key Laboratory of Animal Nutrition, Beijing 100193, P. R. China.
authors.forename: Maiqing
authors.initials: M
authors.lastname: Zheng
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China.
authors.forename: Xiaoqiong
authors.initials: X
authors.lastname: Yu
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China.
authors.forename: Peng
authors.initials: P
authors.lastname: Li
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China State Key Laboratory of Animal Nutrition, Beijing 100193, P. R. China jiewen@iascaas.net.cn.
authors.forename: Jie
authors.initials: J
authors.lastname: Wen
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D005260:Female; D056726:Genetic Association Studies; D008040:Genetic Linkage; D055106:Genome-Wide Association Study; D005838:Genotype; D008297:Male; D010641:Phenotype; D017689:Polydactyly / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D011995:Recombination, Genetic
keywords: GWAS; candidate genes; chicken; linkage analysis; polydactyly
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