title: Genome-Wide Linkage Analysis Identifies Loci for Physical Appearance Traits in Chickens.
abstract: Physical appearance traits, such as feather-crested head, comb size and type, beard, wattles size, and feathered feet, are used to distinguish between breeds of chicken and also may be associated with economic traits. In this study, a genome-wide linkage analysis was used to identify candidate regions and genes for physical appearance traits and to potentially provide further knowledge of the molecular mechanisms that underlie these traits. The linkage analysis was conducted with an F2 population derived from Beijing-You chickens and a commercial broiler line. Single-nucleotide polymorphisms were analyzed using the Illumina 60K Chicken SNP Beadchip. The data were used to map quantitative trait loci and genes for six physical appearance traits. A 10-cM/0.51-Mb region (0.0-10.0 cM/0.00-0.51 Mb) with 1% genome-wide significant level on LGE22C19W28_E50C23 linkage group (LGE22) for crest trait was identified, which is likely very closely linked to the HOXC8. A QTL with 5% chromosome-wide significant level for comb weight, which partly overlaps with a region identified in a previous study, was identified at 74 cM/25.55 Mb on chicken (Gallus gallus; GG) chromosome 3 (i.e., GGA3). For beard and wattles traits, an identical region 11 cM/2.23 Mb (0.0-11.0 cM/0.00-2.23 Mb) including WNT3 and GH genes on GGA27 was identified. Two QTL with 1% genome-wide significant level for feathered feet trait, one 9-cM/2.80-Mb (48.0-57.0/13.40-16.20 Mb) region on GGA13, and another 12-cM/1.45-Mb (41.0-53.0 cM/11.37-12.82 Mb) region on GGA15 were identified. These candidate regions and genes provide important genetic information for the physical appearance traits in chicken.
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China College of Life Science, Longyan University, Longyan, Fujian 364012, People's Republic of China Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Longyan University, Longyan, Fujian 364012, People's Republic of China.
authors.forename: Yanfa
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China State Key Laboratory of Animal Nutrition, Beijing 100193, People's Republic of China.
authors.forename: Ranran
authors.initials: R
authors.lastname: Liu
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China State Key Laboratory of Animal Nutrition, Beijing 100193, People's Republic of China.
authors.forename: Guiping
authors.initials: G
authors.lastname: Zhao
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China State Key Laboratory of Animal Nutrition, Beijing 100193, People's Republic of China.
authors.forename: Maiqing
authors.initials: M
authors.lastname: Zheng
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
authors.forename: Xiaoqiong
authors.initials: X
authors.lastname: Yu
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
authors.forename: Peng
authors.initials: P
authors.lastname: Li
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China State Key Laboratory of Animal Nutrition, Beijing 100193, People's Republic of China jiewen@iascaas.net.cn.
authors.forename: Jie
authors.initials: J
authors.lastname: Wen
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D002874:Chromosome Mapping; D005260:Female; D008040:Genetic Linkage; D055106:Genome-Wide Association Study; D008297:Male; D000067029:Physical Appearance, Body; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable
keywords: beard; chicken; comb; feather-crested head; feathered feet; linkage analysis; physical appearance traits; wattles