title: Study on LOC426217 as a candidate gene for beak deformity in chicken.
abstract: BACKGROUND
  The beak deformity (crossed beaks) was found in some indigenous chickens of China, such as Beijing-You (BJY), Qingyuan Partridge, and Huxu Chickens. Birds with deformed beaks have reduced feed intake and drinking, impeded growth rate, and poor production performance. Beak deformity reduces the economy of poultry industry and affects animal welfare as well. The genetic basis of this malformation remains incompletely understood. LOC426217, also named claw keratin-like, was the most up-regulated gene in the deformed beaks from a previous digital gene expression (DGE) analysis and was selected as an important candidate gene for further analysis.
  
  
  RESULTS
  In the present study, quantitative real-time PCR (qRT-PCR) was firstly performed to determine the expression pattern of LOC426217 gene in deformed and normal beaks to verify the DGE results. Tissue-specific expression profile of this gene in 14 tissues was also determined using qRT-PCR. The LOC426217 was amplified from the genomic DNA of 171 deformed and 164 normal beaks, and sequenced to detect the single nucleotide polymorphisms (SNPs). The results showed that LOC426217 was significantly high-expressed in the deformed beaks, which was in good agreement with the DGE results. This gene was specifically high-expressed in beaks than other tissues. Eight SNPs were detected in LOC426217: -62G > T, 24 T > C, 36G > C, 192A > T, 204C > T, 222 T > C, 285G > T, and 363 T > C. Genotype frequency of G-62 T, T24C, G36C, T222C, and T363C loci was significant different between deformed and normal beaks. Haplotype analysis revealed one block with SNPs T24C and G36C, and one block with SNPs A192T, C204T, T222C, and G285T in normal birds, while the block with SNPs G36C and A192T in deformed ones.
  
  
  CONCLUSIONS
  It was concluded from these results that the over-expression of LOC426217 in the beak maybe related to the malformation. The polymorphisms of LOC426217 gene were associated with the beak deformity trait where the SNPs of G-62 T, T24C, G36C, T222C, and T363C loci maybe used as markers. The specific haplotype block in deformed birds may be a potential linkage marker for this trait.
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. bhowen1027@163.com.
authors.forename: Hao
authors.initials: H
authors.lastname: Bai
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. yanyansun2014@163.com.
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. jingjing19870220@163.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. liunian.14@163.com.
authors.forename: Nian
authors.initials: N
authors.lastname: Liu
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. lidongli20002004@163.com.
authors.forename: Dongli
authors.initials: D
authors.lastname: Li
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. xueguang123@126.com.
authors.forename: Fuguang
authors.initials: F
authors.lastname: Xue
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. mailyunlei@163.com.
authors.forename: Yunlei
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. chen.jilan@163.com.
authors.forename: Jilan
authors.initials: J
authors.lastname: Chen
mesh_terms: D000827:Animal Welfare; D000818:Animals; D030161:Avian Proteins / Q000235:genetics*; D001502:Beak / Q000002:abnormalities*; D000068476:Beijing; D002645:Chickens / Q000235:genetics*; D005786:Gene Expression Regulation; D005787:Gene Frequency; D056426:Genetic Loci; D060005:Genotyping Techniques; D006239:Haplotypes; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D030161:Avian Proteins