title: Identification of genes related to beak deformity of chickens using digital gene expression profiling.
abstract: Frequencies of up to 3% of beak deformity (normally a crossed beak) occur in some indigenous chickens in China, such as and Beijing-You. Chickens with deformed beaks have reduced feed intake, growth rate, and abnormal behaviors. Beak deformity represents an economic as well as an animal welfare problem in the poultry industry. Because the genetic basis of beak deformity remains incompletely understood, the present study sought to identify important genes and metabolic pathways involved in this phenotype. Digital gene expression analysis was performed on deformed and normal beaks collected from Beijing-You chickens to detect global gene expression differences. A total of >11 million cDNA tags were sequenced, and 5,864,499 and 5,648,877 clean tags were obtained in the libraries of deformed and normal beaks, respectively. In total, 1,156 differentially expressed genes (DEG) were identified in the deformed beak with 409 being up-regulated and 747 down-regulated in the deformed beaks. qRT-PCR using eight genes was performed to verify the results of DGE profiling. Gene ontology (GO) analysis highlighted that genes of the keratin family on GGA25 were abundant among the DEGs. Pathway analysis showed that many DEGs were linked to the biosynthesis of unsaturated fatty acids and glycerolipid metabolism. Combining the analyses, 11 genes (MUC, LOC426217, BMP4, ACAA1, LPL, ALDH7A1, GLA, RETSAT, SDR16C5, WWOX, and MOGAT1) were highlighted as potential candidate genes for beak deformity in chickens. Some of these genes have been identified previously, while others have unknown function with respect to thus phenotype. To the best of our knowledge, this is the first genome-wide study to investigate the transcriptome differences in the deformed and normal beaks of chickens. The DEGs identified here are worthy of further functional characterization.
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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, China.
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, China.
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, China.
authors.forename: Ranran
authors.initials: R
authors.lastname: Liu
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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, China.
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, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Wen
authors.affiliation: Key Laboratory of Genetics Resources and Utilization of Livestock, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Jilan
authors.initials: J
authors.lastname: Chen
mesh_terms: D000818:Animals; D001502:Beak / Q000473:pathology*; D015415:Biomarkers / Q000378:metabolism*; D001715:Bird Diseases / Q000235:genetics* / Q000473:pathology; D002645:Chickens; D002681:China; D020869:Gene Expression Profiling; D063990:Gene Ontology; D046228:Microarray Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D015415:Biomarkers; D012333:RNA, Messenger