Abstract
BackgroundThe 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.ResultsIn 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.ConclusionsIt 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0353-x) contains supplementary material, which is available to authorized users.
Highlights
The beak deformity was found in some indigenous chickens of China, such as Beijing-You (BJY), Qingyuan Partridge, and Huxu Chickens
Verification for LOC426217 gene of digital gene expression (DGE) results To verify the previous DGE analysis, where LOC426217 was the most up-regulated in the deformed beaks, qRTPCR was used to estimate the expression of this gene in 9 deformed and 9 normal beaks
Tissue expression profile of LOC426217 As shown in Fig. 3, LOC426217 gene was hardly expressed in brain, heart, bursa, or small intestine
Summary
The beak deformity (crossed beaks) was found in some indigenous chickens of China, such as Beijing-You (BJY), Qingyuan Partridge, and Huxu Chickens. 3 % of beak deformity (normally a crossed beak) were found in various indigenous chickens of China, such as Beijing-You (BJY) (studied here), Silkies, Qingyuan Partridge, and Huxu Chickens. According to our observations in a BJY population, in the absence of known environmental factors contributing to the malformation, birds with deformed beaks present consistently in each generation and cannot be eliminated from a population on the basis of the phenotype. This indicated the genetic effects underlying this trait.
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