Study on LOC426217 as a candidate gene for beak deformity in chicken
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.
[…] The relative abundance of transcripts was calculated from 2−ΔΔCT . All data presented graphically are means ± SEM. The significance level was P < 0.05 or P < 0.01. Student’s t-tests were used to evaluate the relative expression differences of LOC426217 between the RNA samples of deformed and normal beaks. The ANOVA procedure of SAS 8.0 was used to assess the differences expression of LOC426217 in all the tissues. All SNPs were checked for Hardy-Weinberg Equilibrium (HWE) in both groups (P > 0.05 means equilibrium). Allele frequency, genotype frequency, and polymorphism information content (PIC, PIC < 0.25: low polymorphism; 0.25 < PIC < 0.5: moderate polymorphism; PIC > 0.5: high polymorphism) were calculated by PopGene (Version 1.31). Chi-square tests were used to evaluate the genotype frequency differences between deformed and normal beaks. Benjamini & Hochberg method was used for the Bonferroni correction . Linkage Disequilibrium (LD) pattern for the SNPs genotyped was plotted using Haploview (Version 4.2). The sliding window method was used to generate different haplotypes between two groups [, ]. […]
to analyse the site's operation and effectiveness, to display ads tailored to your interests
and to provide you with relevant promotional messages and other information about products,
events and services of ours or our sponsors and partner companies.
These cookies are needed for the site to work and to be optimized.
These cookies are needed to interact with the social network plugins on this site.
These cookies are used to track visitors across websites.
The intention is to display ads that are relevant and engaging for the users.
These cookies are needed in order to better understand how
this site is used and to improve the user experience.
At omicX, we believe trust is of the utmost importance. Transparency allows trust.
This is why we want you to understand what data we collect and how we use it.