Computational protocol: Study on LOC426217 as a candidate gene for beak deformity in chicken

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Protocol publication

[…] 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 [, ]. […]

Pipeline specifications

Software tools POPGENE, Haploview
Applications Population genetic analysis, GWAS
Organisms Gallus gallus
Diseases Abnormalities, Drug-Induced, Musculoskeletal Diseases