Bioinformatics, phylogenetic and variant association analysis of Ovocalyxin-32 gene reveals its contribution to egg production traits in native chickens

Abstract Fars native chicken (FNC) is utilized as a food source, and plays a critical role in earning money in rural areas. However, little attention has been paid to FNC at molecular level and its genetic background is unknown for organizing the breeding programs. For the first time, herein, the effect of Ovocalyxin-32 (OCX-32) variant on egg production traits was investigated. OCX-32 protein plays role in minerals deposition and completion of eggshell. 400 blood samples were collected and a 390-bp fragment including exon 3 in OCX-32 gene (c.193A > C) was amplified and genotyped using RFLP-PCR technique. The bioinformatics analysis showed that the studied SNP is messiness mutation and leads to the substitution of Histidine with Asparagine in protein structure. Two genotypes including AA and AC were identified and effect of genotypes on the age at first egg was significant. Phylogeny analysis indicated that the OCX-32 gene sequences of FNC and Coturnix japonica are genetically categorized into the same group. The gene network analysis showed that there was association among OCX-32 and other important candidate genes affecting body size, digestibility and egg proteins. Therefore, OCX-32 could contribute to overall egg production in chickens.