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

Q4 Biochemistry, Genetics and Molecular Biology

Animal Gene Pub Date : 2020-09-01 DOI:10.1016/j.angen.2020.200108

Parviz Esfandiari , Mohammad Dadpasand , Hamed Kharrati-Koopaee , Hadi Atashi , Amir Gharghi , Ali Niazi

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引用次数: 4

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.

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Ovocalyxin-32基因的生物信息学、系统发育和变异关联分析揭示了其对地方鸡产蛋性状的影响

法尔斯土鸡(FNC)被用作一种食物来源，在农村地区的收入中发挥着关键作用。然而，在分子水平上对FNC的研究很少，其遗传背景也不清楚，难以组织育种计划。本文首次研究了Ovocalyxin-32 (OCX-32)变异对产蛋性状的影响。OCX-32蛋白在蛋壳的矿物质沉积和完成中起作用。收集了400份血样，发现了OCX-32基因外显子3的390 bp片段(c.193A >C)进行扩增，并采用RFLP-PCR技术进行基因分型。生物信息学分析表明，所研究的SNP是一种混乱突变，导致蛋白质结构上组氨酸被天冬酰胺取代。鉴定出AA和AC两种基因型，基因型对初卵龄有显著影响。系统发育分析表明，FNC和Coturnix japonica的OCX-32基因序列在遗传上属于同一类群。基因网络分析表明，OCX-32与其他影响体型、消化率和鸡蛋蛋白的重要候选基因存在关联。因此，OCX-32可以促进鸡的总产蛋量。

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Animal Gene Agricultural and Biological Sciences-Insect Science

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期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.