鸡胰岛素样生长因子2基因(IGF2)外显子区功能性SNP预测与分析

doi:10.11843/j.issn.0366-6964.2020.11.006

Abstract

Abstract: The aim of this study was to use bioinformatics methods to screen non-synonymous single nucleotide polymorphisms (nsSNPs) sites with potential biological functions in chicken IGF2 gene and provide a theoretical basis for carrying out marker-assisted selection to improve important economic traits of chicken. Twelve nsSNPs sites of chicken IGF2 gene were retrieved from dbSNP database. SIFT, Polyphen-2, PhD-SNP, and SNAP were used to predict the possible functional SNPs. The amino acid stability of mutation sites was analyzed by I-Mutant3.0 and Mupro methods. Multiple sequence alignment and conserved prediction of evolutionary sites were carried out on the amino acid sequence encoded by chicken IGF2 gene, and combined with MutPred2 to predict the possible functional consequences caused by mutations. Finally, Sopma was used to predict the secondary structure of IGF2 wild-type and mutant proteins, and I-TASSER was used to construct their tertiary structure. The results showed that rs740391349 (E29G), rs735633122 (T30P), rs739078786 (L31P), rs736255842 (E35G) and rs736800980 (V37G) might affect the protein function of chicken IGF2, and all the mutations reduced the protein stability of IGF2. Multiple sequence alignment and conservative analysis showed that rs740391349 (E29G), rs735633122 (T30P), and rs736255842 (E35G) were highly conserved and exposed functional residues. MutPred2 and secondary structural analysis showed that mutations at rs735633122 (T30P) and rs736255842 (E35G) both led to a decreased percentage of α-helix. Tertiary structural analysis showed that rs735633122 (T30P) and rs736255842 (E35G) could change the spatial structure of IGF2 protein. In summary, mutations at T30P and E35G seriously affect the structure of chicken IGF2 protein and may be the significant functional SNPs affecting chicken growth and body composition traits.

Key words: chicken, IGF2 gene, SNP function prediction, bioinformatics

CLC Number:

S831.2

LI Yudong, WANG Weijia, LI Ziwei, LI Ruichu, ZHANG Changchao, WANG Ning, LI Hui, WANG Shouzhi. Prediction and Analysis of Functional SNP on Exon Region of Insulin-like Growth Factor 2 Gene (IGF2) in Chickens[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(11): 2665-2678.

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Prediction and Analysis of Functional SNP on Exon Region of Insulin-like Growth Factor 2 Gene (IGF2) in Chickens

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