Single nucleotide polymorphism and bioinformatics analysis of IGF2R gene in Hainan cattle

【Objective】 To explore genetic polymorphism of the insulin-like growth factor 2 receptor gene(IGF2R) in Hainan cattle and its genetic distribution in Hainan cattle population, and to provide theoretical basis for revealing regulatory mechanism of gene IGF2R to growth traits of Hainan cattle and sites for molecular marker-assisted selection.【Method】 A DNA pool was constructed, and polymorphism analysis of gene coding regions(CDS) of Hainan cattle IGF2R gene was operated through PCR amplification and sequencing technology. The single nucleotide polymorphism (SNP) sites of missense mutation were screened with Chromas sequence alignment;a total of 202 individuals of Hainan cattle were genotyped by PCR-RFLP and the selected SNP sites were used for linkage disequilibrium and haplotype analysis to evaluate haplotype distribution in Hainan cattle population;effects of haplotypes and SNP sites on mRNA secondary structure, protein physicochemical properties and protein secondary structure of CDS of Hainan cattle IGF2R gene were analyzed by bioinformatics methods.【Result】 Four SNP sites of missense mutation in Hainan cattle IGF2R gene CDS region were detected, including SNP1(g.63977 A>G), SNP2(g.63999 T>C), SNP3(g.69772 G>A), and SNP4 (g.94987 A>C), and a strong linkage disequilibrium between SNP1, SNP2 and SNP3. Four SNP sites showed mediumly polymorphism in the population, and they were in Hardy-Weinberg disequilibrium(P>0.05). Four haplotypes were in Hainan cattle population(F>0.01), namely H1(ATG), H2(GCA), H3(ACA), and H4(GCG);each haplotype and mutated SNP4 influenced secondary structure and minimum free energy of mRNA in the CDS of Hainan cattle IGF2R gene. IGF2R protein was hydrophilic, which had transmembrane structure and a signal peptide and its secondary structure was mainly composed of irregular curls and extended strand, followed by α-helix and β-turn.【Conclusion】 Four missense mutation SNP sites in CDS regions of IGF2R gene in Hainan cattle are detected, and medium polymorphism is detected in Hainan cattle population and are in Hardy-Weinberg disequilibrium. Mutation of SNP sites of IGF2R gene in Hainan cattle may affect mRNA secondary structure and stability, leading to changes of peptide chain conformation of IGF2R protein secondary structure, thus influencing regulation of growth traits in Hainan cattle.