Polymorphisms of 5'-flanking region of SOCS5 gene in cattle

【Objective】SNP sites in the promoter region of SOCS5 gene in cattle were screened in order to analyze the effect of SNPs on function elements of promoter. 【Method】Two cattle breeds(Wuchuan black cattle and Chinese Holstein cow) possessing significant difference in growth performance were selected to construct DNA pools. After direct sequencing, sequence jointing and adjusting were conducted using DNASTAR software. The polymorphisms of SOCS5 gene was analyzed using BLAST. Sequence core promoter region and CpG island were predicted using bioinformatics software. Finally the effects of SNP site on transcription factor binding sites were assayed. 【Result】Three SNPs including C-577T, T-43C and C+61T were found in the 5' flanking region and exon 1 of SOCS5 gene. The C+61T accorded with rs110977810 in SNP database, while C-577T and T-43C were newly found sites. Furthermore, bioinformatics tools were used to predict the core region of promoter and CpG island. It was demonstrated that various novel transcription factors binding sites emerged while a large amount of transcription factors binding sites disappeared. SNP mutation could change transcription factors binding sites but it did not affect the range or initiation site of promoter dramatically, which meant that SNP had no effect on SOCS5 gene expression at the methylation level. 【Conclusion】There were three SNPs existing in the 5' flanking region of SOCS5 gene that had important effects on promoter elements.