Genetic polymorphism screening of CSF3 gene in dairy cow and its bioinformatics analysis

doi:10.3969/j.issn.1004-1524.2020.06.06

›› 2020, Vol. 32 ›› Issue (6): 986-993.DOI: 10.3969/j.issn.1004-1524.2020.06.06

• Animal Science • Previous Articles Next Articles

Genetic polymorphism screening of CSF3 gene in dairy cow and its bioinformatics analysis

WU Jia, CHEN Lang, JIANG Tao, HUANG Guoming, LI Zhuo, LI Yaodong, ZHANG Li, LIU Lixia^*

College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China

Received:2019-10-13 Online:2020-06-25 Published:2020-06-24

Abstract

Abstract: In order to explore the genetic immunization function of colony-stimulating factor 3 (CSF3) gene in dairy cows, the single nucleotide polymorphism (SNP) of 5 exons of CSF3 gene in dairy cows were screened by direct sequencing after amplification by DNA pool, and the open reading frame (ORF) region of CSF3 gene was encoded by bioinformatics. Signal peptide transmembrane region, amino acid physicochemical properties, protein affinity/hydrophobicity, mRNA secondary structure, protein secondary and tertiary structure were predicted and analyzed. The results showed that there were three SNPs in exon 2 of CSF3 gene in cows, which were T⁶⁶C, C⁶⁷A and C¹¹⁸A, all of which were missense mutations, and led to the changes of serine (Ser) and proline (Pro) to histidine (His). The results of mRNA secondary structure prediction showed that T⁶⁶C and C⁶⁷A reduced the secondary structure stability of CSF3 gene mRNA in dairy cows, while C¹¹⁸A increased its stability. The results of physicochemical analysis showed that the CSF3 gene of cows was 1 460 bp in length and encoded a total of 195 amino acids. It is a mixed soluble protein with a signal peptide transmembrane region. The main components of its secondary structure are α-helix and random coli.

Key words: dairy cow, CSF3, SNP, bioinformatics analysis

CLC Number:

S823.9⁺1

WU Jia, CHEN Lang, JIANG Tao, HUANG Guoming, LI Zhuo, LI Yaodong, ZHANG Li, LIU Lixia. Genetic polymorphism screening of CSF3 gene in dairy cow and its bioinformatics analysis[J]. , 2020, 32(6): 986-993.

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Genetic polymorphism screening of CSF3 gene in dairy cow and its bioinformatics analysis

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