IDENTIFICATION AND SNP ANALYSIS OF DIFFERENTIALLY EXPRESSED GENES IN THE SKIN OF CATTLE OF DIFFERENT GENETIC GROUPS IN RESPONSE TO TICK INFESTATION
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Date
2020-02-17
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COLLEGE OF VETERINARY AND ANIMAL SCIENCES, POOKODE WAYANAD
Abstract
The present study was an attempt to identify the genes that are differentially
expressed in the skin of Vechur and crossbred (CBHF) cattle in response to tick
(Rhipicephalus annulatus) infestation using microarray analysis, and to study the
single nucleotide polymorphisms (SNPs) in differentially expressed S100 Calcium
Binding Protein A8 (S100A8) and E selectin (SELE) genes in these genetic groups.
Microarray analysis on Agilent platform revealed significant upregulation of 27
and 26 genes and down regulation of 54 and 52 genes 24 h after tick challenge in
Vechur and CBHF respectively. Functional categorization of these genes
indicated involvement of different major pathways in immune response to tick
infestation in different genetic groups. In Vechur animals, genes in T cell
activation and wound response were upregulated while cell signaling genes,
transcription regulators leading to B cell activation were upregulated in CBHF
animals. The down regulated genes in Vechur animals could be grouped under
genes of metabolic pathway, genes regulating cell migration, transcription factors
affecting T cell differentiation. In CBHF animals, the downregulated functional
categories were lipid and protein metabolism and immune genes involved in
regulation of inflammatory changes. The S100A8 gene and complete coding
sequences of SELE gene were characterised in Vechur, CBHF and Kasargode
Dwarf cattle. A new intronic SNP (189T→C) was identified in fragment 1 of
S100A8 which resulted in change of predicted transcription factor binding sites.
Four novel SNPs were identified in the coding sequence of SELE gene exons 3, 4,
5 and 8 at 396C→T, 475A→G, 574C→ A and 1224C→ T, respectively. The nonsynonymous SNPs in the exons 4 and 5 had neutral effect on the protein function.
Restriction fragment length polymorphism analysis was used to genotype the
animals of the three genetic groups based on the SNPs detected. The observations
made in the present study emphasized the difference in immune response
mechanisms to R. annulatus infestation between cattle of Bos indicus and Bos
taurus lineage. In silico predictions on the structure and functional characters of
the encoded proteins were done using various bioinformatic tools.