Comparative miRNA signatures among Sahiwal and Frieswal cattle breeds during summer stress

Abstract

MicroRNAs (miRNAs) are known to take part in different biological mechanisms, including biotic as well as abiotic cellular stresses. The present investigation was aimed to identify comparative expression profile of differentially expressed miRNAs among Sahiwal (Bos indicus) and Frieswal (Bos indicus × Bos taurus) cattle breeds during summer stress. Stress responses in animals were characterized by recording various physiological parameters, biochemical assays and expression profiling of heat shock protein 70 (Hsp70) during elevated environmental temperature. Ion Torrent-based deep sequencing as well as CLC-genomic analysis identified 322 and 420 Bos taurus annotated miRNAs among Sahiwal and Frieswal, respectively. A total 69 common miRNAs were identified to be differentially expressed during summer among the breeds. Out of the 69, a total 14 differentially expressed miRNAs viz. bta-mir 6536-2, bta-mir-2898, bta-mir-let-7b, bta-mir-425, bta-mir-2332, bta-mir-2478, bta-mir-150, bta-mir142, bta-mir-16a, bta-mir-2311, bta-mir-1839, bta-mir-1248-1, bta-mir-103-2 and bta-mir-181b were randomly selected for qRT-PCR-based validation. bta-mir-2898, bta-mir-6536-1, bta-mir-let-7b, bta-mir-2478, bta-mir-150, bta-mir-16a, bta-mir-2311, bta-mir-1032-b and bta-mir-181-b were significantly (p < 0.01) upregulated during summer among Frieswal in comparison to Sahiwal while, bta-mir 6536-2, bta-mir-2332, bta-mir142, bta-mir-1839 and bta-mir-1248-1 was significantly (p < 0.01) expressed at higher level in Sahiwal in contrast to Frieswal correlation coefficient analysis revealed that bta-mir(s)-150, 16a and 181b are negatively correlated (p < 0.05) with Hsp70 expression. Thus, this study identified that miRNA expression during summer stress can vary between the breeds which may reflect their differential post-transcriptional regulation.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-020-02608-4.

Keywords: Cattle; Differential gene expression; Frieswal; HSP70.1; Sahiwal; miRNAs.

Fig. 1

Different biochemical parameters assessed in plasma samples of Frieswal an Sahiwal breeds of cattle. Estimation of different biochemical parameters revealed significant (p < 0.05) higher levels of plasma catalase activity (nmol/min/ml), GPx (nmol/min/ml) and MDA (μM) concentration during summer seasons in both the breeds. Catalase (CAT) activity (nmol/min/ml); glutathione peroxidase (GPx) level (nmol/min/ml) and c malondialdehyde (MDA) concentration (μM). SZ Summer zone, NZ Normal Zone. *p < 0.05

Fig. 2

Relative mRNA expression (mean ± SEM) of HSP70.1 among Sahiwal and Frieswal during normal vs summer zone. The results highlighted that, during summer, the relative mRNA expression of HSP70.1 was significantly (p < 0.05) higher in comparison to normal zone among the breeds. NZ Normal Zone, SZ Summer Zone. *p < 0.05

Fig. 3

Venn diagram depicting the common differentially expressed miRNAs during elevated environmental temperature among Sahiwal and Frieswal. There was a total of 420 and 322 miRNAs were differentially expressed among Frieswal and Sahiwal breed of cattle, respectively. Among them, a total 69 miRNAs were identified to be common among the breeds

Fig. 4

The heat map of differentially expressed common microRNA among Sahiwal and Frieswal. There are two specific groups. Columns 1 and 2 represent summer and normal zone, respectively in Frieswal while columns 2 and 4 represent summer and normal zone, respectively in Sahiwal. Heat map was generated using a function of heatmap.2 in gplots by R platform.The rows are centred and clustered using vector scaling and Euclidean distance, respectively. The intensity of the different colours specifies the level of variation in the expression of particular miRNA

Fig. 5

Comparative miRNAs expression among Frieswal and Sahiwal cattle breeds during summer stress. A total 14 miRNAs were selected for qRT- PCR assay based on their fold changes. Comparative expression profiling showed that bta-mir-2898, bta-mir-6536-1, bta-mir-let-7b, bta-mir-2478, bta-mir-150, bta-mir-16a, bta-mir-2311, bta-mir-1032-b and bta-mir-181-b having significantly (p < 0.01) higher expression during summer among Frieswal cattle in comparison to Sahiwal, while bta-mir 6536-2, bta-mir-2332, bta-mir142, bta-mir-1839 and bta-mir-1248-1 showing contrasting expression patterns. a Normalized expression values through deep sequencing platform and b relative miRNA expression through RT-PCR *p < 0.01. c RT-PCR products (20–25 bp size) of different miRNAs run in agarose gel electrophoresis. M DNA molecular weight marker