Transcriptome analysis showed differences of two purebred cattle and their crossbreds

The consequences of a cattle crossbreeding programme on the genes expression, signalling and metabolic pathways, molecular networks, and biological functions is still indistinctive. In this study differences of five cattle populations in a crossbreeding programme were studied using high throughput sequencing technology to characterise their transcriptome. Holstein (Bos Taurus origin) and Taleshi (Bos indicus origin) as purebred cattle were compared with their crossbreds including 50% sire Taleshi and dam Holstein (50CSN), 50% sire Holstein and dam Taleshi (50CSH) and 75% Holstein (75C). Differentially expressed genes (DEGs) and their related enriched metabolic pathways, transcription up-stream regulators and biological functions were studied by bioinformatics tools of transcriptome analysis. Total expressed transcripts in all populations were 72,812 with 22,627 annotated genes. We found 2262 DEGs in which 251 genes were uniquely expressed in purebreds or crossbreds. Functional analysis of DEGs showed that the immune and inflammatory responses were the most highly-impacted pathways and functions. Among all significantly enriched pathways, eukaryotic translation initiation factor-2 signalling had the highest activation Z-score (5.3) in crossbred compared to purebred cattle. The majority of up-stream regulators of genes including transcription regulators and cytokines were differentially expressed among populations in which their activation Z-score in purebred was more than crossbred cattle. Crossing of Holstein with Taleshi breed resulted lower activity of pathways related to immunity and inflammatory responses. The analysis revealed that the most important differences between studied genotypes, especially between purebred and crossbred cattle, were related to immune function