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Accession IconSRP072500

Comparison of crossbred and purebred cattle by bioinformatics analysis of differentially expressed transcripts

Organism Icon Bos taurus
Sample Icon 5 Downloadable Samples
Technology Badge IconIllumina HiSeq 2000

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Background: Transcriptomic variation among cattle breeds and their crossbreds may help to better understanding of consequences of crossbreeding and heterosis. In this study the differences in biological functions and pathways of three crossbreds including 50 and 75 percent Holstein were compared with their purebred parents, Holstein and Taleshi (an indigenous breed) cattle. Results: Five populations and their ten comparisons were studied by bioinformatics tools for transcriptome analysis. We pooled blood RNA of at least 8 animals of each population prior to RNA sequencing. The obtained results showed that total expressed transcripts in all populations were 72,812 with 22,627 annotated genes. Functional analysis of differentially expressed genes (DEGs) showed that the genetics information processing and metabolism were the most highly-impacted pathways. Among all significantly enriched pathways, eukaryotic translation initiation factor-2 signaling had the highest activation z-score (5.3) in crossbred compared to purebred cattle. The majority of upstream 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. Conclusions: Crossing of Holstein with Taleshi breed resulted in higher activity of pathways related to genetic information processing and lower activity of pathways related to immunity and inflammatory responses. To the best of our knowledge, this is the first study where the differences in pathways and functions were studied using high throughput sequencing of blood in a cattle crossbreeding program. The analysis revealed that the most important differences between studied genotypes, especially between purebred and crossbred cattle, were related to immune functions and metabolism. Overall design: the blood transcriptome of five cattle populations including two purebreds and the three crossbreds of them. Please note that three crossbreds have different parents and different blood share of their purebred parents; 50CSN is 50 percent crossbred sire Iran native cattle and dam Holstein, 50CSH is 50 percent crossbred sire Holstein and dam Iran native cattle, and 75C is 75 percent Holstein and 25 percent Iran native cattle.
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