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Transcriptome Analysis of Cattle Embryos Based on Single Cell RNA-Seq

Transcriptome Analysis of Cattle Embryos Based on Single Cell RNA-Seq

Jie Wang1, Di Fang1, Jianqing Zhao1, Fei Huang2, Bo Liu2, Weikun Tao2, Baoshan Cui2 and Qinghua Gao1,2,3*

1College of Life Sciences, Tarim University, Alar, Xinjiang 843300, China
2College of Animal Science, Tarim University, Alar, Xinjiang 843300, China
3Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, Xinjiang 843300, China
* Corresponding author:


Over the past few years, transcriptome sequencing has been applied to livestock and poultry, helping to select and investigate candidate genes associated with important traits. Yet, so far, only a few studies have reported differences in single-cell transcriptome between bovine embryos of different genders. In this study, we performed transcriptome analysis of cattle embryos based on a single Cell RNA-Seq. Bovine sex-controlled semen for artificial insemination were used to obtain different stage embryos: bovine 8 cell XX embryo, 8 cell XY embryo, 16 cell XX embryo, 16 cell XY embryo, morula XX embryo, morula XY embryo, blastocyst XX embryo, and blastocyst XY embryo. A sequencing library was constructed by the Smart-Seq2 amplification. The transcriptome was sequenced by Illumina HiSeqXten high-throughput sequence technology, and effective sequences were analyzed by functional annotation and related bioinformatics analysis. We found that Q30 percentage range of eight samples was 91.79-92.37%. The filtration sequence was 44106250-54234844. Compared with the reference genome by TopHat software, the net reading ratio of the bovine reference gene at each stage was 93.17-9 4.23%, the ratio of sequence numbers to multiple sites of the genome was 2.99-4.89. The DEG was identified by using the fold change ≥2 and FDR <0.01 as cut-off values. There were 525 differentially expressed genes. GO and KEGG analysis showed that “cell part”, “organelle”, and organelle part” were significantly enriched in cell composition categories. As for molecular functional categories, DEGs were significantly enriched in cellular process “,” biological regulation “and metabolic process” during biological processes. Moreover, KEGG analysis showed that the most abundant pathways were oxidative phosphorylation and Wnt signaling pathway”,”MAPK signaling pathway “,” Regulation of actin cytoskeleton “and VEGF signaling pathway”. To conclude, these RNA-Seq results confirmed the differential expression of several genes in embryos of different genders during embryonic development. These DEGs partcipate in the transcriptional regulation of bovine embryonic development of different genders.

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Pakistan Journal of Zoology


Pakistan J. Zool., Vol. 56, Iss. 3, pp. 1001-1500


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