Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

Authors: ZHANG, TIANLIU - Chinese Academy Of Agricultural Sciences; WANG, TIANZHEN - Chinese Academy Of Agricultural Sciences; NIU, QUNHAO - Chinese Academy Of Agricultural Sciences; XU, LEI - Chinese Academy Of Agricultural Sciences; CHEN, YAN - Chinese Academy Of Agricultural Sciences; GAO, XUE - Chinese Academy Of Agricultural Sciences; GAO, HUIJIANG - Chinese Academy Of Agricultural Sciences; ZHANG, LUPEI - Chinese Academy Of Agricultural Sciences; Liu, Ge - George; LI, JUNYA - Chinese Academy Of Agricultural Sciences; XU, LINGYANG - Chinese Academy Of Agricultural Sciences

Submitted to: BMC Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/3/2022
Publication Date: 3/29/2022
Citation: Zhang, T., Wang, T., Niu, Q., Xu, L., Chen, Y., Gao, X., Gao, H., Zhang, L., Liu, G., Li, J., Xu, L. 2022. Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. BMC Biology. 20(1):79. https://doi.org/10.1186/s12915-022-01269-4.
DOI: https://doi.org/10.1186/s12915-022-01269-4

Interpretive Summary: Comprehensive analyses of transcriptomes will benefit our understanding of genetic bases for complex traits. We provided a beef cattle tissue-specific RNA expression analysis. These results fill our knowledge gaps and will benefit livestock genetic improvement. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Background: A comprehensive analysis of gene expression profiling across tissues can provide necessary information for in-depth understanding of biological functions. We performed a large-scale gene expression analysis and generated a high-resolution atlas of the transcriptome. Results: This atlas of the transcriptome was generated from 135 adult bovine tissues, covering 51 tissue types for all major organ systems (e.g., muscular system, the digestive system, immune system, reproductive system) in beef cattle. Approximately 94.76% of sequencing reads were successfully mapped to the cattle reference genome assembly ARS-UCD.12. We identified a total of 60,488 transcripts, and 32% of them were newly discovered by the current study. We identified 2,654 housekeeping genes (HKGs) and 477 tissue-specific genes (TSGs) across these tissues. Additionally, we obtained 24 modules and 237 hub genes (HUBGs) by using co-expression analysis. Functional enrichment showed that HKGs mainly maintain the basic biological activities of cells, while TSGs were involved in tissue differentiation and specific physiological processes. HKGs in bovine tissues were also more conserved in terms of expression pattern as compared to TSGs and HUBGs among species. Finally, we observed tissue-specific differentially expressed genes (DEGs) between beef and dairy cattle and identified several candidate genes, which may be involved in important production and health traits during the breed formation. Conclusions: We generated a large-scale gene expression profile across major tissues in beef cattle, providing valuable information for enhancing genome assembly and annotation. HKGs, TSGs and HUBGs further contribute to better understanding the biology and evolution of multiple tissues in cattle. DEGs between two breeds (beef vs. dairy purposes) also fill in the knowledge gaps about that differential transcriptome regulation of bovine tissues underlying important economic traits.