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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #385494

Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Comparative transcriptomic analysis reveals region-specifc expression patterns in diferent beef cuts

Author
item ZHANG, TIANLIU - Chinese Academy Of Agricultural Sciences
item WANG, TIANZHEN - Chinese Academy Of Agricultural Sciences
item NIU, QUNHAO - Chinese Academy Of Agricultural Sciences
item ZHENG, XU - Chinese Academy Of Agricultural Sciences
item LI, HAIPENG - Chinese Academy Of Agricultural Sciences
item GAO, XUE - Chinese Academy Of Agricultural Sciences
item CHEN, YAN - Chinese Academy Of Agricultural Sciences
item GAO, HUIJIANG - Chinese Academy Of Agricultural Sciences
item ZHANG, LUPEI - Chinese Academy Of Agricultural Sciences
item Liu, Ge - George
item LI, JUNYA - Chinese Academy Of Agricultural Sciences
item XU, LINGYANG - Chinese Academy Of Agricultural Sciences

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/30/2022
Publication Date: 5/20/2022
Citation: Zhang, T., Wang, T., Niu, Q., Zheng, X., Li, H., Gao, X., Chen, Y., Gao, H., Zhang, L., Liu, G., Li, J., Xu, L. 2022. Comparative transcriptomic analysis reveals region-specifc expression patterns in diferent beef cuts. Biomed Central (BMC) Genomics. 23(1):387. https://doi.org/10.1186/s12864-022-08527-3.
DOI: https://doi.org/10.1186/s12864-022-08527-3

Interpretive Summary: Gene expression analyses will benefit our understanding of genetic bases for meat quality. We conducted a gene expression analysis and identified 80 region-specific genes in five representative beef cuts (i.e., tenderloin, longissimus dorsi, rump, neck, and chuck). 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: Beef cuts in different regions of the carcass have different meat quality due to their distinct physiological function. The objective of this study was to characterize the region-specific expression differences using comparative transcriptomics analysis among five representative beef cuts (i.e., tenderloin, longissimus dorsi, rump, neck, and chuck) in beef cattle. Results: We totally obtained 15,701 expressed genes in 30 muscle samples across five regions from cattle carcasses. We identified a total of 80 region-specific genes (RSGs), ranging from 3 (identified in the rump cut) to 30 (identified in the longissimus doris cut), and detected 25 transcription factors (TFs) for RSGs. Using a co-expression network analysis, we detected seven region-specific modules, including three positive correlation modules (i.e., MEpink, MEgreen, MEmagenta) and four negative correlation modules (i.e., MEblue, MEgrey60, MElightyellow, MEroyalblue). We finally obtained 91 candidate genes related to meat quality, and the functional enrichment analyses showed that these genes were mainly involved in muscle fiber structural (e.g., TNNI1, TNNT1), fatty acid process (e.g., SCD, LPL), amino acids (ALDH2, IVD, ACADS), ion channel binding (i.e., PHPT1, SNTA1, SUMO1, CNBP), protein processing (e.g., CDC37, GAPDH, NRBP1), as well as energy production and conversion (e.g., ATP8, COX8B, NDUFB6). Conclusions: Our results provide valuable insights into understanding the transcriptome regulation of meat quality in different beef cuts, and these findings may further help to improve the selection for health-beneficial meat quality in beef cattle.