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Zhang T, Wang T, Niu Q, Zheng X, Li H, Gao X, Chen Y, Gao H, Zhang L, Liu GE, Li J, Xu L. Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts. BMC Genomics 2022; 23:387. [PMID: 35596128 PMCID: PMC9123670 DOI: 10.1186/s12864-022-08527-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
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 (tenderloin, longissimus lumborum, rump, neck, chuck). RESULTS We obtained 15,701 expressed genes in 30 muscle samples across five regions from carcass meat. We identified a total of 80 region-specific genes (RSGs), ranging from three (identified in the rump cut) to thirty (identified in the longissimus lumborum cut), and detected 25 transcription factors (TFs) for RSGs. Using a co-expression network analysis, we detected seven region-specific modules, including three positively correlated modules and four negatively correlated modules. 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 structure (e.g., TNNI1, TNNT1), fatty acids (e.g., SCD, LPL), amino acids (ALDH2, IVD, ACADS), ion channel binding (PHPT1, SNTA1, SUMO1, CNBP), protein processing (e.g., CDC37, GAPDH, NRBP1), as well as energy production and conversion (e.g., ATP8, COX8B, NDUFB6). Moreover, four candidate genes (ALDH2, CANX, IVD, PHPT1) were validated using RT-qPCR analyses which further supported our RNA-seq results. 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 in beef cattle.
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Affiliation(s)
- Tianliu Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Tianzhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Qunhao Niu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Xu Zheng
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Haipeng Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture-Agricultural Research Services, Beltsville, MD, 20705, USA
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China.
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China.
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Zalewska M, Puppel K, Sakowski T. Associations between gene polymorphisms and selected meat traits in cattle - A review. Anim Biosci 2021; 34:1425-1438. [PMID: 33561332 PMCID: PMC8495340 DOI: 10.5713/ab.20.0672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Maintaining a high level of beef consumption requires paying attention not only to quantitative traits but also to the quality and dietary properties of meat. Growing consumer demands do not leave producers many options for how animals are selected for breeding and animal keeping. Meat and carcass fatness quality traits, which are influenced by multiple genes, are economically important in beef cattle breeding programs. The recent availability of genome sequencing methods and many previously identified molecular markers offer new opportunities for animal breeding, including the use of molecular information in selection programs. Many gene polymorphisms have thus far been analyzed and evaluated as potential candidates for molecular markers of meat quality traits. Knowledge of these markers can be further applied to breeding programs through marker-assisted selection. In this literature review, we discuss the most promising and well-described candidates and their associations with selected beef production traits.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
| | - Kamila Puppel
- Institute of Animal Science, Warsaw University of Life Sciences, Warsaw 02-786, Poland
| | - Tomasz Sakowski
- Department of Biotechnology and Nutrigenomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences (PAS), Magdalenka 05-552, Poland
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