Transcriptome Analysis of Compensatory Growth and Meat Quality Alteration after Varied Restricted Feeding Conditions in Beef Cattle
Abstract
:1. Introduction
2. Results
2.1. Animal Performance of Growth and Meat
2.2. Evaluation of RNA-Seq Data
2.3. Identification of DEGs in Longissimus Dorsi Muscle
2.4. Functional Enrichment Analysis of DEGs
2.5. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA)
2.6. Weighted Gene Co-Expression Network Analysis
2.7. Integrated Analysis to Identify Key Genes
3. Discussion
4. Materials and Methods
4.1. Animal and Experiment Design
4.2. Meta Quality and Composition
4.2.1. pH
4.2.2. Shear Force
4.2.3. Water Holding Capacity
4.2.4. Cooking Loss
4.2.5. Protein Content
4.2.6. Fat
4.2.7. Moisture
4.3. RNA Extraction and Sequencing
4.4. Transcriptomic Data Analysis
4.5. Developing the GO Database
4.6. Gene Ontology Enrichment Analysis of DEGs
4.7. Gene Set Enrichment Analysis
4.8. Gene Set Variation Analysis
4.9. Co-Expression Analysis Based on WGCNA
4.10. Screening of Key Genes and PPI Network
4.11. Statistical Analyses and Graphs
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Trait/Variable | ALF | RF75 | RF50 | SED | PANOVA |
---|---|---|---|---|---|
Body weight (BW), kg | |||||
Start, d0 | 375.76 | 379.41 | 375.74 | 42.95 | 0.991 |
Mid of RF_d28 | 415.24 Aa1 | 391.43 a | 358.52 b | 55.16 | 0.001 |
End of RF, d49 | 447.46 A | 401.43 B | 363.52 C | 50.46 | <0.001 |
Realimentation_d135 | 538.33 Aa | 529.37 a | 495.07 Bb | 50.35 | 0.007 |
Realimentation_d165 | 577.89 Aa | 572.32 a | 537.96 Bb | 50.06 | 0.01 |
Slaughter, d380 | 767.18 | 774.05 | 759.9 | 59.00 | 0.751 |
Average daily weight gain (ADG), kg/d | |||||
RF_d0–28 | 1.52 A | 0.52 B | −0.61 C | 1.01 | <0.001 |
RF_d28–49 | 1.4 A | 0.43 B | 0.22 B | 0.79 | <0.001 |
RF, d0–49 | 1.46 A | 0.45 B | −0.25 B | 0.78 | <0.001 |
Realimentation_d49_135 | 1.04 B | 1.47 A | 1.51 A | 0.31 | <0.001 |
Realimentation_d135_165 | 1.32 | 1.46 | 1.43 | 0.45 | 0.552 |
Realimentation_d165_380 | 0.82 | 0.93 | 0.96 | 0.28 | 0.196 |
Realimentation, d49–380 | 0.93 B | 1.12 A | 1.15 A | 0.21 | <0.001 |
Entire Period | 1.00 | 1.04 | 0.97 | 0.17 | 0.45 |
Trait/Variable | ALF | RF75 | RF50 | SED | PANOVA |
---|---|---|---|---|---|
Carcass trait | |||||
Carcass Weight, kg | 414.2 | 419.36 | 404.00 | 31.98 | 0.30 |
Striploin 1, kg | 6.40 | 6.41 | 6.23 | 0.76 | 0.70 |
High-rib, kg | 11.60 | 12.00 | 11.69 | 1.47 | 0.66 |
Tenderloin, kg | 4.12 | 4.10 | 3.99 | 0.51 | 0.68 |
EMA 3 | 104.6 | 108.71 | 106.25 | 11.16 | 0.5 |
Meat Quality | |||||
pH24 | 5.45 Aa2 | 5.80 Bb | 5.65 b | 0.29 | <0.001 |
Shear Force | 9.21 | 9.01 | 9.19 | 2.70 | 0.966 |
WHC | 0.38 | 0.36 | 0.37 | 0.04 | 0.208 |
Cooking Loss | 0.3 b | 0.29 ab | 0.24 a | 0.06 | 0.029 |
Meat Composition | |||||
Protein, % | 23.55 a | 22.77 b | 23.26 ab | 0.78 | 0.014 |
Fat, % | 2.98 a | 3.8 b | 3.34 ab | 0.93 | 0.042 |
Moisture, % | 72.89 | 72.06 | 72.33 | 1.22 | 0.146 |
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Deng, T.; Liang, M.; Du, L.; Li, K.; Li, J.; Qian, L.; Xue, Q.; Qiu, S.; Xu, L.; Zhang, L.; et al. Transcriptome Analysis of Compensatory Growth and Meat Quality Alteration after Varied Restricted Feeding Conditions in Beef Cattle. Int. J. Mol. Sci. 2024, 25, 2704. https://doi.org/10.3390/ijms25052704
Deng T, Liang M, Du L, Li K, Li J, Qian L, Xue Q, Qiu S, Xu L, Zhang L, et al. Transcriptome Analysis of Compensatory Growth and Meat Quality Alteration after Varied Restricted Feeding Conditions in Beef Cattle. International Journal of Molecular Sciences. 2024; 25(5):2704. https://doi.org/10.3390/ijms25052704
Chicago/Turabian StyleDeng, Tianyu, Mang Liang, Lili Du, Keanning Li, Jinnan Li, Li Qian, Qingqing Xue, Shiyuan Qiu, Lingyang Xu, Lupei Zhang, and et al. 2024. "Transcriptome Analysis of Compensatory Growth and Meat Quality Alteration after Varied Restricted Feeding Conditions in Beef Cattle" International Journal of Molecular Sciences 25, no. 5: 2704. https://doi.org/10.3390/ijms25052704