Integration of Long Non-Coding RNA and mRNA Profiling Reveals the Mechanisms of Different Dietary NFC/NDF Ratios Induced Rumen Development in Calves
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animals and Experimental Design
2.2. Feed Intake and Growth Performance
2.3. Preparation and Observation of Rumen Sections
2.4. RNA Extraction, Library Construction, and Sequencing
2.5. Data Mapping and Transcriptome Assembly
2.6. LncRNA Prediction
2.7. Structural and Conservative Analysis
2.8. Quantitation of Gene Expression
2.9. Prediction of lncRNA Targets
2.10. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes Analysis
2.11. Quantitative Real-Time PCR Analysis
2.12. Statistical Analysis
3. Results
3.1. Feed Intake and Growth Performance
3.2. Rumen Fermentation Parameters and Morphological Observation of Rumen Tissue
3.3. High-Throughput Sequencing and Quality Control
3.4. Identification of lncRNAs and mRNAs in Calves Rumen
3.5. Differential Expression Analysis of lncRNAs and mRNAs
3.6. Target Gene Prediction and Functional Enrichment Analysis
3.7. Integrated Analysis of Differentially Expressed lncRNAs and mRNA
3.8. The qRT-PCR Validation of the Sequencing Data
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Treatment (1) | |||
---|---|---|---|
Items | H Group | M Group | L Group |
Ingredients (% of dry matter) | |||
Corn | 43.62 | 48.00 | 30.03 |
Wheat bran | 15.00 | 0.00 | 0.00 |
Soybean meal | 2.90 | 4.30 | 2.57 |
Dried distiller’s grains with soluble | 15.00 | 15.00 | 15.00 |
Alfafa | 20.00 | 25.00 | 35.00 |
Chinese wild rye | 0.00 | 5.00 | 15.00 |
Limestone | 0.20 | 0.61 | 0.21 |
CaHPO4 | 1.78 | 0.59 | 0.69 |
Premix (2) | 1.00 | 1.00 | 1.00 |
NaCl | 0.50 | 0.50 | 0.50 |
Total | 100.00 | 100.00 | 100.00 |
Nutrient levels (% of dry matter, unless noted) | |||
Dry matter | 91.8 | 90.5 | 91.58 |
Crude protein | 16.34 | 16.42 | 16.38 |
Ether extract | 3.71 | 3.54 | 3.82 |
Ash | 7.57 | 7.93 | 7.44 |
Neutral detergent fiber | 34.43 | 37.14 | 45.33 |
Acid detergent fiber | 15.34 | 18.33 | 25.44 |
Calcium | 1.05 | 1.08 | 1.14 |
Phosphorus | 0.45 | 0.45 | 0.47 |
ME/(MJ/kg) (3) | 11.20 | 10.87 | 9.79 |
NFC/NDF (4) | 1.10 | 0.94 | 0.60 |
Accession NO. | Gene Symbol | Primer Sequence (5′ to 3′) | Annealing Temperature (°C) | Product Size |
---|---|---|---|---|
NM_174314.2 | FABP4 | F: AGTTTGAATGGGGGTGTGGT | 58 | 199 bp |
R: CGAGTTTTCTCTTTATGGTGGT | ||||
NM_001037319.1 | SLC16A1 | F: ATGCCACCACCAGTGAAGTG | 60 | 216 bp |
R: GCCCAAGACCTCCAATGACT | ||||
NM_001192369.1 | PAX9 | F: AGTATTCGTGAACGGGAGGC | 60 | 164 bp |
R: GCAAGATCGAGCCTGTCTCA | ||||
NM_001192245.1 | PLK2 | F: TCTCCATCACAAGCACGTCG | 60 | 273 bp |
R: GCCAAACCAAAGTCCCCAAC | ||||
NM_001109981.2 | ITGA6 | F: CGAAGCAGGAATCCCGAGAC | 60 | 296 bp |
R: TCCACCAACTTCATAAGGCCC | ||||
NM_181024.2 | PPARG | F: CAAGAGCTGACCCGATGGTT | 60 | 193 bp |
R: CCTGACGCTTTATCCCCACA | ||||
NM_001045949.2 | ESPL1 | F: TGAAGCCAGGCACCTATCC | 58 | 195 bp |
R: CCATCTTGACCCGAACCCA |
Items | Treatment 1 | SEM 2 | p-Value | ||
---|---|---|---|---|---|
H Group | M Group | L Group | |||
Initial body weight/kg | 95.04 | 93.82 | 93.23 | 9.27 | 0.481 |
Final body weight/kg | 190.88 | 183.43 | 171.27 | 2.96 | 0.964 |
Body weight gain/kg | 92.73 a | 77.07 b | 70.87 b | 3.12 | 0.009 |
Average daily gain/kg | 1.14 a | 1.00 b | 0.93 b | 0.03 | 0.008 |
Dry matter intake/(kg/d) | 4.09 | 3.81 | 3.85 | 0.11 | 0.605 |
Feed to gain ratio | 3.65 | 3.81 | 4.15 | 0.09 | 0.169 |
Items | Treatments 1 | SEM 2 | p-Value | ||
---|---|---|---|---|---|
H Group | M Group | L Group | |||
pH | 6.81 | 7.00 | 6.83 | 0.06 | 0.419 |
Acetate | 53.43 b | 59.92 a | 60.71 a | 1.24 | 0.026 |
Propionate (mmol/L) | 25.77 a | 21.66 ab | 18.96 b | 1.01 | 0.014 |
Butyrate (mmol/L) | 13.36 | 12.26 | 12.76 | 0.80 | 0.875 |
Papillae length (mm) | 0.75 b | 0.92 b | 1.11 a | 0.08 | 0.023 |
Papillae width (mm) | 0.38 a | 0.34 a | 0.24 b | 0.01 | <0.001 |
Muscle layer thickness (mm) | 1.21 | 1.23 | 1.35 | 0.04 | 0.144 |
Items | H-1 1 | H-2 2 | H-3 3 | L-1 4 | L-2 5 | L-3 6 |
---|---|---|---|---|---|---|
Raw reads | 129,008,240 | 97,533,606 | 113,893,888 | 84,213,254 | 89,185,784 | 99,002,628 |
Clean reads | 126,165,758 | 95,293,260 | 111,116,586 | 81,352,198 | 87,101,750 | 96,764,402 |
Percentage (%) | 97.80 | 97.70 | 97.56 | 96.60 | 97.66 | 97.74 |
Mapped reads | 104,668,662 | 80,985,576 | 93,383,745 | 67,890,749 | 72,068,883 | 82,345,847 |
Mapping rate (%) | 82.96 | 84.99 | 84.04 | 83.45 | 82.74 | 85.10 |
Q30 (%) | 93.64 | 93.23 | 92.68 | 91.93 | 93.83 | 93.33 |
Spliced reads (%) | 20.59 | 18.07 | 21.56 | 22.23 | 20.8 | 22.1 |
Non-spliced reads (%) | 59.65 | 64.54 | 59.59 | 57.47 | 58.57 | 60.21 |
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Li, J.; Xue, M.; Zhang, L.; Li, L.; Lian, H.; Li, M.; Gao, T.; Fu, T.; Tu, Y. Integration of Long Non-Coding RNA and mRNA Profiling Reveals the Mechanisms of Different Dietary NFC/NDF Ratios Induced Rumen Development in Calves. Animals 2022, 12, 650. https://doi.org/10.3390/ani12050650
Li J, Xue M, Zhang L, Li L, Lian H, Li M, Gao T, Fu T, Tu Y. Integration of Long Non-Coding RNA and mRNA Profiling Reveals the Mechanisms of Different Dietary NFC/NDF Ratios Induced Rumen Development in Calves. Animals. 2022; 12(5):650. https://doi.org/10.3390/ani12050650
Chicago/Turabian StyleLi, Jichao, Mingming Xue, Liyang Zhang, Lanjie Li, Hongxia Lian, Ming Li, Tengyun Gao, Tong Fu, and Yan Tu. 2022. "Integration of Long Non-Coding RNA and mRNA Profiling Reveals the Mechanisms of Different Dietary NFC/NDF Ratios Induced Rumen Development in Calves" Animals 12, no. 5: 650. https://doi.org/10.3390/ani12050650
APA StyleLi, J., Xue, M., Zhang, L., Li, L., Lian, H., Li, M., Gao, T., Fu, T., & Tu, Y. (2022). Integration of Long Non-Coding RNA and mRNA Profiling Reveals the Mechanisms of Different Dietary NFC/NDF Ratios Induced Rumen Development in Calves. Animals, 12(5), 650. https://doi.org/10.3390/ani12050650