Transcriptomic Analysis of Skin Tissue Reveals Molecular Mechanisms of Thermal Adaptation in Cold-Exposed Lambs
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Location, Animals, and Their Management
2.2. Experimental Design and Treatments
2.3. Sample Collection and Physiological Response Variables
2.4. Wool and Skin Response Variables
2.5. Transcriptome Sequencing and Differentially Expressed Gene Analyses
2.6. Functional Enrichment and Co-Expression Module Analysis
2.7. Validation with Reverse Transcription-Quantitative PCR (RT-qPCR)
2.8. Statistical Analyses
3. Results
3.1. Changes in Physiological Traits, Wool, and Skin Characteristics
3.2. Quality Assessment of RNA-Seq Data and Genome Alignment
3.3. Gene Expression Level and Cluster Analysis
3.3.1. Temperature Contrasts Across Breeds and Breed Contrasts Across Temperatures
3.3.2. Temperature Contrast Within Breed
3.3.3. Breed Contrast Within the Same Temperature
3.4. GO Analysis of the DEGs
3.5. KEGG Analysis of DEGs
3.5.1. Temperature Contrast Between Breeds
3.5.2. Temperature Contrast Within the Same Breed
3.5.3. Breed Contrasts at the Same Temperature
3.6. Co-Expression Network Construction and Analysis
3.7. Validation of RNA-Seq Data by RT-qPCR
4. Discussion
4.1. The Impact of Temperature on Physiological Traits, Wool and Skin Characteristics of the Lambs
4.2. Changes in the Immune and Endocrine System, Development and Regeneration, and Signal Transduction in Sheep in Colder Environments
4.3. Special Adaptations of Signal Transduction, Membrane Transport, Excretory and Endocrine System, and Metabolism in Hulunbuir Sheep at −20 °C
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ABCA2 | ATP binding cassette subfamily A member 2 |
APOLD1 | Apolipoprotein L domain containing 1 |
ATF3 | Activating transcription factor 3 |
CACNA1E | Calcium voltage-gated channel subunit alpha1 E |
CREB3L4 | cAMP responsive element binding protein 3 like 4 |
DUSP1 | Dual specificity phosphatase 1 |
EGR1 | Early growth response 1 |
FAM71A | Family with sequence similarity 71, member A |
FCGR2B | Fc gamma receptor IIb |
FOS | Fos proto-oncogene |
FOSB | FosB proto-oncogene |
GNLY | Granulysin |
IL1A | Interleukin 1 alpha |
JUN | Jun proto-oncogene |
JUNB | JunB proto-oncogene |
KLF2 | KLF transcription factor 2 |
LIF | LIF interleukin 6 family cytokine |
LIPE | Lipase E, hormone-sensitive type |
MSRA | Methionine sulfoxide reductase A |
MYLK3 | Myosin light chain kinase 3 |
NDST3 | N-deacetylase and N-sulfotransferase 3 |
NOS3 | Nitric oxide synthase 3 |
NOX1 | NADPH oxidase 1 |
NR4A1 | Nuclear receptor subfamily 4 group A member 1 |
OGT | O-linked N-acetylglucosamine (GlcNAc) transferase |
PTGS2 | Prostaglandin-endoperoxide synthase 2 |
RYR3 | Ryanodine receptor 3 |
SERPINE1 | Serpin family E member 1 |
SOCS3 | Suppressor of cytokine signaling 3 |
TNFAIP3 | TNF alpha induced protein 3 |
TSPAN13 | Tetraspanin 13 |
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Ingredient | Nutrient 2 | ||
---|---|---|---|
Alfalfa hay (%) | 25.35 | DM (%) | 96.26 |
Rice husk (%) | 4.65 | ME (MJ/kg) | 10.28 |
Corn (%) | 31.70 | Crude protein (%) | 14.01 |
Cottonseed meal (%) | 2.30 | Ca (%) | 0.54 |
Soybean meal (%) | 12.50 | P (%) | 0.26 |
Corn starch (%) | 18.50 | ||
Bypass fat powder (%) | 3.50 | ||
Limestone (%) | 0.30 | ||
NaCl (%) | 0.70 | ||
Premix 1 | 0.50 | ||
Rate of concentrate to roughage | 70:30 |
Gene Name | Primer Sequence (5′-3′) | Product Size (bp) | Tm (°C) |
---|---|---|---|
ACTB | GGTCATCACCATCGGCAAT | 113 | 60 |
CGTAGAGGTCTTTGCGGATG | |||
FOS | TACAATGGCTAGTGCAGCCC | 163 | 60 |
TTGGTCTGTCTCCGCTTGGA | |||
JUN | GCTTCCAAGTGCCGGAAAAG | 184 | 60 |
GCTGCGTTAGCATGAGTTGG | |||
PTGS2 | TAACACGCTCTACCACTGGC | 176 | 60 |
GATTCCTACGACCAGCGACC | |||
SERPINE1 | AAGAGCACCGTCCAGAGAGA | 130 | 60 |
ACATCTGCATCCTGAATTTCTCAA |
Characteristic | 15 °C | −20 °C | Hu | Hulunbuir | SEM | p-Value | ||
---|---|---|---|---|---|---|---|---|
Temperature | Breed | Interaction | ||||||
WGL (cm) | 1.1 ± 0.04 | 1.7 ± 0.10 | 1.3 ± 0.09 | 1.4 ± 0.15 | 0.09 | <0.001 | 0.243 | 0.046 |
FWMFD (µm) | 20.5 ± 0.58 | 21.1 ± 0.42 | 21.7 ± 0.40 | 19.8 ± 0.41 | 0.35 | 0.344 | 0.004 | 0.262 |
WY (g) | 0.3 ± 0.02 | 0.3 ± 0.03 | 0.3 ± 0.02 | 0.3 ± 0.03 | 0.02 | 0.140 | 0.037 | 0.139 |
HFD (/mm2) | 38.7 ± 2.39 | 33.0 ± 1.45 | 33.5 ± 1.74 | 38.1 ± 2.31 | 1.51 | 0.044 | 0.094 | 0.208 |
ET (µm) | 15.2 ± 0.65 | 18.7 ± 0.79 | 16.5 ± 0.60 | 17.3 ± 1.15 | 0.64 | 0.002 | 0.431 | 0.050 |
ADG (g/d) | 105.5 ± 17.03 | 59.6 ± 10.44 | 75.2 ± 17.44 | 89.8 ± 14.14 | 11.05 | 0.037 | 0.480 | 0.286 |
RT (°C) | 38.8 ± 0.04 | 38.1 ± 0.09 | 38.4 ± 0.14 | 38.4 ± 0.12 | 0.09 | <0.001 | 0.923 | 0.923 |
RR (breaths/min) | 22.4 ± 1.42 | 16.0 ± 0.84 | 18.7 ± 1.36 | 19.7 ± 1.75 | 1.09 | 0.001 | 0.526 | 0.213 |
Characteristic | −20 °C | 15 °C | p-Value | |||||
---|---|---|---|---|---|---|---|---|
HU−20 | HB−20 | HU+15 | HB+15 | HU+15 vs. HU−20 | HB+15 vs. HB−20 | HU−20 vs. HB−20 | HU+15 vs. HB+15 | |
WGL (cm) | 1.5 ± 0.12 | 1.8 ± 0.13 | 1.1 ± 0.08 | 1.0 ± 0.46 | 0.028 | <0.001 | 0.096 | 0.310 |
FWMFD (µm) | 21.7 ± 0.69 | 20.4 ± 0.35 | 21.8 ± 0.48 | 19.2 ± 0.67 | 0.903 | 0.147 | 0.144 | 0.014 |
WY (g) | 0.3 ± 0.15 | 0.4 ± 0.03 | 0.3 ± 0.03 | 0.3 ± 0.03 | 0.999 | 0.074 | 0.025 | 0.630 |
HFD (/mm2) | 32.4 ± 2.20 | 33.6 ± 2.11 | 34.7 ± 2.87 | 42.7 ± 3.06 | 0.549 | 0.041 | 0.702 | 0.092 |
ET (µm) | 17.3 ± 0.64 | 20.0 ± 1.20 | 15.8 ± 0.97 | 14.6 ± 0.87 | 0.240 | 0.006 | 0.076 | 0.370 |
ADG (g/d) | 41.2 ± 7.16 | 77.9 ± 16.44 | 109.3 ± 27.16 | 101.6 ± 23.66 | 0.042 | 0.435 | 0.074 | 0.837 |
HCW (kg) | 19.5 ± 0.47 | 19.8 ± 0.72 | 21.1 ± 0.39 | 20.2 ± 0.62 | 0.030 | 0.732 | 0.736 | 0.221 |
RT (°C) | 38.1 ± 0.16 | 38.1 ± 0.10 | 38.8 ± 0.07 | 38.8 ± 0.04 | 0.004 | <0.001 | 0.918 | 1.000 |
RR (breaths/min) | 16.5 ± 1.37 | 15.5 ± 1.08 | 20.8 ± 2.05 | 24.0 ± 1.89 | 0.122 | 0.004 | 0.559 | 0.284 |
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Feng, M.; Ji, K.; Li, Y.; Alexandre, P.A.; Jiao, D.; Liang, Y.; Du, X.; Cheng, X.; Zhou, H.; Hickford, J.G.H.; et al. Transcriptomic Analysis of Skin Tissue Reveals Molecular Mechanisms of Thermal Adaptation in Cold-Exposed Lambs. Animals 2025, 15, 1405. https://doi.org/10.3390/ani15101405
Feng M, Ji K, Li Y, Alexandre PA, Jiao D, Liang Y, Du X, Cheng X, Zhou H, Hickford JGH, et al. Transcriptomic Analysis of Skin Tissue Reveals Molecular Mechanisms of Thermal Adaptation in Cold-Exposed Lambs. Animals. 2025; 15(10):1405. https://doi.org/10.3390/ani15101405
Chicago/Turabian StyleFeng, Mengyu, Kaixi Ji, Yutao Li, Pâmela Almeida Alexandre, Dan Jiao, Yanping Liang, Xia Du, Xindong Cheng, Huitong Zhou, Jon G. H. Hickford, and et al. 2025. "Transcriptomic Analysis of Skin Tissue Reveals Molecular Mechanisms of Thermal Adaptation in Cold-Exposed Lambs" Animals 15, no. 10: 1405. https://doi.org/10.3390/ani15101405
APA StyleFeng, M., Ji, K., Li, Y., Alexandre, P. A., Jiao, D., Liang, Y., Du, X., Cheng, X., Zhou, H., Hickford, J. G. H., & Yang, G. (2025). Transcriptomic Analysis of Skin Tissue Reveals Molecular Mechanisms of Thermal Adaptation in Cold-Exposed Lambs. Animals, 15(10), 1405. https://doi.org/10.3390/ani15101405