Integrated Analysis of Phenotypic and Hepatic Transcriptomic Profiles Reveals Enhanced Cold Tolerance in Triploid Crucian Carp
Abstract
1. Introduction
2. Materials and Methods
2.1. Experimental Design
2.2. Histopathology Assay
2.3. Hepatopancreas Transcriptome Sequencing and Analysis
2.4. Quantitative Real-Time PCR (qRT-PCR) Validation
2.5. Statistical Analysis
3. Results
3.1. Triploid 3nRCR Exhibits Superior Behavioral Cold Tolerance During Gradual Cooling
3.2. Gill and Liver Histopathology Reveals Ploidy-Dependent Tissue Damage and Inflammation
3.3. Transcriptomic Profiling Identifies Triploid-Specific Stress Adaptation Networks in Hepatopancreas
3.3.1. Global Transcriptional Changes and Quality Control
3.3.2. Alternative Splicing Dynamics Highlight Transcriptional Stability in Triploids
3.3.3. Functional Enrichment Reveals Ploidy-Specific Pathways
3.4. Validation of Gene Expression by qRT-PCR
3.5. Differential Gene Expression and Functional Annotation-ER Stress-Immune Crosstalk Differentiates Survival Strategies
4. Discussion
4.1. Ploidy-Specific Transcriptional Remodeling and Genomic Flexibility
4.2. ER Stress and Apoptosis: Balancing Survival and Damage Control
4.3. Immune Modulation and Metabolic Reprogramming
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
RCC | Improved diploid red crucian carp |
3nRCR | triploid Xiangyun crucian carp 2 |
4nAT | Improved tetraploids |
PFA | paraformaldehyde |
H&E | hematoxylin and eosin |
RIN | RNA integrity number |
qRT-PCR | Quantitative Real-Time PCR |
SD | standard deviation |
ANOVA | one-way analysis of variance |
AS | alternative splicing |
DEGs | differentially expressed genes |
GO | Gene Ontology |
NLR | NOD-like receptor |
TLR | Toll-like receptor |
ER | endoplasmic reticulum |
ISR | integrated stress response |
IFN | I interferon |
LOE | Loss of equilibrium |
NO | nitric oxide |
ROS | Reactive Oxygen Species |
OXPHOS | Oxidative Phosphorylation |
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Tao, S.; Zhou, Z.; Chen, S.; Cui, J.; Wang, Y.; Luo, K.; Liu, W.; Liu, Q.; Li, W.; Liu, S. Integrated Analysis of Phenotypic and Hepatic Transcriptomic Profiles Reveals Enhanced Cold Tolerance in Triploid Crucian Carp. Fishes 2025, 10, 519. https://doi.org/10.3390/fishes10100519
Tao S, Zhou Z, Chen S, Cui J, Wang Y, Luo K, Liu W, Liu Q, Li W, Liu S. Integrated Analysis of Phenotypic and Hepatic Transcriptomic Profiles Reveals Enhanced Cold Tolerance in Triploid Crucian Carp. Fishes. 2025; 10(10):519. https://doi.org/10.3390/fishes10100519
Chicago/Turabian StyleTao, Suifei, Zexun Zhou, Shandong Chen, Jialin Cui, Yude Wang, Kaikun Luo, Wei Liu, Qingfeng Liu, Wuhui Li, and Shaojun Liu. 2025. "Integrated Analysis of Phenotypic and Hepatic Transcriptomic Profiles Reveals Enhanced Cold Tolerance in Triploid Crucian Carp" Fishes 10, no. 10: 519. https://doi.org/10.3390/fishes10100519
APA StyleTao, S., Zhou, Z., Chen, S., Cui, J., Wang, Y., Luo, K., Liu, W., Liu, Q., Li, W., & Liu, S. (2025). Integrated Analysis of Phenotypic and Hepatic Transcriptomic Profiles Reveals Enhanced Cold Tolerance in Triploid Crucian Carp. Fishes, 10(10), 519. https://doi.org/10.3390/fishes10100519