Transcriptome Analysis Elucidates the Potential Key Genes Involved in Rib Development in bmp6-Deficient Silver Carp (Hypophthalmichthys molitrix)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Experimental Fish and Maintenance
2.2. Bmp6 Gene Editing by CRISPR/Cas9
2.3. Mutant Fish Identification
2.4. Phenotypic Observation
2.5. Total RNA Isolation and Sequencing
2.6. Differentially Expressed Genes Analysis
2.7. Quantitative Real-Time PCR (qRT-PCR) Analysis
2.8. Statistical Analysis
3. Results
3.1. Bmp6 Gene Editing in Silver Carp
3.2. Phenotypic Observation in P0 Chimeras
3.3. Analysis of Differential Expression Gene
3.4. Functional Analysis of DEGs
3.5. DEGs in Bone Development-Related Pathways
3.6. Validation of RNA-Seq Data Using qRT-PCR
4. Discussion
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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Classification | Wild-Type Silver Carp | P0 Chimeras |
---|---|---|
Bmp6 knockout efficiency | - | 86.11% |
Survival percentage | 79.2% | 77.4% |
Normal physical appearance | 100% | 100% |
Fish exhibiting diminished IBs | 0/15 | 13/18 |
The mean quantity of Ibs | 113 | 74 |
The reduction ratio of Ibs | - | 34.5% |
Fish exhibiting rib bifurcation | 0/15 | 3/18 |
Fish exhibiting rib bending | 0/15 | 6/18 |
Gene Abbreviation | Gene Description | Fold Change (WT vs. CH) | |
---|---|---|---|
qPCR | RNA-Seq | ||
ctgf | Connective tissue growth factor | 2.54 | 2.50 |
fos | Proto-oncogene | 4.30 | 5.80 |
metk | S-adenosyl methionine synthase isoform | 3.50 | 3.05 |
igh | Ig mu chain C region membrane-bound | 0.51 | 0.44 |
irak4 | Interleukin-1 receptor-associated kinase | 0.62 | 0.39 |
got1 | Aspartate aminotransferase, cytoplasmic | 0.41 | 0.47 |
bhmt | Betaine—homocysteine S-methyltransferase 1 | 0.33 | 0.36 |
card11 | Caspase recruitment domain-containing protein 11 | 0.63 | 0.45 |
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Li, X.; Zhang, C.; Feng, C.; Zhang, Z.; Feng, N.; Sha, H.; Luo, X.; Zou, G.; Liang, H. Transcriptome Analysis Elucidates the Potential Key Genes Involved in Rib Development in bmp6-Deficient Silver Carp (Hypophthalmichthys molitrix). Animals 2024, 14, 1451. https://doi.org/10.3390/ani14101451
Li X, Zhang C, Feng C, Zhang Z, Feng N, Sha H, Luo X, Zou G, Liang H. Transcriptome Analysis Elucidates the Potential Key Genes Involved in Rib Development in bmp6-Deficient Silver Carp (Hypophthalmichthys molitrix). Animals. 2024; 14(10):1451. https://doi.org/10.3390/ani14101451
Chicago/Turabian StyleLi, Xiaohui, Chunyan Zhang, Cui Feng, Zewen Zhang, Nannan Feng, Hang Sha, Xiangzhong Luo, Guiwei Zou, and Hongwei Liang. 2024. "Transcriptome Analysis Elucidates the Potential Key Genes Involved in Rib Development in bmp6-Deficient Silver Carp (Hypophthalmichthys molitrix)" Animals 14, no. 10: 1451. https://doi.org/10.3390/ani14101451