Analysis of Transcriptomic Differences in the Ovaries of High- and Low-Laying Ducks
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals and Sample Collection
2.2. Serum Physiological and Biochemical Index Testing
2.3. RNA Extraction, Library Preparation, and Illumina Hiseq Sequencing
2.4. RNA-Seq Data Processing and Analysis
2.5. Gene Ontology and KEGG Pathway Analysis of DEGs
2.6. Protein–Protein Interaction Network Analysis and Module Selection
2.7. Quantitative Real-Time PCR Analysis
2.8. Statistical Analysis
3. Results
3.1. Egg Quality Differences between the HEP and LEP Groups
3.2. Serum Physiological and Biochemical Differences between the HEP and LEP Groups
3.3. Transcriptome Alignment and Mapping Statistics
3.4. Differentially Expressed Genes (DEG) between the HEP and LEP Groups
3.5. Gene Ontology (GO) and KEGG Analyses for DEGs
3.6. Identification of Hub Genes and Pathways through PPI Network Analysis of DEGs
3.7. Validation of RNA-Seq Results by qRT-PCR
4. Discussion
4.1. Differences between Egg Quality in High- and Low-Egg-Production Shan Ma Ducks
4.2. Blood Physiological and Biochemical Indicators
4.3. Analysis of DEGs
4.4. Functional Classification Analysis
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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Item | LEP | HEP | p-Value |
---|---|---|---|
Egg production | 184.33 ± 4.55 | 215.50 ± 13.52 ** | 0.002 |
Eggshell thickness (mm) | 0.44 ± 0.02 | 0.42 ± 0.04 | 0.069 |
Egg weight (g) | 69.53 ± 7.43 | 78.55 ± 7.43 ** | 0.008 |
Ovary weight (g) | 2.58 ± 0.95 | 3.03 ± 1.08 | 0.784 |
Egg shape index | 1.31 ± 0.06 | 1.32 ± 0.06 | 0.279 |
Egg yolk color | 11.25 ± 0.45 | 11.36 ± 0.50 | 0.909 |
Eggshell strength (kg/cm2) | 4.74 ± 0.37 | 4.77 ± 0.79 | 0.151 |
Hastelloy unit | 63.87 ± 17.86 | 69.93 ± 12.36 | 0.002 |
Item | LEP | HEP | p-Value |
---|---|---|---|
Follicle-stimulating hormone (mIU/mL) | 1.77 ± 0.26 | 3.07 ± 0.19 ** | 0.000 |
Luteinizing hormone (mIU/mL) | 5.64 ± 0.83 | 8.22 ± 1.44 * | 0.021 |
Estradiol (pg/mL) | 31.55 ± 6.14 | 47.20 ± 5.45 ** | 0.009 |
Progesterone (ng/mL) | 12.12 ± 0.92 | 8.26 ± 0.90 ** | 0.001 |
Growth hormone (ng/mL) | 4.70 ± 0.72 | 7.06 ± 0.56 * | 0.002 |
Prolactin (μIU/mL) | 99.80 ± 2.86 | 87.12 ± 6.46 ** | 0.012 |
Triiodothyronine (ng/mL) | 0.73 ± 0.17 | 1.06 ± 0.09 * | 0.015 |
Thyroxine (ng/mL) | 9.14 ± 0.64 | 12.71 ± 1.09 ** | 0.001 |
Total protein (g/L) | 37.51 ± 5.99 | 57.55 ± 7.35 ** | 0.006 |
Albumin (g/L) | 13.15 ± 1.01 | 15.81 ± 0.88 ** | 0.007 |
Globulin (g/L) | 32.03 ± 1.25 | 36.24 ± 2.49 * | 0.023 |
Total cholesterol (mmol/L) | 1.98 ± 0.10 | 3.65 ± 0.38 ** | 0.000 |
Triglycerides (mmol/L) | 9.30 ± 1.95 | 17.49 ± 2.75 ** | 0.003 |
High-density lipoprotein (mmol/L) | 1.74 ± 0.50 | 0.90 ± 0.14 * | 0.019 |
Low-density lipoprotein (mmol/L) | 0.88 ± 0.19 | 1.16 ± 0.11 * | 0.045 |
Aspartate transaminase (U/L) | 48.90 ± 7.19 | 115.96 ± 56.41 | 0.056 |
Alanine transaminase (U/L) | 60.99 ± 5.25 | 82.22 ± 6.71 ** | 0.002 |
Gene ID | Read Count (LEP) | Read Count (HEP) | Log2 Fold-Change (HEP/LEP) | Up/Down (HEP/LEP) | p-Value | Gene Description |
---|---|---|---|---|---|---|
LOC101797718 | 0.58 | 54.78 | 6.55 | up | 0.00 | Apovitellenin-1-like precursor |
LOC101805018 | 0.00 | 0.86 | 9.76 | up | 0.00 | Prostatic acid phosphatase-like |
MAL | 0.03 | 2.03 | 6.16 | up | 0.00 | Myelin and lymphocyte protein |
LOC110354597 | 0.00 | 2.13 | 11.05 | up | 0.00 | Cygnin |
FGA | 0.03 | 2.12 | 6.10 | up | 0.00 | Fibrinogen alpha chain |
FGB | 0.05 | 3.07 | 6.04 | up | 0.00 | Fibrinogen beta chain |
ALB | 0.20 | 10.51 | 5.73 | up | 0.00 | Serum albumin precursor |
LOC101793493 | 0.00 | 1.46 | 10.51 | up | 0.00 | Fatty acid-binding protein, liver |
PHOX2A | 0.01 | 0.79 | 5.80 | up | 0.00 | Paired mesoderm homeobox Protein 2A |
PNMT | 0.00 | 2.20 | 11.10 | up | 0.00 | Phenylethanolamine N-methyltransferase |
LOC110351439 | 5.40 | 0.14 | −5.28 | down | 0.00 | Histone H3 |
LOC101799083 | 1.67 | 0.03 | −5.58 | down | 0.00 | Trefoil factor 2 |
LOC119716807 | 2.07 | 0.06 | −5.00 | down | 0.00 | Putative short transient receptor potential channel 2-like protein |
TMEM196 | 9.33 | 0.23 | −5.32 | down | 0.00 | Transmembrane protein 196 isoform X3 |
GJD2 | 2.05 | 0.07 | −4.95 | down | 0.00 | Gap junction delta-2 protein |
IHH | 1.96 | 0.04 | −5.55 | down | 0.00 | Indian hedgehog protein |
LOC119718687 | 1.86 | 0.05 | −5.29 | down | 0.00 | Butyrophilin subfamily 1 member A1-like |
SFTPC | 6.33 | 0.21 | −4.89 | down | 0.00 | Pulmonary surfactant-associated protein C isoform X1 |
LOC110354773 | 7.78 | 0.33 | −4.57 | down | 0.00 | Pulmonary surfactant-associated protein C-like |
LOC119715269 | 0.40 | 0.00 | −8.66 | down | 0.00 | Trypsin-3-like |
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Chang, Y.; Guo, R.; Zeng, T.; Sun, H.; Tian, Y.; Han, X.; Cao, Y.; Xu, L.; Duan, M.; Lu, L.; et al. Analysis of Transcriptomic Differences in the Ovaries of High- and Low-Laying Ducks. Genes 2024, 15, 181. https://doi.org/10.3390/genes15020181
Chang Y, Guo R, Zeng T, Sun H, Tian Y, Han X, Cao Y, Xu L, Duan M, Lu L, et al. Analysis of Transcriptomic Differences in the Ovaries of High- and Low-Laying Ducks. Genes. 2024; 15(2):181. https://doi.org/10.3390/genes15020181
Chicago/Turabian StyleChang, Yuguang, Rongbing Guo, Tao Zeng, Hanxue Sun, Yong Tian, Xue Han, Yongqing Cao, Ligen Xu, Mingcai Duan, Lizhi Lu, and et al. 2024. "Analysis of Transcriptomic Differences in the Ovaries of High- and Low-Laying Ducks" Genes 15, no. 2: 181. https://doi.org/10.3390/genes15020181
APA StyleChang, Y., Guo, R., Zeng, T., Sun, H., Tian, Y., Han, X., Cao, Y., Xu, L., Duan, M., Lu, L., & Chen, L. (2024). Analysis of Transcriptomic Differences in the Ovaries of High- and Low-Laying Ducks. Genes, 15(2), 181. https://doi.org/10.3390/genes15020181