Transcriptome Analysis and Identification of Genes Associated with Cotton Seed Size
Abstract
:1. Introduction
2. Results
2.1. Obtaining and Phenotypic Analysis of Cotton Seed Size Materials
2.2. Transcriptome Assembly and Sample Clustering
2.3. Cottonseed Growth Curve and Gene Expression Network
2.4. Transcriptome Differences between N10 and N12 during Seed Development
2.5. Temporal Pattern Clusters of N10 and N12
2.6. Establishment of Weighed Gene Co-Expression Network Analysis (WGCNA)
2.7. Cottonseed Size Candidate Gene Screening
2.8. GhUXS5 Is a Candidate Gene That Affects Seed Size Function
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Sampling
4.2. RNA Extraction, Library Construction, and RNA-Seq Analysis
4.3. Principal Component Analysis, Ovule In Vitro Culture, and Growth Curves
4.4. Gene Expression Network
4.5. Differential Expression Analysis
4.6. Clusters of Temporal Patterns
4.7. WGCNA Pipeline
4.8. Phenotypic Identification of Arabidopsis Overexpressed GhUXS5
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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Year | Location | HSW | SA | SG | SL | SW | SD | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
N10 | N12 | N10 | N12 | N10 | N12 | N10 | N12 | N10 | N12 | N10 | N12 | ||
2017 | Alaer | 12.71 | 7.37 | 44.21 | 28.17 | 27.91 | 21.99 | 10.32 | 8.12 | 5.75 | 4.69 | 7.49 | 5.98 |
Shihezi | 12.51 | 7.42 | 45.91 | 28.71 | 28.31 | 22.15 | 10.59 | 8.32 | 5.75 | 4.63 | 7.63 | 6.04 | |
Anyang | 12.82 | 7.48 | 44.89 | 29.41 | 28.19 | 22.61 | 10.51 | 8.39 | 5.66 | 4.78 | 7.55 | 6.10 | |
Xingtai | 14.28 | 8.16 | 50.40 | 30.38 | 29.98 | 23.15 | 11.06 | 8.62 | 6.06 | 4.82 | 8.00 | 6.21 | |
2018 | Alaer | 11.38 | 8.05 | 41.95 | 29.92 | 27.09 | 22.33 | 10.32 | 8.53 | 5.40 | 4.74 | 7.26 | 6.17 |
Shihezi | 10.68 | 6.91 | 43.00 | 25.67 | 27.12 | 20.63 | 10.33 | 7.82 | 5.57 | 4.39 | 7.39 | 5.71 | |
Anyang | 11.41 | 8.21 | 43.80 | 30.69 | 27.66 | 22.77 | 10.39 | 8.58 | 5.61 | 4.86 | 7.46 | 6.24 | |
Xingtai | 13.83 | 7.63 | 49.90 | 28.94 | 29.59 | 22.23 | 11.04 | 8.33 | 5.97 | 4.70 | 7.96 | 6.06 |
Year | Location | HKW | KA | KG | KL | KW | KD | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
N10 | N12 | N10 | N12 | N10 | N12 | N10 | N12 | N10 | N12 | N10 | N12 | ||
2017 | Alaer | 7.50 | 4.42 | 28.38 | 17.86 | 22.81 | 17.55 | 8.80 | 6.78 | 4.21 | 3.49 | 6.00 | 4.76 |
Shihezi | 7.41 | 4.64 | 28.59 | 18.92 | 23.22 | 18.64 | 9.01 | 7.18 | 4.19 | 3.50 | 6.02 | 4.90 | |
Anyang | 8.28 | 5.28 | 30.34 | 20.39 | 23.85 | 18.72 | 9.24 | 7.23 | 4.34 | 3.78 | 6.21 | 5.09 | |
Xingtai | 9.02 | 5.28 | 32.00 | 19.96 | 24.59 | 18.78 | 9.50 | 7.17 | 4.46 | 3.74 | 6.38 | 5.04 | |
2018 | Alaer | 7.33 | 5.02 | 27.04 | 19.18 | 22.12 | 18.13 | 8.81 | 7.16 | 4.02 | 3.54 | 5.86 | 4.94 |
Shihezi | 6.17 | 4.33 | 26.10 | 17.52 | 22.72 | 17.45 | 9.00 | 6.73 | 3.86 | 3.46 | 5.76 | 4.72 | |
Anyang | 6.99 | 5.29 | 26.39 | 20.22 | 22.33 | 18.67 | 8.97 | 7.30 | 3.85 | 3.71 | 5.79 | 5.07 | |
Xingtai | 9.92 | 5.00 | 34.37 | 19.71 | 24.82 | 18.61 | 9.56 | 7.19 | 4.76 | 3.69 | 6.61 | 5.00 |
Primer Name | Sequence |
---|---|
GhUXS5-F | GGGGACAAGTTTGTACAAAAAAGCAGGCTTAATGGCAGCAAATTCATCAAATG |
GhUXS5-R | GGGGACCACTTTGTACAAGAAAGCTGGGTAGTTCTCTTTGGAGACTCCGAG |
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Jia, B.; Feng, P.; Song, J.; Zhou, C.; Wang, Y.; Zhang, B.; Wu, M.; Zhang, J.; Chen, Q.; Yu, J. Transcriptome Analysis and Identification of Genes Associated with Cotton Seed Size. Int. J. Mol. Sci. 2024, 25, 9812. https://doi.org/10.3390/ijms25189812
Jia B, Feng P, Song J, Zhou C, Wang Y, Zhang B, Wu M, Zhang J, Chen Q, Yu J. Transcriptome Analysis and Identification of Genes Associated with Cotton Seed Size. International Journal of Molecular Sciences. 2024; 25(18):9812. https://doi.org/10.3390/ijms25189812
Chicago/Turabian StyleJia, Bing, Pan Feng, Jikun Song, Caoyi Zhou, Yajie Wang, Bingbing Zhang, Man Wu, Jinfa Zhang, Quanjia Chen, and Jiwen Yu. 2024. "Transcriptome Analysis and Identification of Genes Associated with Cotton Seed Size" International Journal of Molecular Sciences 25, no. 18: 9812. https://doi.org/10.3390/ijms25189812