In-Depth Sequence Analysis of Bread Wheat VRN1 Genes
Abstract
:1. Introduction
2. Results
2.1. CNV of VRN1 Homoeologs
2.2. VRN1 Sequence Variability and Gene Expression
2.2.1. Sequence Analysis of VRN-A1 Genes and Promoters
2.2.2. Sequence Analysis of VRN-B1 Genes and Promoters
2.2.3. Sequence Analysis of VRN-D1 Genes and Promoters
2.2.4. Comparison of VRN1 Homoeologous Promoter Regions
2.3. Effect of VRN-A1 CNV on Heading Time
3. Discussion
3.1. VRN1 Sequence Variability
3.2. VRN1 Promoter Secondary Structures
3.3. VRN1 Copy Number Variation
4. Materials and Methods
4.1. Plant Material
4.2. DNA Extraction and Genotyping
4.3. A Chromosome Sorting by Flow Cytometry
4.4. CNV of VRN1 Homoeologs and Ppd-B1
4.5. Sequencing of VRN1 Homoeologs
4.5.1. Sanger Sequencing
4.5.2. Illumina Sequencing
4.5.3. Oxford Nanopore Sequencing
4.5.4. Different Variants of the vrn-A1 Promoter
4.6. Sequencing Data Analysis
4.7. Growth Conditions
4.8. RNA Extraction and Gene Expression
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Oligo ID | 5′–3′ Sequence and Modifications | Amplicon Length | Reference |
---|---|---|---|
Ta-3D_F | CTCATCTCAGGCTGTCTAATTAA | 167 bp | [36] |
Ta-3D_R | CATAGATCCCTCCTTGAAGGA | ||
Ta-3D_taq | VIC-CCTCACTCAAGCACCACATCG-QSY | ||
CNV_VRNB1_F | CAGCATTCATCCAGCGGCAT | 114 bp | [28] |
CNV_VRNB1_R | CTTCAGCCGTTGATGTGGCTA | ||
CNV_VRNB1_taq | FAM-CAGAGGATGCGGCAGTGCAG-QSY | ||
CNV_VRND1_F | AAATTCTTGAACGGTATGAGCGCTAC | 109 bp | This study |
CNV_VRND1_R | GCTAAAGGAAAGCAAACCATTTG | ||
CNV_VRND1_taq | FAM-TGCAGAAAAGGTTCTCGTTTCAAGTG-QSY |
CNV | Winter Wheats | Spring Wheats | |||||||
---|---|---|---|---|---|---|---|---|---|
vrn-A1 | vrn-B1 | vrn-D1 | vrn-A1 | Vrn-A1a | Vrn-A1B | VRN-B1 | VRN-D1 | Vrn-D4 | |
1 | 4 | 65 | 65 | 4 | 15 | - | 40 | 40 | 1 |
2 | 18 | - | - | 6 | 8 | 3 | - | - | - |
3 | 41 | - | - | 4 | - | - | - | - | - |
4 | 2 | - | - | - | - | - | - | - | - |
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Strejčková, B.; Milec, Z.; Holušová, K.; Cápal, P.; Vojtková, T.; Čegan, R.; Šafář, J. In-Depth Sequence Analysis of Bread Wheat VRN1 Genes. Int. J. Mol. Sci. 2021, 22, 12284. https://doi.org/10.3390/ijms222212284
Strejčková B, Milec Z, Holušová K, Cápal P, Vojtková T, Čegan R, Šafář J. In-Depth Sequence Analysis of Bread Wheat VRN1 Genes. International Journal of Molecular Sciences. 2021; 22(22):12284. https://doi.org/10.3390/ijms222212284
Chicago/Turabian StyleStrejčková, Beáta, Zbyněk Milec, Kateřina Holušová, Petr Cápal, Tereza Vojtková, Radim Čegan, and Jan Šafář. 2021. "In-Depth Sequence Analysis of Bread Wheat VRN1 Genes" International Journal of Molecular Sciences 22, no. 22: 12284. https://doi.org/10.3390/ijms222212284