Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material and Inoculation
2.2. RNA Extraction and Sequencing
2.3. Sequence Quality Control and Read Alignments
2.4. Differential Gene Expression (DGE)
2.5. SNP Discovery and Variant Prediction
2.6. Population Study
2.7. Sampling DNA from Rice Varieties
2.8. Data Mining and Functional Annotation
3. Results
3.1. Transcriptome Analyses
3.2. SNP Marker Discovery and Variant Cause Prediction
3.3. Double Haploid Population Study
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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SNP | Substitution Type | CCDR | MCR |
---|---|---|---|
A→G | Transition | 8703 | 11,102 |
T→C | Transition | 8896 | 11,228 |
G→A | Transition | 8735 | 11,420 |
C→T | Transition | 8878 | 11,622 |
G→C | Transversion | 2817 | 3523 |
C→G | Transversion | 2730 | 3559 |
T→G | Transversion | 3274 | 4108 |
G→T | Transversion | 3367 | 4158 |
A→C | Transversion | 3316 | 3964 |
C→A | Transversion | 3339 | 4175 |
T→A | Transversion | 3734 | 4428 |
A→T | Transversion | 3685 | 4397 |
Total SNPs | 61,474 | 77,684 | |
Total Indels | Insertions and deletions | 3647 | 4609 |
Total variants | 65,121 | 82,293 |
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Al-Bader, N.; Meier, A.; Geniza, M.; Gongora, Y.S.; Oard, J.; Jaiswal, P. Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance. Genes 2023, 14, 1673. https://doi.org/10.3390/genes14091673
Al-Bader N, Meier A, Geniza M, Gongora YS, Oard J, Jaiswal P. Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance. Genes. 2023; 14(9):1673. https://doi.org/10.3390/genes14091673
Chicago/Turabian StyleAl-Bader, Noor, Austin Meier, Matthew Geniza, Yamid Sanabria Gongora, James Oard, and Pankaj Jaiswal. 2023. "Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance" Genes 14, no. 9: 1673. https://doi.org/10.3390/genes14091673
APA StyleAl-Bader, N., Meier, A., Geniza, M., Gongora, Y. S., Oard, J., & Jaiswal, P. (2023). Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance. Genes, 14(9), 1673. https://doi.org/10.3390/genes14091673