Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel pi21 Haplotype Conferring Basal Resistance to Rice Blast Disease
Abstract
:1. Introduction
2. Results
2.1. Evaluation of 02428 and LXG in Basal Resistance to Rice Blast Disease
2.2. SNP and Short InDel Polymorphism Profiling
2.3. QTL Mapping and Heritability Estimation
2.4. Identification of a New Haplotype of pi21 as a Candidate Gene of qBBR-4
2.5. Assessment of the pi21-2428 Haplotype in 325 Rice Accessions
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Blast Isolates
4.2. Rice Blast Inoculations
4.3. Bulking, DNA Extraction, and Whole-Genome Resequencing
4.4. Analysis of Reads and Variants
4.5. QTL Analysis
4.6. Detection of Haplotypes of Pi21
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
References
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Chr. | Length | SNP | Short InDel | ||
---|---|---|---|---|---|
Number | Density (per kb) | Number | Density (per kb) | ||
Chr1 | 43,270,923 | 48,669 | 1.12 | 7735 | 0.18 |
Chr2 | 35,937,250 | 67,302 | 1.87 | 9069 | 0.25 |
Chr3 | 36,413,819 | 20,399 | 0.56 | 3336 | 0.09 |
Chr4 | 35,502,694 | 42,156 | 1.19 | 5558 | 0.16 |
Chr5 | 29,958,434 | 67,386 | 2.25 | 9189 | 0.31 |
Chr6 | 31,248,787 | 34,848 | 1.12 | 5309 | 0.17 |
Chr7 | 29,697,621 | 25,681 | 0.86 | 4040 | 0.14 |
Chr8 | 28,443,022 | 56,474 | 1.99 | 7152 | 0.25 |
Chr9 | 23,012,720 | 23,331 | 1.01 | 2965 | 0.13 |
Chr10 | 23,207,287 | 36,435 | 1.57 | 4062 | 0.18 |
Chr11 | 29,021,106 | 31,309 | 1.08 | 4680 | 0.16 |
Chr12 | 27,531,856 | 15,522 | 0.56 | 2671 | 0.10 |
Total | 373,245,519 | 469,512 | 1.26 | 65,766 | 0.18 |
QTL | Chr. | AFD value a | Pos. (Mb) b | Interval (Mp) c | Max. NLP d | (%) e | (%) f |
---|---|---|---|---|---|---|---|
qBBR-4 | 4 | 0.278 | 20.46 | 18.90–22.10 | 0.90 | 2.09 | 7.82 |
qBBR-7 | 7 | 0.172 | 0.86 | 0–2.91 | 0.65 | 0.89 | 0.26 |
qBBR-8 | 8 | 0.227 | 10.63 | 3.89–18.09 | 0.85 | 1.56 | 0.01 |
qBBR-11 | 11 | 0.226 | 0.02 | 0–6.21 | 0.73 | 1.54 | 3.50 |
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Liang, T.; Chi, W.; Huang, L.; Qu, M.; Zhang, S.; Chen, Z.-Q.; Chen, Z.-J.; Tian, D.; Gui, Y.; Chen, X.; et al. Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel pi21 Haplotype Conferring Basal Resistance to Rice Blast Disease. Int. J. Mol. Sci. 2020, 21, 2162. https://doi.org/10.3390/ijms21062162
Liang T, Chi W, Huang L, Qu M, Zhang S, Chen Z-Q, Chen Z-J, Tian D, Gui Y, Chen X, et al. Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel pi21 Haplotype Conferring Basal Resistance to Rice Blast Disease. International Journal of Molecular Sciences. 2020; 21(6):2162. https://doi.org/10.3390/ijms21062162
Chicago/Turabian StyleLiang, Tingmin, Wenchao Chi, Likun Huang, Mengyu Qu, Shubiao Zhang, Zi-Qiang Chen, Zai-Jie Chen, Dagang Tian, Yijie Gui, Xiaofeng Chen, and et al. 2020. "Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel pi21 Haplotype Conferring Basal Resistance to Rice Blast Disease" International Journal of Molecular Sciences 21, no. 6: 2162. https://doi.org/10.3390/ijms21062162