Genome Resequencing for Autotetraploid Rice and Its Closest Relatives Reveals Abundant Variation and High Potential in Rice Breeding
Abstract
:1. Introduction
2. Results
2.1. Breeding and Field Performance of Superior Hybrid Rice HTRM12
2.2. Comparison of Agronomic Traits of HT2, HT4, HTRM2, and HTRM12
2.3. Genome-Wide Polymorphism Detection in HT2, HT4, HTRM2, and HTRM12
2.4. SNP and InDel Site Annotation and Mutation Type Analysis of HT2, HT4, HTRM2, and HTRM12
2.5. GO Terms and KEGG Enrichment Analysis of SNP Mutant Genes of HT2, HT4, HTRM2, and HTRM12
2.6. GO Terms and KEGG Enrichment Analysis of InDel Mutant Genes of HT2, HT4, HTRM2, and HTRM12
2.7. Identification and Comparison of Copy Number Variation (CNV) for HT4, HTRM2, and HTRM12
3. Discussion
4. Materials and Methods
4.1. Rice Material and Phenotype Examination
4.2. The Disease and Pest Resistance Test
4.3. The High Temperature Resistance Test
4.4. Genome Sequencing and Data Quality Assessment
4.5. Analysis of Variation Information
4.6. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Enrichment Analyses
4.7. GWAS Phenotype Enrichment Analysis
4.8. Identification and Comparative Analysis of Copy Number Variation Intervals
4.9. Statistical Methods
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Variety | Susceptibility Index of Rice Blast | Susceptibility Index of Bacterial Leaf Blight | Susceptibility Index of Brown Planthopper |
---|---|---|---|
HTRM12 | 5.2 | 5 | 9 |
FLY4 (CK) | 6.5 | 5 | 9 |
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Zhang, Y.; Du, A.; Tong, L.; Yan, G.; Lu, L.; Yin, Y.; Fu, X.; Yang, H.; Li, H.; Huang, W.; et al. Genome Resequencing for Autotetraploid Rice and Its Closest Relatives Reveals Abundant Variation and High Potential in Rice Breeding. Int. J. Mol. Sci. 2024, 25, 9012. https://doi.org/10.3390/ijms25169012
Zhang Y, Du A, Tong L, Yan G, Lu L, Yin Y, Fu X, Yang H, Li H, Huang W, et al. Genome Resequencing for Autotetraploid Rice and Its Closest Relatives Reveals Abundant Variation and High Potential in Rice Breeding. International Journal of Molecular Sciences. 2024; 25(16):9012. https://doi.org/10.3390/ijms25169012
Chicago/Turabian StyleZhang, Yachun, Anping Du, Liqi Tong, Gui Yan, Longxiang Lu, Yanni Yin, Xingyue Fu, Huixin Yang, Hui Li, Weizao Huang, and et al. 2024. "Genome Resequencing for Autotetraploid Rice and Its Closest Relatives Reveals Abundant Variation and High Potential in Rice Breeding" International Journal of Molecular Sciences 25, no. 16: 9012. https://doi.org/10.3390/ijms25169012