Allelic diversity of flowering-time regulatory gene Hd3a in rice

References

• Abbai, R., V. K. Singh, V. V. Nachimuthu, P. Sinha, R. Selvaraj, A. K. Vipparla, A. K. Singh, U. M. Singh, R. K. Varshney, and A. Kumar. 2019. “Haplotype Analysis of Key Genes Governing Grain Yield and Quality Traits across 3K RG Panel Reveals Scope for the Development of Tailor-made Rice with Enhanced Genetic Gains.” Plant Biotechnology Journal 17 (8): 1612–1622. doi:10.1111/pbi.13087.
   PubMed Web of Science ®Google Scholar
• Bimolata, W., A. Kumar, and R. M. Sundaram. 2015. “Nucleotide Diversity Analysis of Three Major Bacterial Blight Resistance Genes in Rice.” PloS One 10 (3): e0120186. doi:10.1371/journal.pone.0120186.
   PubMed Web of Science ®Google Scholar
• Chen, A., U. Baumann, G. B. Fincher, and N. C. Collins. 2009. “Flt-2L, a Locus in Barley Controlling Flowering Time, Spike Density, and Plant Height.” Functional & Integrative Genomics 9 (2): 243–254. doi:10.1007/s10142-009-0114-2.
   PubMed Web of Science ®Google Scholar
• Chow, C. N., H. Q. Zheng, N. Y. Wu, C. H. Chien, H. D. Huang, T. Y. Lee, Y. F. Chiang-Hsieh, P. F. Hou, T. Y. Yang, and W. C. Chang. 2015. “PlantPAN 2.0: An Update of Plant Promoter Analysis Navigator for Reconstructing Transcriptional Regulatory Networks in Plants.” Nucleic Acids Research 44 (D1): D1154–1160. doi:10.1093/nar/gkv1035.
   PubMed Web of Science ®Google Scholar
• Kearse, M., R. Moir, A. Wilson, S. Stones-Havas, M. Cheung, S. Sturrock, S. Buxton, A. Cooper, S. Markowitz, and C. Duran. 2012. “Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data.” Bioinformatics 28 (12): 1647–1649. doi:10.1093/bioinformatics/bts199.
   PubMed Web of Science ®Google Scholar
• Lee, Y. S., and G. An. 2015. “Regulation of Flowering Time in Rice.” Journal of Plant Biology 58 (6): 353–360. doi:10.1007/s12374-015-0425-x.
   Web of Science ®Google Scholar
• Lestari, P., G. Lee, T. H. Ham, M. O. Woo, R. Piao, W. Jiang, S. H. Chu, J. Lee, and H. J. Koh. 2011. “Single Nucleotide Polymorphisms and Haplotype Diversity in Rice Sucrose Synthase 3.” Journal of Heredity 102 (6): 735–746. doi:10.1093/jhered/esr094.
   PubMed Web of Science ®Google Scholar
• Lu, L., W. Yan, W. Xue, D. Shao, Y. Xing. 2012. “Evolution and Association Analysis of Ghd7 in Rice.” PloS One 7 (5): e34021. doi:10.1371/journal.pone.0034021.
   PubMed Web of Science ®Google Scholar
• Mansueto, L., R. R. Fuentes, F. N. Borja, J. Detras, J. M. Abriol-Santos, D. Chebotarov, M. Sanciangco, K. Palis, D. Copetti, and A. Poliakov. 2016. “Rice SNP-Seek Database Update: New SNPs, Indels, and Queries.” Nucleic Acids Research 45 (D1): D1075–D1081. doi:10.1093/nar/gkw1135.
   PubMed Web of Science ®Google Scholar
• Nanayakkara, N. H. L. D. L., D., . V. Herath, and D. V. Jayatilake. 2018. “Haplotype Diversity Analysis of Bacterial Leaf Blight Resistance Gene Xa21 in Rice.” Tropical Agricultural Research 30 (1): 56–68. doi:10.4038/tar.v30i1.8278.
   Google Scholar
• Ogiso-Tanaka, E., K. Matsubara, S. Yamamoto, Y. Nonoue, J. Wu, H. Fujisawa, H. Ishikubo, et al. 2013. “Natural Variation of the Rice Flowering Locus T 1 Contributes to Flowering Time Divergence in Rice.” PloS One 8 (10): e75959. doi:10.1371/journal.pone.0075959.
   PubMed Web of Science ®Google Scholar
• Okonechnikov, K., O. Golosova, and M. Fursov; UGENE team. 2012. “Unipro UGENE: A Unified Bioinformatics Toolkit.” Bioinformatics 28 (8): 1166–1167. doi:10.1093/bioinformatics/bts091.
   PubMed Web of Science ®Google Scholar
• Putterill, J., R. Laurie, and R. Macknight. 2004. “It’s Time to Flower: The Genetic Control of Flowering Time.” Bioessays 26 (4): 363–373. doi:10.1002/bies.20021.
   PubMed Web of Science ®Google Scholar
• Rozas, J., A. Ferrer-Mata, J. C. Sánchez-DelBarrio, S. Guirao-Rico, P. Librado, S. E. Ramos-Onsins, and A. Sánchez-Gracia. 2017. “DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.” Molecular Biology and Evolution 34 (12): 3299–3302. doi:10.1093/molbev/msx248.
   PubMed Web of Science ®Google Scholar
• Snyder, M. W., A. Adey, J. O. Kitzman, and J. Shendure. 2015. “Haplotype-Resolved Genome Sequencing: Experimental Methods and Applications.” Nature Reviews Genetics 16 (6): 344–358. doi:10.1038/nrg3903.
   PubMed Web of Science ®Google Scholar
• Takahashi, Y., K. M. Teshima, S. Yokoi, H. Innan, and K. Shimamoto. 2009. “Variations in Hd1 Proteins, Hd3a Promoters, and Ehd1 Expression Levels Contribute to Diversity of Flowering Time in Cultivated Rice.” Proceedings of the National Academy of Sciences of the United States of America 106 (11): 4555–4560. doi:10.1073/pnas.0812092106.
   PubMed Web of Science ®Google Scholar
• Yano, M., Y. Katayose, M. Ashikari, U. Yamanouchi, L. Monna, T. Fuse, T. Baba, K. Yamamoto, Y. Umehara, and Y. Nagamura. 2000. “Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS.” The Plant Cell 12 (12): 2473–2483. doi:10.1105/tpc.12.12.2473.
   PubMed Web of Science ®Google Scholar
• Yano, M., S. Kojima, Y. Takahashi, H. Lin, and T. Sasaki. 2001. “Genetic Control of Flowering Time in Rice, a Short-Day Plant.” Plant Physiology 127 (4): 1425–1429. doi:10.1104/pp.010710.
   PubMed Web of Science ®Google Scholar
• Yu, P., X. M. Wang, X. P. Yuan, C. H. Wang, Q. Xu, Y. Feng, H. Y. Yu, Y. P. Wang, and X. H. Wei. 2016. “Sequence Variations and Haplotypes of the Bacterial Blight Resistance Gene Xa13 in Rice.” Journal of Plant Pathology 98 (1): 167–170. doi:10.4454/JPP.V98I1.035.
   Web of Science ®Google Scholar
• Zhang, F., Z. C. Wu, M. M. Wang, F. Zhang, M. Dingkuhn, J. L. Xu, Y. L. Zhou, and Z. K. Li. 2017. “Genome-Wide Association Analysis Identifies Resistance Loci for Bacterial Blight in a Diverse Collection of Indica Rice Germplasm.” PloS One 12 (3): e0174598. doi:10.1371/journal.pone.0174598.
   PubMed Web of Science ®Google Scholar