Tamaki S, Matsuo S, Wong HL, Yokoi S, Shimamoto K. Hd3a protein is a mobile flowering signal in rice. Science. 2007;316:1033–6.

Article  CAS  PubMed  Google Scholar 

Komiya R, Ikegami A, Tamaki S, Yokoi S, Shimamoto K. Hd3a and RFT1 are essential for flowering in rice. Development. 2008;135:767–74.

Article  CAS  PubMed  Google Scholar 

Komiya R, Yokoi S, Shimamoto K. A gene network for long-day flowering activates RFT1 encoding a mobile flowering signal in rice. Development. 2009;136:3443–50.

Article  CAS  PubMed  Google Scholar 

Taoka K, Ohki I, Tsuji H, Furuita K, Hayashi K, Yanase T, Yamaguchi M, Nakashima C, Purwestri YA, Tamaki S, Ogaki Y, Shimada C, Nakagawa A, Kojima C, Shimamoto K. 14–3-3 proteins act as intracellular receptors for rice Hd3a florigen. Nature. 2011;476(7360):332–5. https://doi.org/10.1038/nature10272.

Article  CAS  PubMed  Google Scholar 

Liu L, Liu C, Hou X, Xi W, Shen L, Tao Z, Wang Y, Yu H. FTIP1 is an essential regulator required for florigen transport. PLoS Biol. 2012;10: e1001313.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Song S, Chen Y, Liu L, Wang Y, Bao S, Zhou X, Teo ZW, Mao C, Gan Y, Yu H. OsFTIP1-mediated regulation of florigen transport in rice is negatively regulated by the ubiquitin-like domain kinase OsUbDK?4. Plant Cell. 2017;29(3):491–507. https://doi.org/10.1105/tpc.16.00728.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A. Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev. 2004;18(8):926–36. https://doi.org/10.1101/gad.1189604.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, et al. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell. 2000;12:2473–84.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet. 2008;40:761–7.

Article  CAS  PubMed  Google Scholar 

Shen C, Liu H, Guan Z, Yan J, Zheng T, Yan W, Wu C, Zhang Q, Yin P, Xing Y. Structural insight into DNA recognition by CCT/NF-YB/YC complexes in plant photoperiodic flowering. Plant Cell. 2020;32:3469–84.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Du A, Tian W, Wei M, Yan W, He H, Zhou D, Huang X, Li S, Ouyang X. The DTH8-Hd1 module mediates day-length-dependent regulation of rice flowering. Mol Plant. 2017;10:948–61.

Article  CAS  PubMed  Google Scholar 

Goretti D, Martignago D, Landini M, Brambilla V, Gómez-Ariza J, Gnesutta N, Galbiati F, Collani S, Takagi H, Terauchi R, Mantovani R, Fornara F. Transcriptional and posttranscriptional mechanisms limit heading date 1 (Hd1) function to adapt rice to high latitudes. PLoS Genet. 2017;13: e1006530.

Article  PubMed  PubMed Central  Google Scholar 

Roy S, Banerjee A, Mawkhlieng B, Misra AK, Pattanayak A, Harish GD, et al. Genetic diversity and population structure in aromatic and quality rice (Oryza sativa L.) landraces from North-Eastern India. PLoS ONE. 2015;10(6): e0129607.

Article  PubMed  PubMed Central  Google Scholar 

Das A, Kesari V, Rangan L. Aromatic Joha rice of Assam: a review. Agric Rev. 2010;31(1):1–10.

Google Scholar 

Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE. The gene for fragrance in rice. Plant Biotechnol J. 2005;3:363–70.

Article  CAS  PubMed  Google Scholar 

Sashankar P, Chidambaranathan P, Anandan A, Sathyanarayana N. Downregulation of badh2 gene is responsible for aroma in Kon Joha rice (Oryza sativa L.) of Assam. Nucleus. 2024. https://doi.org/10.1007/s13237-024-00476-4.

Article  Google Scholar 

Morita R, Kusaba M, Iida S, Yamaguchi H, Nishio T, Nishimura M. Molecular characterization of mutations induced by gamma irradiation in rice. Genes Genet Syst. 2009;84:361–70. https://doi.org/10.1266/ggs.84.361.

Article  CAS  PubMed  Google Scholar 

Viana VE, Pegoraro C, Busanello C, de Oliveira AC. Mutagenesis in Rice: the basis for breeding a new super plant. Front Plant Sci. 2019;10:1326. https://doi.org/10.3389/fpls.2019.01326.

Article  PubMed  PubMed Central  Google Scholar 

Riviello-Flores ML, Cadena-Iñiguez J, Ruiz-Posadas LDM, Arévalo-Galarza ML, Castillo-Juárez I, Soto Hernández M, Castillo-Martínez CR. Use of gamma radiation for the genetic improvement of underutilized plant varieties. Plants. 2022;11(9):1161. https://doi.org/10.3390/plants11091161.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fu HW, Li YF, Shu QY. A revisit of mutation induction by gamma rays in rice (Oryza sativa L.): implications of microsatellite markers for quality control. Mol Breed. 2008;22:281–8. https://doi.org/10.1007/s11032-008-9173-7.

Article  CAS  Google Scholar 

Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol. 2004;135(3):1198–205. https://doi.org/10.1104/pp.103.038463.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lima JM, Nath M, Dokku P, Raman KV, Kulkarni KP, Vishwakarma C, Sahoo SP, Mohapatra UB, Amitha Mithra SV, Chinnusamy V, Robin S, Sarla N, Sheshashayee M, Singh K, Singh AK, Singh NK, Sharma RP, Mohapatra T. Physiological, anatomical and transcriptional alterations in a rice mutant leading to enhanced water stress tolerance. AoB Plants. 2015;7: plv023. https://doi.org/10.1093/aobpla/plv023.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shoba D, Raveendran M, Manonmani S, Utharasu S, Dhivyapriya D, Subhasini G, Ramchandar S, Valarmathi R, Grover N, Krishnan SG, Singh AK, Jayaswal P, Kale P, Ramkumar MK, Mithra SVA, Mohapatra T, Singh K, Singh NK, Sarla N, Sheshshayee MS, Kar MK, Robin S, Sharma RP. Development and genetic characterization of a novel herbicide (Imazethapyr) tolerant mutant in rice (Oryza sativa L.). Rice. 2017;10(1):10. https://doi.org/10.1186/s12284-017-0151-8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Michelmore RW, Paran I, Kesseli RV. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA. 1991;88:9828–32.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. https://doi.org/10.1093/bioinformatics/btp352.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cingolani P, Platts A, le Wang, L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6(2):80–92. https://doi.org/10.4161/fly.19695.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res. 1994;22(22):4673–80. https://doi.org/10.1093/nar/22.22.4673.

Article  CAS  PubMed