| [1] |
Ziska LH, Gealy DR, Burgos N, Caicedo AL, Gressel J, et al. 2015. Weedy (red) rice: an emerging constraint to global rice production. Advances in Agronomy 129:181−228 doi: 10.1016/bs.agron.2014.09.003 |
| [2] |
Olsen KM, Caicedo A, Jia Y. 2007. Evolutionary genomics of weedy rice in the USA. Journal of Integrative Plant Biology 49:811−16 |
| [3] |
Roma-Burgos N, San Sudo MP, Olsen KM, Werle I, Song BK. 2021. Weedy rice (Oryza spp.): what's in a name? Weed Science 69:505−13 doi: 10.1017/wsc.2021.22 |
| [4] |
Ellstrand NC, Heredia SM, Leak-Garcia JA, Heraty JM, Burger JC, et al. 2010. Crops gone wild: evolution of weeds and invasives from domesticated ancestors. Evolutionary Applications 3:494−504 doi: 10.1111/j.1752-4571.2010.00140.x |
| [5] |
Li LF, Li YL, Jia Y, Caicedo AL, Olsen KM. 2017. Signatures of adaptation in the weedy rice genome. Nature Genetics 49:811−14 doi: 10.1038/ng.3825 |
| [6] |
He Q, Kim KW, Park YJ. 2017. Population genomics identifies the origin and signatures of selection of Korean weedy rice. Plant Biotechnology Journal 15:357−66 doi: 10.1111/pbi.12630 |
| [7] |
Qiu J, Zhou Y, Mao L, Ye C, Wang W, et al. 2017. Genomic variation associated with local adaptation of weedy rice during de-domestication. Nature Communications 8:15323 doi: 10.1038/ncomms15323 |
| [8] |
Sun J, Ma D, Tang L, Zhao M, Zhang G, et al. 2019. Population genomic analysis and de novo assembly reveal the origin of weedy rice as an evolutionary game. Molecular Plant 12:632−47 doi: 10.1016/j.molp.2019.01.019 |
| [9] |
Qiu J, Jia L, Wu D, Weng X, Chen L, et al. 2020. Diverse genetic mechanisms underlie worldwide convergent rice feralization. Genome Biology 21:70 doi: 10.1186/s13059-020-01980-x |
| [10] |
Li LF, Pusadee T, Wedger MJ, Li YL, Li MR, et al. 2024. Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia. Nature Communications 15:1182 doi: 10.1038/s41467-024-45447-0 |
| [11] |
Sun J, Qian Q, Ma DR, Xu ZJ, Liu D, et al. 2013. Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China. New Phytologist 197:290−99 doi: 10.1111/nph.12012 |
| [12] |
Song ZJ, Wang Z, Feng Y, Yao N, Yang J, et al. 2015. Genetic divergence of weedy rice populations associated with their geographic location and coexisting conspecific crop: Implications on adaptive evolution of agricultural weeds. Journal of Systematics and Evolution 53:330−38 doi: 10.1111/jse.12152 |
| [13] |
Imaizumi T, Ebana K, Kawahara Y, Muto C, Kobayashi H, et al. 2021. Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution. Communications Biology 4:952 doi: 10.1038/s42003-021-02484-5 |
| [14] |
Huang Z, Young ND, Reagon M, Hyma KE, Olsen KM, et al. 2017. All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza. Molecular Ecology 26:3151−67 doi: 10.1111/mec.14120 |
| [15] |
Presotto A, Hernández F, Vercellino RB, Kruger RD, Fontana ML, et al. 2024. Introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice. Molecular Ecology 33:e17368 doi: 10.1111/mec.17368 |
| [16] |
Reagon M, Thurber CS, Gross BL, Olsen KM, Jia Y, et al. 2010. Genomic patterns of nucleotide diversity in divergent populations of US weedy rice. BMC Evolutionary Biology 10:180 doi: 10.1186/1471-2148-10-180 |
| [17] |
Zhu M, Yong K, Xu K, Cong J, Zhou X, et al. 2024. Landrace introgression contributed to the recent feralization of weedy rice in East China. Plant Communications 5:101066 doi: 10.1016/j.xplc.2024.101066 |
| [18] |
Olsen KM, Wendel JF. 2013. A bountiful harvest: genomic insights into crop domestication phenotypes. Annual Review of Plant Biology 64:47−70 doi: 10.1146/annurev-arplant-050312-120048 |
| [19] |
Gu XY, Foley ME, Horvath DP, Anderson JV, Feng J, et al. 2011. Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates abscisic acid and flavonoid synthesis in weedy red rice. Genetics 189:1515−24 doi: 10.1534/genetics.111.131169 |
| [20] |
Zhou W, Wang X, Zhou D, Ouyang Y, Yao J. 2017. Overexpression of the 16-kDa α-amylase/trypsin inhibitor RAG2 improves grain yield and quality of rice. Plant Biotechnology Journal 15:568−80 doi: 10.1111/pbi.12654 |
| [21] |
Song BK, Chuah TS, Tam SM, Olsen KM. 2014. Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia. Molecular Ecology 23:5003−17 doi: 10.1111/mec.12922 |
| [22] |
Vigueira CC, Qi X, Song BK, Li LF, Caicedo AL, et al. 2019. Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia. Evolutionary Applications 12:93−104 doi: 10.1111/eva.12581 |
| [23] |
Wu D, Xie L, Sun Y, Huang Y, Jia L, et al. 2023. A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Genome Biology 24:179 doi: 10.1186/s13059-023-03017-5 |
| [24] |
Jiang Z, Xia H, Basso B, Lu BR. 2012. Introgression from cultivated rice influences genetic differentiation of weedy rice populations at a local spatial scale. Theoretical and Applied Genetics 124:309−22 doi: 10.1007/s00122-011-1706-5 |
| [25] |
Wedger MJ, Roma-Burgos N, Olsen KM. 2022. Genomic revolution of US weedy rice in response to 21st century agricultural technologies. Communications Biology 5:885 doi: 10.1038/s42003-022-03803-0 |
| [26] |
Lin YL, Wu DH, Wu CC, Huang YF. 2021. Explore the genetics of weedy traits using rice 3K database. Botanical Studies 62:2 doi: 10.1186/s40529-020-00309-y |
| [27] |
Yao N, Wang L, Yan H, Liu Y, Lu BR. 2015. Mapping quantitative trait loci (QTL) determining seed-shattering in weedy rice: evolution of seed shattering in weedy rice through de-domestication. Euphytica 204:513−22 doi: 10.1007/s10681-014-1331-x |
| [28] |
Li X, Lowey D, Lessard J, Caicedo AL. 2024. Comparative histology of abscission zones reveals the extent of convergence and divergence in seed shattering in weedy and cultivated rice. Journal of Experimental Botany 75:4837−50 doi: 10.1093/jxb/erae221 |
| [29] |
Qi X, Liu Y, Vigueira CC, Young ND, Caicedo AL, et al. 2015. More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms. Molecular Ecology 24:3329−44 doi: 10.1111/mec.13256 |
| [30] |
Li X, Zhang S, Lowey D, Hissam C, Clevenger J, et al. 2023. A derived weedy rice × ancestral cultivar cross identifies evolutionarily relevant weediness QTLs. Molecular Ecology 32:5971−85 doi: 10.1111/mec.17172 |
| [31] |
Wei X, Chen M, Zhang Q, Gong J, Liu J, et al. 2024. Genomic investigation of 18, 421 lines reveals the genetic architecture of rice. Science 385:eadm8762 doi: 10.1126/science.adm8762 |
| [32] |
Cao S, Chen K, Lu K, Chen S, Zhang X, et al. 2023. Asymmetric variation in DNA methylation during domestication and de-domestication of rice. The Plant Cell 35:3429−43 doi: 10.1093/plcell/koad160 |
| [33] |
Wang H, Lu H, Yang Z, Zhang Z, Li M, et al. 2023. Characterization of lodging variation of weedy rice. Journal of Experimental Botany 74:1403−19 doi: 10.1093/jxb/erac480 |
| [34] |
Xie H, Han Y, Li X, Dai W, Song X, et al. 2020. Climate-dependent variation in cold tolerance of weedy rice and rice mediated by OsICE1 promoter methylation. Molecular Ecology 29:121−37 doi: 10.1111/mec.15305 |
| [35] |
Zhang G, Liu Y, Gui R, Wang Z, Li Z, et al. 2021. Comparative multi-omics analysis of hypoxic germination tolerance in weedy rice embryos and coleoptiles. Genomics 113:3337−48 doi: 10.1016/j.ygeno.2021.07.021 |
| [36] |
Zhang G, Wang X, Wang Y, Hua D, Lv H, et al. 2024. Combined transcriptome and metabolome analyses reveal the mechanism of abundant bioactive compounds and high antioxidant activity in germinated weedy rice. Journal of Food Science 89:5517−30 doi: 10.1111/1750-3841.17229 |
| [37] |
Chauhan BS. 2013. Strategies to manage weedy rice in Asia. Crop Protection 48:51−56 doi: 10.1016/j.cropro.2013.02.015 |
| [38] |
Chauhan BS, Singh K, Ladha JK, Kumar V, Saharawat YS, et al. 2013. Weedy rice: an emerging threat for direct-seeded rice production systems in India. Journal of Rice Research 1:106 doi: 10.4172/jrr.1000106 |
| [39] |
Zhang Z, Gao PL, Dai WM, Song XL, Hu F, et al. 2019. Effect of tillage and burial depth and density of seed on viability and seedling emergence of weedy rice. Journal of Integrative Agriculture 18:1914−23 doi: 10.1016/S2095-3119(19)62583-9 |
| [40] |
Wang HQ, Dai WM, Zhang ZX, Li MS, Meng LC, et al. 2023. Occurrence pattern and morphological polymorphism of Chinese weedy rice. Journal of Integrative Agriculture 22:149−69 doi: 10.1016/j.jia.2022.08.001 |
| [41] |
Jin M, Chen L, Deng XW, Tang X. 2022. Development of herbicide resistance genes and their application in rice. The Crop Journal 10:26−35 doi: 10.1016/j.cj.2021.05.007 |
| [42] |
Li J, Meng X, Zong Y, Chen K, Zhang H, et al. 2016. Gene replacements and insertions in rice by intron targeting using CRISPR–Cas9. Nature Plants 2:16139 doi: 10.1038/nplants.2016.139 |
| [43] |
Deng W, Yang Q, Zhang Y, Jiao H, Mei Y, et al. 2017. Cross-resistance patterns to acetolactate synthase (ALS)-inhibiting herbicides of flixweed (Descurainia sophia L.) conferred by different combinations of ALS isozymes with a Pro-197-Thr mutation or a novel Trp-574-Leu mutation. Pesticide Biochemistry and Physiology 136:41−45 doi: 10.1016/j.pestbp.2016.08.006 |
| [44] |
Shimatani Z, Fujikura U, Ishii H, Terada R, Nishida K, et al. 2018. Herbicide tolerance-assisted multiplex targeted nucleotide substitution in rice. Data in Brief 20:1325−31 doi: 10.1016/j.dib.2018.08.124 |
| [45] |
Liu L, Kuang Y, Yan F, Li S, Ren B, et al. 2020. Developing a novel artificial rice germplasm for dinitroaniline herbicide resistance by base editing of OsTubA2. Plant Biotechnology Journal 19:5−7 |
| [46] |
Engku AK, Norida M, Juraimi AS, Rafii MY, Abdullah SNA, et al. 2016. Gene flow from Clearfield® rice to weedy rice under field conditions. Plant, Soil and Environment 62:16−22 doi: 10.17221/616/2015-PSE |
| [47] |
Zhang J, Kang Y, Valverde BE, Dai W, Song X, et al. 2018. Feral rice from introgression of weedy rice genes into transgenic herbicide-resistant hybrid-rice progeny. Journal of Experimental Botany 69:3855−65 doi: 10.1093/jxb/ery210 |
| [48] |
Vigueira CC, Olsen KM, Caicedo A. 2013. The red queen in the corn: agricultural weeds as models of rapid adaptive evolution. Heredity 110:303−11 doi: 10.1038/hdy.2012.104 |
| [49] |
Wu D, Qiu J, Sun J, Song BK, Olsen KM, et al. 2022. Weedy rice, a hidden gold mine in the paddy field. Molecular Plant 15:566−68 doi: 10.1016/j.molp.2022.01.008 |
| [50] |
Bhupenchandra I, Chongtham SK, Gangarani Devi A, Dutta P, Lamalakshmi E, et al. 2025. Harnessing weedy rice as functional food and source of novel traits for crop improvement. Plant, Cell & Environment 48:2498−521 doi: 10.1111/pce.14868 |
| [51] |
Osakina A, Jia Y. 2023. Genetic diversity of weedy rice and its potential application as a novel source of disease resistance. Plants 12:2850 doi: 10.3390/plants12152850 |
| [52] |
Wang W, Zhao M, Zhang G, Liu Z, Hua Y, et al. 2020. Weedy rice as a novel gene resource: a genome-wide association study of anthocyanin biosynthesis and an evaluation of nutritional quality. Frontiers in Plant Science 11:878 doi: 10.3389/fpls.2020.00878 |
| [53] |
Han B, Cui D, Ma X, Cao G, Zhang H, et al. 2022. Evidence for evolution and selection of drought-resistant genes based on high-throughput resequencing in weedy rice. Journal of Experimental Botany 73:1949−62 doi: 10.1093/jxb/erab515 |
| [54] |
Sun J, Zhang G, Cui Z, Kong X, Yu X, et al. 2022. Regain flood adaptation in rice through a 14-3-3 protein OsGF14h. Nature Communications 13:5664 doi: 10.1038/s41467-022-33320-x |
| [55] |
Niu XM, Xu YC, Li ZW, Bian YT, Hou XH, et al. 2019. Transposable elements drive rapid phenotypic variation in Capsella rubella. Proceedings of the National Academy of Sciences of the United States of America 116:6908−13 doi: 10.1073/pnas.1811498116 |
| [56] |
Gressel J. 2015. Dealing with transgene flow of crop protection traits from crops to their relatives. Pest Management Science 71:658−67 doi: 10.1002/ps.3850 |
| [57] |
Yan H, Li L, Liu P, Jiang X, Wang L, et al. 2017. Reduced weed seed shattering by silencing a cultivated rice gene: strategic mitigation for escaped transgenes. Transgenic Research 26:465−75 doi: 10.1007/s11248-017-0016-3 |
| [58] |
Zhang Y, Gao J, Cen H, Lu Y, Yu X, et al. 2019. Automated spectral feature extraction from hyperspectral images to differentiate weedy rice and barnyard grass from a rice crop. Computers and Electronics in Agriculture 159:42−49 doi: 10.1016/j.compag.2019.02.018 |
| [59] |
Yuan C, Liu T, Gao F, Zhang R, Seng X. 2023. YOLOv5s-CBAM-DMLHead: a lightweight identification algorithm for weedy rice (Oryza sativa f. spontanea) based on improved YOLOv5. Crop Protection 172: 106342 |
| [60] |
Yu H, Lin T, Meng X, Du H, Zhang J, et al. 2021. A route to de novo domestication of wild allotetraploid rice. Cell 184:1156−1170.E14 doi: 10.1016/j.cell.2021.01.013 |
| [61] |
Pisias MT, Bakala HS, McAlvay AC, Mabry ME, Birchler JA, et al. 2022. Prospects of feral crop de novo redomestication. Plant & Cell Physiology 63:1641−53 doi: 10.1093/pcp/pcac072 |
| [62] |
Kong M, He X, Yin Z, Chen X, Zhang Y, et al. 2023. Removing harmful pericarp character of weedy rice as the first step of domestication towards direct-seeding rice using CRISPR/Cas9-targeted mutagenesis. Agronomy 13:1130 doi: 10.3390/agronomy13041130 |
| [63] |
Wei X, Qiu J, Yong K, Fan J, Zhang Q, et al. 2021. A quantitative genomics map of rice provides genetic insights and guides breeding. Nature Genetics 53:243−53 doi: 10.1038/s41588-020-00769-9 |