doi:10.48130/SeedBio-2023-0004

[1]

Fukagawa NK, Ziska LH. 2019. Rice: Importance for Global Nutrition. Journal of Nutritional Science and Vitaminology 65:S2−S3

doi: 10.3177/jnsv.65.S2

[2]

Hiei Y, Ohta S, Komari T, Kumashiro T. 1994. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. The Plant Journal 6:271−82

doi: 10.1046/j.1365-313X.1994.6020271.x

[3]

Lin YJ, Zhang Q. 2005. Optimising the tissue culture conditions for high efficiency transformation of indica rice. Plant Cell Reports 23:540−47

doi: 10.1007/s00299-004-0843-6

[4]

Ge X, Chu Z, Lin Y, Wang S. 2006. A tissue culture system for different germplasms of indica rice. Plant Cell Reports 25:392−402

doi: 10.1007/s00299-005-0100-7

[5]

Hiei Y, Komari T. 2008. Agrobacterium-mediated transformation of rice using immature embryos or calli induced from mature seed. Nature Protocols 3:824−34

doi: 10.1038/nprot.2008.46

[6]

Ozawa K. 2009. Establishment of a high efficiency Agrobacterium-mediated transformation system of rice (Oryza sativa L.). Plant Science 176:522−27

doi: 10.1016/j.plantsci.2009.01.013

[7]

Susanto FA, Wijayanti P, Fauzia AN, Komalasari RD, Nuringtyas TR, et al. 2020. Establishment of a plant tissue culture system and genetic transformation for agronomic improvement of Indonesian black rice (Oryza sativa L.). Plant Cell, Tissue and Organ Culture (PCTOC) 141:605−17

doi: 10.1007/s11240-020-01819-0

[8]

Molina-Risco M, Ibarra O, Faion-Molina M, Kim B, Septiningsih EM, et al. 2021. Optimizing Agrobacterium-mediated transformation and CRISPR-Cas9 gene editing in the tropical Japonica rice variety presidio. International Journal of Molecular Sciences 22:10909

doi: 10.3390/ijms222010909

[9]

Matsumoto TK, Gonsalves D. 2012. Biolistic and other non-Agrobacterium technologies of plant transformation. In Plant Biotechnology and Agriculture, eds. Altman A, Hasegawa PM. Academic Press. pp. 117−29. https://doi.org/10.1016/B978-0-12-381466-1.00008-0

[10]

Kwak SY, Lew TTS, Sweeney CJ, Koman VB, Wong MH, et al. 2019. Chloroplast-selective gene delivery and expression in planta using chitosan-complexed single-walled carbon nanotube carriers. Nature Nanotechnology 14:447−55

doi: 10.1038/s41565-019-0375-4

[11]

Njiti VN, Myers O Jr, Schroeder D, Lightfoot DA. 2003. Roundup Ready Soybean: Glyphosate Effects on Fusarium solani Root Colonization and Sudden Death Syndrome. Agronomy Journal 95:1140−45

doi: 10.2134/agronj2003.1140

[12]

Vuorinen AL, Nieminen A, Gaba V, Sikorskaite S, Valkonen JP. 2013. Biolistic DNA delivery to leaf tissue of plants with the non-vacuum gene gun (HandyGun). In Biolistic DNA Delivery. Methods in Molecular Biology, eds. Sudowe S, Reske-Kunz AB. 940: XIV,415. New Jersey: Humana Totowa. pp. 45−51. https://doi.org/10.1007/978-1-62703-110-3_4

[13]

Gu Z, Biswas A, Zhao M, Tang Y. 2011. Tailoring nanocarriers for intracellular protein delivery. Chemical Society Reviews 40:3638−55

doi: 10.1039/c0cs00227e

[14]

Zhang K, Su J, Xu M, Zhou Z, Zhu X, et al. 2020. A common wild rice-derived BOC1 allele reduces callus browning in indica rice transformation. Nature Communications 11:443

doi: 10.1038/s41467-019-14265-0

[15]

Elakhdar A, Fukuda M, Kubo T. 2021. Agrobacterium-mediated transformation of Japonica rice using mature embryos and regenerated transgenic plants. Bio-protocol 11:e4143

doi: 10.21769/BioProtoc.4143

[16]

Chen K, Łyskowski A, Jaremko Ł, Jaremko M. 2021. Genetic and molecular factors determining grain weight in rice. Frontiers in Plant Science 12:605799

doi: 10.3389/fpls.2021.605799

[17]

Xu R, Duan P, Yu H, Zhou Z, Zhang B, et al. 2018. Control of Grain Size and Weight by the OsMKKK10-OsMKK4-OsMAPK6 Signaling Pathway in Rice. Molecular Plant 11:860−73

doi: 10.1016/j.molp.2018.04.004

[18]

Xu R, Yu H, Wang J, Duan P, Zhang B, et al. 2018. A mitogen-activated protein kinase phosphatase influences grain size and weight in rice. The Plant Journal 95:937−46

doi: 10.1111/tpj.13971

[19]

Guo T, Chen K, Dong N, Shi C, Ye W, et al. 2018. GRAIN SIZE AND NUMBER1 Negatively Regulates the OsMKKK10-OsMKK4-OsMPK6 Cascade to Coordinate the Trade-off between Grain Number per Panicle and Grain Size in Rice. The Plant Cell 30:871−88

doi: 10.1105/tpc.17.00959

[20]

Wang T, Zou T, He Z, Yuan G, Luo T, et al. 2019. GRAIN LENGTH AND AWN 1 negatively regulates grain size in rice. Journal of Integrative Plant Biology 61:1036−42

doi: 10.1111/jipb.12736

[21]

Ministry of Agriculture and Rural Affairs of the People's Republic of China. 2020. Ministry of Agriculture and Rural Affairs of the People's Republic of China Announcement No. 360. www.zzj.moa.gov.cn/gsgg/202012/t20201202_6357482.htm

[22]

Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, et al. 2015. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Molecular Plant 8:1274−84

doi: 10.1016/j.molp.2015.04.007

[23]

Xie X, Ma X, Zhu Q, Zeng D, Li G, et al. 2017. CRISPR-GE: A convenient software toolkit for CRISPR-based genome editing. Molecular Plant 10:1246−49

doi: 10.1016/j.molp.2017.06.004

[24]

Zhao W, Zheng S, Ling H. 2011. An efficient regeneration system and Agrobacterium-mediated transformation of Chinese upland rice cultivar Handao297. Plant Cell, Tissue and Organ Culture (PCTOC) 106:475−83

doi: 10.1007/s11240-011-9946-2

[25]

Duan YB, Zhao FL, Chen HD, Li H, Ni DH, et al. 2015. A simplified genomic DNA extraction protocol for pre-germination genotyping in rice. Genet Mol Res 14:6369−75

doi: 10.4238/2015.June.11.12

[26]

Rao X, Huang X, Zhou Z, Lin X. 2013. An improvement of the 2^−ΔΔCᴛ method for quantitative real-time polymerase chain reaction data analysis. Biostatistics, Bioinformatics and Biomathematics 3:71−85

[27]

Toki S, Hara N, Ono K, Onodera H, Tagiri A, et al. 2006. Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice. The Plant Journal 47:969−76

doi: 10.1111/j.1365-313X.2006.02836.x

[28]

Sahoo KK, Tripathi AK, Pareek A, Sopory SK, Singla-Pareek SL. 2011. An improved protocol for efficient transformation and regeneration of diverse indica rice cultivars. Plant Methods 7:49

doi: 10.1186/1746-4811-7-49

[29]

Lin H, Xia P, Wing R, Zhang Q, Luo M. 2012. Dynamic intra-japonica subspecies variation and resource application. Molecular Plant 5:218−30

doi: 10.1093/mp/ssr085

[30]

Zhang J, Li C, Wu C, Xiong L, Chen G, et al. 2006. RMD: a rice mutant database for functional analysis of the rice genome. Nucleic Acids Research 34:D745−D748

doi: 10.1093/nar/gkj016

[31]

Chen S, Wang A, Li W, Wang Z, Cai X. 2008. Establishing a gene trap system mediated by T-DNA(GUS) in rice. 10.1111/j.1744-7909.2007.00611.x 50:742−51

doi: 10.1111/j.1744-7909.2007.00611.x

[32]

Saika H, Toki S. 2010. Mature seed-derived callus of the model indica rice variety Kasalath is highly competent in Agrobacterium-mediated transformation. Plant Cell Reports 29:1351−64

doi: 10.1007/s00299-010-0921-x

[33]

Zhou X, Chen D, Guo J, Chen P, Li L, et al. 2021. Genetic improvement of grain quality traits in indica inbred rice cultivars developed in South China during 1956–2020. Euphytica 218:8

doi: 10.1007/s10681-021-02953-2

[34]

Zhang W, Dewey RE, Boss W, Phillippy BQ, Qu R. 2013. Enhanced Agrobacterium-mediated transformation efficiencies in monocot cells is associated with attenuated defense responses. Plant Molecular Biology 81:273−86

doi: 10.1007/s11103-012-9997-8

[35]

Li S, Yan S, Wang A, Zou G, Huang X, et al. 2013. Identification of QTLs associated with tissue culture response through sequencing-based genotyping of RILs derived from 93-11 × Nipponbare in rice (Oryza sativa). Plant Cell Reports 32:103−16

doi: 10.1007/s00299-012-1345-6

[36]

Liu X, Zhou C, Zhao Y, Zhou S, Wang W, Zhou DX. 2014. The rice enhancer of zeste [E(z)] genes SDG711 and SDG718 are respectively involved in long day and short day signaling to mediate the accurate photoperiod control of flowering time. Frontiers in Plant Science 5:591

doi: 10.3389/fpls.2014.00591

[37]

Coudert Y, Le VAT, Adam H, Bès M, Vignols F, et al. 2015. Identification of CROWN ROOTLESS1-regulated genes in rice reveals specific and conserved elements of postembryonic root formation. New Phytologist 206:243−54

doi: 10.1111/nph.13196

[38]

Khanday I, Skinner D, Yang B, Mercier R, Sundaresan V. 2019. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature 565:91−95

doi: 10.1038/s41586-018-0785-8

[39]

Liang Y, Biswas S, Kim B, Bailey-Serres J, Septiningsih EM. 2021. Improved transformation and regeneration of Indica rice: Disruption of SUB1A as a test case via CRISPR-Cas9. International Journal of Molecular Sciences 22:6989

doi: 10.3390/ijms22136989

[40]

Luu VT, Stiebner M, Maldonado PE, Valdés S, Marín D, et al. 2020. Efficient Agrobacterium-mediated transformation of the Elite-Indica rice variety Komboka. Bio-protocol 10:e3739

doi: 10.21769/BioProtoc.3739

[41]

Demirer GS, Zhang H, Matos JL, Goh NS, Cunningham FJ, et al. 2019. High aspect ratio nanomaterials enable delivery of functional genetic material without DNA integration in mature plants. Nature Nanotechnology 14:456−64

doi: 10.1038/s41565-019-0382-5

[42]

Dunbar T, Tsakirpaloglou N, Septiningsih EM, Thomson MJ. 2022. Carbon Nanotube-Mediated Plasmid DNA Delivery in Rice Leaves and Seeds. International Journal of Molecular Sciences 23:4081

doi: 10.3390/ijms23084081

[43]

Geng L, Li Q, Jiao L, Xiang Y, Deng Q, et al. 2023. WOX11 and CRL1 act synergistically to promote crown root development by maintaining cytokinin homeostasis in rice. New Phytologist 237:204−16

doi: 10.1111/nph.18522

[44]

Luo W, Tan J, Li T, Feng Z, Ding Z, et al. 2023. Overexpression of maize GOLDEN2 in rice and maize calli improves regeneration by activating chloroplast development. Science China Life Sciences 66:340−49

doi: 10.1007/s11427-022-2149-2

[45]

Debernardi JM, Tricoli DM, Ercoli MF, Hayta S, Ronald P, et al. 2020. A GRF-GIF chimeric protein improves the regeneration efficiency of transgenic plants. Nature Biotechnology 38:1274−79

doi: 10.1038/s41587-020-0703-0

[46]

Chen Z, Debernardi JM, Dubcovsky J, Gallavotti A. 2022. The combination of morphogenic regulators BABY BOOM and GRF-GIF improves maize transformation efficiency. BioRxiv Preprint

doi: 10.1101/2022.09.02.506370

[47]

Chen E, Zhang P, Zuo S, Li A, Zhang Y, et al. 2004. Factors affecting Agrobacterium-mediated transformation efficiency in rice. Rice Science 11:181−85

[48]

Li S, Wang S, Yin F, Zou L, Qi D, et al. 2005. Some factors affecting Agrobacterium-mediated transformation frequency in rice. Chinese Journal of Rice Science 19:231−37

doi: 10.3321/j.issn:1001-7216.2005.03.006

[49]

Guo T, Lu Z, Shan J, Ye W, Dong N, et al. 2020. ERECTA1 Acts Upstream of the OsMKKK10-OsMKK4-OsMPK6 Cascade to Control Spikelet Number by Regulating Cytokinin Metabolism in Rice. The Plant Cell 32:2763−79

doi: 10.1105/tpc.20.00351