Fromont-Racine, M., Rain, J.-C. & Legrain, P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat. Genet. 16, 277–282 (1997).
Google Scholar
Jefferson, R. A., Kavanagh, T. A. & Bevan, M. W. Gus fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. Embo J. 6, 3901–3907 (1987).
Google Scholar
Smale, S. T. Luciferase assay. Cold Spring Harb. Protoc. 2010, pdb.prot5421 (2010).
Google Scholar
Kain, S. R. et al. Green fluorescent protein as a reporter of gene-expression and protein localization. Biotechniques 19, 650–655 (1995).
Google Scholar
He, Y., Zhang, T., Sun, H., Zhan, H. & Zhao, Y. A reporter for noninvasively monitoring gene expression and plant transformation. Hortic. Res. 7, 152 (2020).
Google Scholar
Fonseca, J. P. et al. Iron-sulfur cluster protein NITROGEN FIXATION S-LIKE1 and its interactor FRATAXIN function in plant immunity. Plant Physiol. 184, 1532–1548 (2020).
Google Scholar
Wang, Z. et al. Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes. Sci. Rep. 7, 4910 (2017).
Google Scholar
Wang, K., Kang, L., Anand, A., Lazarovits, G. & Mysore, K. S. Monitoring in planta bacterial infection at both cellular and whole-plant levels using the green fluorescent protein variant GFPuv. N. Phytol. 174, 212–223 (2007).
Google Scholar
Werner, S., Breus, O., Symonenko, Y., Marillonnet, S. & Gleba, Y. High-level recombinant protein expression in transgenic plants by using a double-inducible viral vector. Proc. Natl Acad. Sci. USA 108, 14061–14066 (2011).
Google Scholar
Gelvin, S. B. Agrobacterium-mediated plant transformation: the biology behind the “gene-jockeying” tool. Microbiol Mol. Biol. Rev. 67, 16–37 (2003).
Google Scholar
Hwang, H. H., Yu, M. & Lai, E. M. Agrobacterium-mediated plant transformation: biology and applications. Arabidopsis Book 15, e0186 (2017).
Google Scholar
Mao, Y. F., Botella, J. R., Liu, Y. G. & Zhu, J. K. Gene editing in plants: progress and challenges. Natl Sci. Rev. 6, 421–437 (2019).
Google Scholar
Yang, X. et al. Plant biosystems design research roadmap 1.0. BioDesign Res. 2020, 8051764 (2020).
Google Scholar
Harrison, S. J. et al. A rapid and robust method of identifying transformed Arabidopsis thaliana seedlings following floral dip transformation. Plant Methods 2, 19 (2006).
Google Scholar
Bhalla, P. L. & Singh, M. B. Agrobacterium-mediated transformation of Brassica napus and Brassica oleracea. Nat. Protoc. 3, 181–189 (2008).
Google Scholar
Shimizu, A., Shiratori, I., Horii, K. & Waga, I. Molecular evolution of versatile derivatives from a GFP-like protein in the marine copepod Chiridius poppei. PLoS ONE 12, e0181186 (2017).
Google Scholar
Chin, D. P. et al. Generation of brilliant green fluorescent petunia plants by using a new and potent fluorescent protein transgene. Sci. Rep. 8, 16556 (2018).
Google Scholar
Sannigrahi, P., Ragauskas, A. J. & Tuskan, G. A. Poplar as a feedstock for biofuels: a review of compositional characteristics. Biofuel Bioprod. Bior 4, 209–226 (2010).
Google Scholar
Liu, Y. Q., Heying, E. & Tanumihardjo, S. A. History, global distribution, and nutritional importance of Citrus fruits. Compr. Rev. Food Sci. F. 11, 530–545 (2012).
Google Scholar
Yamasaki, S. et al. Arabidopsis thaliana cold-regulated 47 gene 5′-untranslated region enables stable high-level expression of transgenes. J. Biosci. Bioeng. 125, 124–130 (2018).
Google Scholar
Matsui, T., Sawada, K., Takita, E. & Kato, K. The longer version of Arabidopsis thaliana heat shock protein 18.2 gene terminator contributes to higher expression of stably integrated transgenes in cultured tobacco cells. Plant Biotechnol. 31, 191–194 (2014).
Google Scholar
Gutierrez-Valdes, N. et al. Hairy root cultures—A versatile tool with multiple applications. Front. Plant Sci. 11, 33 (2020).
Google Scholar
Gomes, C., Dupas, A., Pagano, A., Grima-Pettenati, J. & Paiva, J. A. P. Hairy root transformation: a useful tool to explore gene function and expression in Salix spp. recalcitrant to transformation. Front. Plant Sci. 10, 1427 (2019).
Google Scholar
Ma, Y. et al. Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet Genom. 36, 267–276 (2009).
Google Scholar
Ye, X. D. et al. Enhanced production of single copy backbone-free transgenic plants in multiple crop species using binary vectors with a pRi replication origin in Agrobacterium tumefaciens. Transgenic Res. 20, 773–786 (2011).
Google Scholar
Maher, M. F. et al. Plant gene editing through de novo induction of meristems. Nat. Biotechnol. 38, 84–89 (2020).
Google Scholar
Breyer, D., Kopertekh, L. & Reheul, D. Alternatives to antibiotic resistance marker genes for in vitro selection of genetically modified plants – scientific developments, current use, operational access and biosafety considerations. Crit. Rev. Plant Sci. 33, 286–330 (2014).
Google Scholar
Verma, S. S., Chiinnusarny, V. & Bansal, K. C. A simplified floral dip method for transformation of Brassica napus and B. carinata. J. Plant Biochem Biot. 17, 197–200 (2008).
Google Scholar
Liu, Z. Q. et al. Systematic comparison of 2A peptides for cloning multi-genes in a polycistronic vector. Sci. Rep. 7, 2193 (2017).
Google Scholar
Yuan, G. et al. Biosystems design to accelerate C3-to-CAM progression. BioDesign Res. 2020, 3686791 (2020).
Google Scholar
Hernandez-Garcia, C. M. & Finer, J. J. Identification and validation of promoters and cis-acting regulatory elements. Plant Sci. 217, 109–119 (2014).
Google Scholar
Notaguchi, M. & Okamoto, S. Dynamics of long-distance signaling via plant vascular tissues. Front. Plant Sci. 6, 161 (2015).
Google Scholar
Dietz-Pfeilstetter, A. Stability of transgene expression as a challenge for genetic engineering. Plant Sci. 179, 164–167 (2010).
Google Scholar
Rigoulot, S. B. et al. Imaging of multiple fluorescent proteins in canopies enables synthetic biology in plants. Plant Biotechnol. J. 19, 830–843 (2021).
Google Scholar
Xie, M. et al. A 5-enolpyruvylshikimate 3-phosphate synthase functions as a transcriptional repressor in Populus. Plant Cell 30, 1645–1660 (2018).
Google Scholar
Yuan, G. et al. PROTEIN PHOSHATASE 2A B’α and β maintain centromeric sister chromatid cohesion during meiosis in. Arabidopsis. Plant Physiol. 178, 317–328 (2018).
Google Scholar
Li, X. Infiltration of Nicotiana benthamiana protocol for transient expression via Agrobacterium. Bio-Protoc. 1, e95 (2011).
Chen, L. Z. et al. A method for the production and expedient screening of CRISPR/Cas9-mediated non-transgenic mutant plants. Hortic. Res. 5, 13 (2018).
Google Scholar
Filichkin, S. A. et al. Alcohol-inducible gene expression in transgenic. Populus. Plant Cell Rep. 25, 660–667 (2006).
Google Scholar
Weigel, D. & Glazebrook, J. Quick miniprep for plant DNA isolation. Cold Spring Harb. Protoc. 2009, pdb.prot5179 (2009).
Google Scholar
Wang, Y. et al. Validation of reference genes for gene expression by quantitative real-time RT-PCR in stem segments spanning primary to secondary growth in Populus tomentosa. Plos ONE 11, e0157370 (2016).
Google Scholar
Lu, H. W. et al. RNA interference suppression of AGAMOUS and SEEDSTICK alters floral organ identity and impairs floral organ determinacy, ovule differentiation, and seed-hair development in Populus. New Phytologist 222, 923–937 (2019).
Google Scholar
Lu, H. W., Gordon, M. I., Amarasinghe, V. & Strauss, S. H. Extensive transcriptome changes during seasonal leaf senescence in field-grown black cottonwood (Populus trichocarpa Nisqually-1). Sci. Rep. 10, 6581 (2020).
Google Scholar
Qiao, Z. & Libault, M. Unleashing the potential of the root hair cell as a single plant cell type model in root systems biology. Front. Plant Sci. 4, 484 (2013).
Google Scholar
Zhang, F., LeBlanc, C., Irish, V. F. & Jacob, Y. Rapid and efficient CRISPR/Cas9 gene editing in Citrus using the YAO promoter. Plant Cell Rep. 36, 1883–1887 (2017).
Google Scholar
