Transformation efficiency of Arabidopsis thaliana ecotypes with differential tolerance to submergence stress

References

• AAT Bioquest. Quest Graph™ LC50 Calculator. 18 Aug. 2021, https://www.aatbio.com/tools/lc50-calculator.
   Google Scholar
• Bailey-Serres J, Parker JE, Ainsworth EA, Oldroyd GED, Schroeder JI. 2019. Genetic strategies for improving crop yields. Nature. 575 (7781):109-118. doi:10.1038/s41586-019-1679-0.
   PubMed Web of Science ®Google Scholar
• Bui LT, Shukla V, Giorgi FM, Trivellini A, Perata P, Licausi F, Giuntoli B. 2020. Differential submergence tolerance between juvenile and adult arabidopsis plants involves the ANAC017 transcription factor. Plant J. 104(4):979–994. doi: 10.1111/tpj.14975.
   PubMed Web of Science ®Google Scholar
• Clough SJ, Bent AF. 1998. Floral dip: a simplified method forAgrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16(6):735–743. doi: 10.1046/j.1365-313x.1998.00343.x.
   PubMed Web of Science ®Google Scholar
• Fukao T, Barrera-Figueroa BE, Juntawong P, Peña-Castro JM. 2019. Submergence and waterlogging stress in plants: A review highlighting research opportunities and understudied aspects. Front Plant Sci. 10(340). doi: 10.3389/fpls.2019.00340.
   PubMedGoogle Scholar
• Ghedira R, De Buck S, Nolf J, Depicker A. 2013. The efficiency of arabidopsis thaliana floral Dip transformation Is determined Not only by the agrobacterium strain used but also by the physiology and the ecotype of the dipped plant. Mol Plant Microbe Interact. 26(7):823–832. doi: 10.1094/MPMI-11-12-0267-R.
   PubMed Web of Science ®Google Scholar
• Giuntoli B, Lee SC, Licausi F, Kosmacz M, Oosumi T, van Dongen JT, Bailey-Serres J, Perata P. 2014. A trihelix DNA binding protein counterbalances hypoxia-responsive transcriptional activation in arabidopsis. PLoS Biol. 12(9):e1001950. doi: 10.1371/journal.pbio.1001950.
   PubMed Web of Science ®Google Scholar
• Lee SC, Mustroph A, Sasidharan R, Vashisht D, Pedersen O, Oosumi T, Voesenek LA, Bailey-Serres J. 2011. Molecular characterization of the submergence response of the arabidopsis thaliana ecotype columbia. New Phytol. 190(2):457–471. doi:10.1111/j.1469-8137.2010.03590.x.
   PubMed Web of Science ®Google Scholar
• Licausi F, Kosmacz M, Weits DA, Giuntoli B, Giorgi FM, Voesenek LA, Perata P, van Dongen JT. 2011. Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization. Nature. 479(7373):419–422.
   PubMed Web of Science ®Google Scholar
• Mendiondo GM, Gibbs DJ, Szurman-Zubrzycka M, Korn A, Marquez J, Szarejko I, Maluszynski M, King J, Axcell B, Smart K, et al. 2016. Enhanced waterlogging tolerance in barley by manipulation of expression of the N-end rule pathway E3 ligase PROTEOLYSIS6. Plant Biotechnol J. 14(1):40–50. doi: 10.1111/pbi.12334.
   PubMed Web of Science ®Google Scholar
• Meng X, Li L, Narsai R, De Clercq I, Whelan J, Berkowitz O. 2020. Mitochondrial signalling is critical for acclimation and adaptation to flooding in arabidopsis thaliana. Plant J. 103(1):227–247. doi: 10.1111/tpj.14724.
   PubMed Web of Science ®Google Scholar
• Mickelbart MV, Hasegawa PM, Bailey-Serres J. 2015. Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat Rev Genet. 16(4):237–251. doi: 10.1038/nrg3901.
   PubMed Web of Science ®Google Scholar
• Morales A, de Boer HJ, Douma JC, Elsen S, Engels S, Glimmerveen T, Sajeev N, Huber M, Luimes M, Luitjens E, et al. 2022. Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of arabidopsis thaliana. AoB Plants. 14(4):plac029. doi:10.1101/2021.12.10.472073.
   PubMed Web of Science ®Google Scholar
• Mustroph A. 2018. Improving flooding tolerance of crop plants. Agronomy. 8(9):160. doi:10.3390/agronomy8090160.
   Google Scholar
• National Academies of Sciences, Engineering, and Medicine. 2019. Reproducibility and replicability in science. Washington, DC: The National Academies Press.
   Google Scholar
• National Academies of Sciences, Engineering, and Medicine. 2019. Science breakthroughs to advance food and agricultural research by 2030. Washington, DC: The National Academies Press.
   Google Scholar
• Nonaka S, Someya T, Kadota Y, Nakamura K, Ezura H. 2019. Super-Agrobacterium ver. 4: improving the transformation frequencies and genetic engineering possibilities for crop plants. Front Plant Sci. 10:1204. doi:10.3389/fpls.2019.01204.
   PubMed Web of Science ®Google Scholar
• Nosek BA, Errington TM. 2020. What is replication? PLoS Biol. 18(3):e3000691. doi:10.1371/journal.pbio.3000691.
   PubMed Web of Science ®Google Scholar
• Oltmanns H, Frame B, Lee LY, Johnson S, Li B, Wang K, Gelvin SB. 2010. Generation of backbone-free, Low transgene copy plants by launching T-DNA from the agrobacterium chromosome. Plant Physiol. 152(3):1158–1166. doi:10.1104/pp.109.148585.
   PubMed Web of Science ®Google Scholar
• Peña-Castro JM, van Zanten M, Lee SC, Patel MR, Voesenek LA, Fukao T, Bailey-Serres J. 2011. Expression of rice SUB1A and SUB1C transcription factors in arabidopsis uncovers flowering inhibition as a submergence tolerance mechanism. Plant J. 67; 67(3):434-446. doi:10.1111/j.1365-313X.2011.04605.x.
   PubMed Web of Science ®Google Scholar
• Sasidharan R, Bailey-Serres J, Ashikari M, Atwell BJ, Colmer TD, Fagerstedt K, Fukao T, Geigenberger P, Hebelstrup KH, Hill RD, et al. 2017. Community recommendations on terminology and procedures used in flooding and low oxygen stress research. New Phytol. 214(4):1403–1407. doi:10.1111/nph.14519.
   PubMed Web of Science ®Google Scholar
• Sasidharan R, Hartman S, Liu Z, Martopawiro S, Sajeev N, van Veen H, Yeung E, Voesenek LACJ. 2018. Signal dynamics and interactions during flooding stress. Plant Physiol. 176(2):1106–1117. doi: 10.1104/pp.17.01232.
   PubMed Web of Science ®Google Scholar
• Singh US, Dar MH, Singh S, Zaidi NW, Bari MA, Mackill DJ, Collard BCY, Singh VN, Singh JP, Reddy JN, et al. 2013. Field performance, dissemination, impact and tracking of submergence tolerant (Sub1) rice varieties in south Asia. SABRAO J Breed Genet. 45(1):112–131.
   Google Scholar
• Spitzer M, Wildenhain J, Rappsilber J, Tyers M. 2014. Boxplotr: a web tool for generation of box plots. Nat Methods. 11(2):121–122. doi: 10.1038/nmeth.2811.
   PubMed Web of Science ®Google Scholar
• Tsai KJ, Lin CY, Ting CY, Shih MC. 2016. Ethylene-regulated glutamate dehydrogenase fine-tunes metabolism during anoxia-reoxygenation. Plant Physiol. 172(3):1548–1562. doi: 10.1104/pp.16.00985.
   PubMed Web of Science ®Google Scholar
• van Veen H, Vashisht D, Akman M, Girke T, Mustroph A, Reinen E, Hartman S, Kooiker M, van Tienderen P, Schranz ME, et al. 2016. Transcriptomes of eight arabidopsis thaliana accessions reveal core conserved, genotype- and organ-specific responses to flooding stress. Plant Physiol. 172(2):pp.00472.2016–689. doi:10.1104/pp.16.00472.
   Web of Science ®Google Scholar
• Vashisht D, Hesselink A, Pierik R, Ammerlaan JM, Bailey-Serres J, Visser EJ, Pedersen O, van Zanten M, Vreugdenhil D, Jamar DC, et al. 2011. Natural variation of submergence tolerance among arabidopsis thaliana accessions. New Phytol. 190(2):299–310. doi:10.1111/j.1469-8137.2010.03552.x.
   PubMed Web of Science ®Google Scholar
• Weits DA, Giuntoli B, Kosmacz M, Parlanti S, Hubberten HM, Riegler H, Hoefgen R, Perata P, van Dongen JT, Licausi F. 2014. Plant cysteine oxidases control the oxygen-dependent branch of the N-end-rule pathway. Nat Commun. 5:3425. doi: 10.1038/ncomms4425.
   PubMed Web of Science ®Google Scholar
• Yeung E, van Veen H, Vashisht D, Sobral Paiva AL, Hummel M, Rankenberg T, Steffens B, Steffen-Heins A, Sauter M, de Vries M, et al. 2018. A stress recovery signaling network for enhanced flooding tolerance in arabidopsis thaliana. Proc Natl Acad Sci U S A. 115(26):E6085–E6094. doi:10.1073/pnas.1803841115.
   PubMed Web of Science ®Google Scholar
• Zhang X, Henriques R, Lin SS, Niu QW, Chua NH. 2006. Agrobacterium-mediated transformation of arabidopsis thaliana using the floral dip method. Nat Protoc. 1(2):641–646. doi: 10.1038/nprot.2006.97.
   PubMed Web of Science ®Google Scholar