Abstract
Rice (Oryza sativa L.) is one of the most important dietary carbohydrate sources for half of the world’s population. However, it is not well adapted to environmental stress conditions, necessitating to create new and improved varieties to help ensure sufficient rice production in the face of rising populations and shrinking arable land. Recently, the development of the CRISPR/Cas9 gene editing system has allowed researchers to study functional genomics and engineer new rice varieties with great efficiency compared to conventional methods. In this study, we investigate the involvement of OsGER4, a germin-like protein identified by a genome-wide association study that is associated with rice root development under a stress hormone jasmonic acids treatment. Analysis of the OsGER4 promoter region revealed a series of regulatory elements that connect this gene to ABA signaling and water stress response. Under heat stress, osger4 mutant lines produce a significantly lower crown root than wild-type Kitaake rice. The loss of OsGER4 also led to the reduction of lateral root development. Using the GUS promoter line, OsGER4 expression was detected in the epidermis of the crown root primordial, in the stele of the crown root, and subsequently in the primordial of the lateral root. Taken together, these results illustrated the involvement of OsGER4 in root development under heat stress by regulating auxin transport through plasmodesmata, under control by both ABA and auxin signaling.
This is a preview of subscription content, log in via an institution to check access.
Data availability
All relevant data can be found within the manuscript and its supporting materials.
References
Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K (1997) Role of arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell 9:1859–1868. https://doi.org/10.1105/tpc.9.10.1859
Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15:63–78. https://doi.org/10.1105/TPC.006130
Anders C, Niewoehner O, Duerst A, Jinek M (2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513:569–573. https://doi.org/10.1038/nature13579
Balasubramaniam T, Wijewardene I, Hu R, Shen G, Zhang J, Zhang H (2022) Co-overexpression of AVP1, PP2A-C5, and AtCLCc in Arabidopsis thaliana greatly increases tolerance to salt and drought stresses. Environ Exp Botany 200:104934. https://doi.org/10.1016/j.envexpbot.2022.104934
Band LR (2021) Auxin fluxes through plasmodesmata. The New phytologist, 231(5): 1686–1692. https://doi.org/10.1111/nph.17517
Band LR (2022) Plasmodesmata play a key role in leaf vein patterning PLOS Biology 20(9): e3001806. https://doi.org/10.1371/journal.pbio.3001806
Brown RL, Kazan K, McGrath KC, Maclean DJ, Manners JM (2003) A role for the GCC-box in jasmonate-mediated activation of the PDF1.2 gene of Arabidopsis. Plant Physiol 132:1020–1032. https://doi.org/10.1104/pp.102.017814
Da Costa CT, de Almeida MR, Ruedell CM, Schwambach J, Maraschin FS, Fett-Neto AG (2013) When stress and development go hand in hand: main hormonal controls of adventitious rooting in cuttings. Front Plant Sci 4:133. https://doi.org/10.3389/FPLS.2013.00133/BIBTEX
Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE (2014) Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation. Nat Biotechnol 32:1262–1267. https://doi.org/10.1038/nbt.3026
Doyle, J. (1991). DNA Protocols for Plants. In: Hewitt, G.M., Johnston, A.W.B., Young, J.P.W. (eds) Molecular Techniques in Taxonomy. NATO ASI Series, vol 57. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-83962-7_18
Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang D-L, Wang Z, Zhang Z, Zheng R, Yang L, Zeng L, Liu X, Zhu J-K (2014) Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc Natl Acad Sci U S A 111:4632–4637. https://doi.org/10.1073/pnas.1400822111
Gao S, Fang J, Xu F, Wang W, Sun X, Chu J, Cai B, Feng Y, Chu C (2014) Cytokinin oxidase/dehydrogenase4 integrates cytokinin and auxin signaling to control rice crown root formation. Plant Physiol 165:1035–1046. https://doi.org/10.1104/pp.114.238584
Gómez-Porras JL, Riaño-Pachón DM, Dreyer I, Mayer JE, Mueller-Roeber B (2007) Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics 8:260. https://doi.org/10.1186/1471-2164-8-260
Guilfoyle TJ, Hagen G (2007) Auxin response factors. Curr Opin Plant Biol 10:453–460. https://doi.org/10.1016/j.pbi.2007.08.014
Haworth M, Marino G, Brunetti C, Killi D, De Carlo A, Centritto M (2018) the impact of heat stress and water deficit on the photosynthetic and stomatal physiology of olive (olea europaea l.)—a case study of the 2017 heat wave. Plants (Basel) 7:76. https://doi.org/10.3390/plants7040076
He J, Li C, Hu N, Zhu Y, He Z, Sun Y, Wang Z, Wang Y (2022) ECERIFERUM1-6A is required for the synthesis of cuticular wax alkanes and promotes drought tolerance in wheat. Plant Physiol 190:1640–1657. https://doi.org/10.1093/plphys/kiac394
Hewitt S, Hernández-Montes E, Dhingra A, Keller M (2023) Impact of heat stress, water stress, and their combined effects on the metabolism and transcriptome of grape berries. Sci Rep 13:9907. https://doi.org/10.1038/s41598-023-36160-x
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31:827–832. https://doi.org/10.1038/nbt.2647
Huysmans M, Buono RA, Skorzinski N, Radio MC, De Winter F, Parizot B, Mertens J, Karimi M, Fendrych M, Nowack MK (2018) NAC Transcription factors ANAC087 and ANAC046 control distinct aspects of programmed cell death in the Arabidopsis columella and lateral root cap. Plant Cell 30:2197–2213. https://doi.org/10.1105/tpc.18.00293
Inukai Y, Sakamoto T, Ueguchi-Tanaka M, Shibata Y, Gomi K, Umemura I, Hasegawa Y, Ashikari M, Kitano H, Matsuoka M (2005) Crown rootless1, which is essential for crown root formation in rice, is a target of an auxin response factor in auxin signaling. Plant Cell 17:1387–1396. https://doi.org/10.1105/TPC.105.030981
Jeong JS, Kim YS, Baek KH, Jung H, Ha S-H, Do Choi Y, Kim M, Reuzeau C, Kim J-K (2010) Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol 153:185–197. https://doi.org/10.1104/pp.110.154773
Jeong JS, Kim YS, Redillas MCFR, Jang G, Jung H, Bang SW, Choi YD, Ha S-H, Reuzeau C, Kim J-K (2013) OsNAC5 overexpression enlarges root diameter in rice plants leading to enhanced drought tolerance and increased grain yield in the field. Plant Biotechnol J 11:101–114. https://doi.org/10.1111/pbi.12011
Jiang M, Hu H, Kai J, Traw MB, Yang S, Zhang X (2019) Different knockout genotypes of OsIAA23 in rice using CRISPR/Cas9 generating different phenotypes. Plant Mol Biol 100:467–479. https://doi.org/10.1007/s11103-019-00871-5
Jumrani K, Bhatia VS (2019) Interactive effect of temperature and water stress on physiological and biochemical processes in soybean. Physiol Mol Biol Plants 25:667–681. https://doi.org/10.1007/s12298-019-00657-5
Jun N, Gaohang W, Zhenxing Z, Huanhuan Z, Yunrong W, Ping W (2011) OsIAA23-mediated auxin signaling defines postembryonic maintenance of QC in rice. Plant J 68:433–442. https://doi.org/10.1111/j.1365-313X.2011.04698.x
Kámán-Tóth E, Pogány M, Dankó T, Szatmari A, Bozsó Z (2018) A simplified and efficient Agrobacterium tumefaciens electroporation method 3 Biotech 8. https://doi.org/10.1007/s13205-018-1171-9
Kaplan B, Davydov O, Knight H, Galon Y, Knight MR, Fluhr R, Fromm H (2006) Rapid transcriptome changes induced by cytosolic Ca2+ transients reveal ABRE-related sequences as Ca2+-responsive cis elements in Arabidopsis. Plant Cell 18:2733–2748. https://doi.org/10.1105/tpc.106.042713
Kim Y, Chung YS, Lee E, Tripathi P, Heo S, Kim K-H (2020) Root response to drought stress in rice (Oryza sativa L.). Int J Mol Sci 21:1513. https://doi.org/10.3390/ijms21041513
Leah R, Band (2022) plasmodesmata play a key role in leaf vein patterning. PLoS Biol 20(9);e3001806. https://doi.org/10.1371/journal.pbio.3001806
Lee D-K, Chung PJ, Jeong JS, Jang G, Bang SW, Jung H, Kim YS, Ha S-H, Choi YD, Kim J-K (2017) The rice OsNAC6 transcription factor orchestrates multiple molecular mechanisms involving root structural adaptions and nicotianamine biosynthesis for drought tolerance. Plant Biotechnol J 15:754–764. https://doi.org/10.1111/pbi.12673
Li C, Brant E, Budak H et al (2021) CRISPR/Cas: a Nobel prize award-winning precise genome editing technology for gene therapy and crop improvement. J Zhejiang Univ Sci B 22:253–284. https://doi.org/10.1631/jzus.B2100009
Li X, Xu S, Fuhrmann-Aoyagi MB, Yuan S, Iwama T, Kobayashi M, Miura K (2022) CRISPR/Cas9 technique for temperature, drought, and salinity stress responses. Curr Issues Mol Biol 44:2664–2682. https://doi.org/10.3390/cimb44060182
Lin H, Arrivault S, Coe RA, Karki S, Covshoff S, Bagunu E, Lunn JE, Stitt M, Furbank RT, Hibberd JM Quick WP (2020) A Partial C4 Photosynthetic Biochemical Pathway in Rice. Front Plant Sci. 15(11): 564463. https://doi.org/10.3389/fpls.2020.564463
Linh NM, Scarpella E (2022) Correction: Leaf vein patterning is regulated by the aperture of plasmodesmata intercellular channels. PLoS biology, 20(10): e3001869. https://doi.org/10.1371/journal.pbio.3001869
Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J, Edbali O, Madhusoodanan N, Kolesnikov A, Lopez R (2022) Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res 50:W276–W279. https://doi.org/10.1093/nar/gkac240
Meng F, Xiang D, Zhu J, Li Y (2019Jan 10) Mao C (2019) Molecular Mechanisms of Root Development in Rice. Rice (N Y). 12(1):1. https://doi.org/10.1186/s12284-018-0262-x
Mellor NL, Voß U, Janes G, Bennett MJ, Wells DM, Band LR, (2020) auxin fluxes through plasmodesmata modify root-tip auxin distribution abstract. Development 147(6) https://doi.org/10.1242/dev.181669
Miao C, Xiao L, Hua K, Zou C, Zhao Y, Bressan RA, Zhu J-K (2018) Mutations in a subfamily of abscisic acid receptor genes promote rice growth and productivity. Proc Natl Acad Sci 115:6058–6063. https://doi.org/10.1073/pnas.1804774115
Miras M, Pottier M, Schladt TM, Ejike JO, Redzich L, Frommer WB, Kim J-Y (2022) Plasmodesmata and their role in assimilate translocation. J Plant Physiol 270:153633. https://doi.org/10.1016/j.jplph.2022.153633
Mohidem NA, Hashim N, Shamsudin R, Che Man H (2022) Rice for food security: revisiting its production, diversity, rice milling process and nutrient content. Agriculture 12:741. https://doi.org/10.3390/agriculture12060741
Muhammad Aslam M, Waseem M, Jakada BH, Okal EJ, Lei Z, Saqib HSA, Yuan W, Xu W, Zhang Q (2022) Mechanisms of abscisic acid-mediated drought stress responses in plants. Int J Mol Sci 23:1084. https://doi.org/10.3390/ijms23031084
Nguyen T, Pham T, Tien Do P, Vo K, Thi Van Anh L, Tran TA, Chu H, Jeon JS, To H (2023) The plasmodesmal protein Osger4 is involved in auxin mediated crown root development in rice. bioRxiv. Preprint. https://doi.org/10.21203/rs.3.rs-3108300/v1
Nishimura A, Aichi I, Matsuoka M (2006) A protocol for Agrobacterium-mediated transformation in rice. Nat Protoc 1:2796–2802. https://doi.org/10.1038/nprot.2006.469
Ogata T, Ishizaki T, Fujita M, Fujita Y (2020) CRISPR/Cas9-targeted mutagenesis of OsERA1 confers enhanced responses to abscisic acid and drought stress and increased primary root growth under nonstressed conditions in rice. PLOS ONE 15:e0243376. https://doi.org/10.1371/journal.pone.0243376
Pushpam R, Manonmani S, Varthini V, Robin S (2018) Studies on yield, root characters related to drought tolerance and their association in upland rice genotypes. Electronic J Plant Breed 9:856. https://doi.org/10.5958/0975-928X.2018.00106.0
Poonam Mehra, Bipin K., Pandey Dalia, Melebari Jason, Banda Nicola, Leftley Valentin, Couvreur James, Rowe Moran, Anfang Hugues, De Gernier Emily, Morris Craig J., Sturrock Sacha J., Mooney Ranjan, Swarup Christine, Faulkner Tom, Beeckman Rishikesh P., Bhalerao Eilon, Shani Alexander M., Jones Ian C., Dodd Robert E., Sharp Ari, Sadanandom Xavier, Draye Malcolm J., Bennett (2022) hydraulic flux–responsive hormone redistribution determines root branching lateral root development. Science 378(6621) 762-768 https://doi.org/10.1126/science.add3771
Prerostova S, Jarosova J, Dobrev PI, Hluskova L, Motyka V, Filepova R, Knirsch V, Gaudinova A, Kieber J, Vankova R, (2022) Heat Stress targeting individual organs reveals the central role of roots and crowns in rice stress responses. Front Plant Sci 12. https://doi.org/10.3389/fpls.2021.799249
Rao MJ, Wang L (2021) CRISPR/Cas9 technology for improving agronomic traits and future prospective in agriculture. Planta 254:68. https://doi.org/10.1007/s00425-021-03716-y
Redillas MCFR, Jeong JS, Kim YS, Jung H, Bang SW, Choi YD, Ha S-H, Reuzeau C, Kim J-K (2012) The overexpression of OsNAC9 alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions. Plant Biotechnol J 10:792–805. https://doi.org/10.1111/j.1467-7652.2012.00697.x
Rouster J, Leah R, Mundy J, Cameron-Mills V (1997) Identification of a methyl jasmonate-responsive region in the promoter of a lipoxygenase 1 gene expressed in barley grain. Plant J 11:513–523. https://doi.org/10.1046/j.1365-313X.1997.11030513.x
Sager RE, Lee JY, (2018) plasmodesmata at a glance abstract. J Cell Sci. 131(11) https://doi.org/10.1242/jcs.209346
Sager R, Wang X, Hill K, Yoo B-C, Caplan J, Nedo A, Tran T, Bennett MJ, Lee J-Y (2020) Auxin-dependent control of a plasmodesmal regulator creates a negative feedback loop modulating lateral root emergence. Nat Commun 11:364. https://doi.org/10.1038/s41467-019-14226-7
Shinozaki K, Yamaguchi-Shinozaki K, Seki M (2003) Regulatory network of gene expression in the drought and cold stress responses. Curr Opin Plant Biol 6:410–417. https://doi.org/10.1016/S1369-5266(03)00092-X
Simpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Two different novel cis-acting elements of erd1, a clpA homologous Arabidopsis gene function in induction by dehydration stress and dark-induced senescence. Plant J 33:259–270. https://doi.org/10.1046/j.1365-313x.2003.01624.x
Song H, Ahn J-Y, Yan F, Ran Y, Koo O, Lee G-J (2022) Genetic dissection of CRISPR-Cas9 mediated inheritance of independently targeted alleles in tobacco α-1,3-fucosyltransferase 1 and β-1,2-xylosyltransferase 1 loci. Int J Mol Sci 23:2450. https://doi.org/10.3390/ijms23052450
Sudianto E, Beng-Kah S, Ting-Xiang N, Saldain NE, Scott RC, Burgos NR (2013) Clearfield® rice: its development, success, and key challenges on a global perspective. Crop Prot 49:40–51. https://doi.org/10.1016/j.cropro.2013.02.013
Swamy BPM, Marathi B, Ribeiro-Barros AIF, Calayugan MIC, Ricachenevsky FK (2021) Iron Biofortification in Rice: an update on quantitative trait loci and candidate genes. Front Plant Sci. 2021 May 26;12:647341. https://doi.org/10.3389/fpls.2021.647341
To HTM, Pham DT, Thi VAL, Nguyen TT, Tran TA, Ta AS, Chu HH, Do PT (2022) The Germin-like protein OsGER4 is involved in promoting crown root development under exogenous jasmonic acid treatment in rice. Plant J 112:860–874. https://doi.org/10.1111/TPJ.15987
Tran L-SP, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K, Fujita M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2004) Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell 16:2481–2498. https://doi.org/10.1105/tpc.104.022699
Trang Hieu N, To H, Moukouanga D, Lebrun M, Bellafiore S (2020) Champion A (2020) CRISPR/Cas9-mediated gene editing of the jasmonate biosynthesis OsAOC gene in rice. Methods Mol Biol. 2085:199–209. https://doi.org/10.1007/978-1-0716-0142-6_15
Uga Y, Sugimoto K, Ogawa S, Rane J, Ishitani M, Hara N, Kitomi Y, Inukai Y, Ono K, Kanno N, Inoue H, Takehisa H, Motoyama R, Nagamura Y, Wu J, Matsumoto T, Takai T, Okuno K, Yano M (2013) Control of root system architecture by deeper rooting 1 increases rice yield under drought conditions. Nat Genet 45:1097–1102. https://doi.org/10.1038/ng.2725
Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki K (1993) An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. Plant Cell 5:1529–1539. https://doi.org/10.1105/tpc.5.11.1529
Wang X, Tu M, Wang D, Liu J, Li Y, Li Z, Wang Y, Wang X (2018) CRISPR/Cas9-mediated efficient targeted mutagenesis in grape in the first generation. Plant Biotechnol J 16:844–855. https://doi.org/10.1111/pbi.12832
Xu M, Zhu L, Shou H, Wu P (2005) A PIN1 family gene, OsPIN1, involved in auxin-dependent adventitious root emergence and tillering in rice. Plant Cell Physiol 46:1674–1681. https://doi.org/10.1093/PCP/PCI183
Zafar K, Sedeek KEM, Rao GS, Khan MZ, Amin I, Kamel R, Mukhtar Z, Zafar M, Mansoor S, Mahfouz MM (2020) Genome editing technologies for rice improvement: progress, prospects, and safety concerns. Front Genome Ed 2
Zemlyanskaya EV, Wiebe DS, Omelyanchuk NA, Levitsky VG (2016Apr) Mironova VV (2016) Meta-analysis of transcriptome data identified TGTCNN motif variants associated with the response to plant hormone auxin in Arabidopsis thaliana L. J Bioinform Comput Biol. 14(2):1641009. https://doi.org/10.1142/S0219720016410092
Zhang X-H, Tee LY, Wang X-G, Huang Q-S, Yang S-H (2015) Off-target effects in CRISPR/Cas9-mediated genome engineering. Mol Ther Nucleic Acids 4:e264. https://doi.org/10.1038/mtna.2015.37
Zhang T, Li R, Xing J, Yan L, Wang R, Zhao Y (2018) The YUCCA-auxin-WOX11 module controls crown root development in rice. Front Plant Sci 9:523. https://doi.org/10.3389/fpls.2018.00523
Zhu X, Xu Y, Yu S, Lu L, Ding M, Cheng J, Song G, Gao X, Yao L, Fan D, Meng S, Zhang X, Hu S, Tian Y (2014) An efficient genotyping method for genome-modified animals and human cells generated with CRISPR/Cas9 system. Sci Rep 4:6420. https://doi.org/10.1038/srep06420
Zou Y, Liu X, Wang Q, Chen Y, Liu C, Qiu Y, Zhang W (2014) OsRPK1, a novel leucine-rich repeat receptor-like kinase, negatively regulates polar auxin transport and root development in rice. Biochim Biophys Acta 1840:1676–1685. https://doi.org/10.1016/j.bbagen.2014.01.003
Acknowledgements
We thank Ms. Thuy Dương, Ms. Nguyen Thi Linh, Ms. Hoang Thi Huyen Trang, and Dr. Nguyen Van Doai for much support in this project.
Funding
This research was supported by the Vietnam Academy of Science and Technology under grant number VAST02.05/22–23 to Huong TM To.
Author information
Authors and Affiliations
Contributions
NTT, PTD, TTMH performed the vector construction and phenotyping. NTHN, DTP performed the transformation and genotyping of transgenic lines. All authors wrote the manuscript and approved it for publication.
Corresponding author
Ethics declarations
Ethical approval and consent to participate
Not applicable.
Competing interests
The authors declare no competing interests.
Additional information
Publisher's note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Nguyen, T.T., Pham, D.T., Nguyen, N.H. et al. The Germin-like protein gene OsGER4 is involved in heat stress response in rice root development. Funct Integr Genomics 23, 271 (2023). https://doi.org/10.1007/s10142-023-01201-1
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s10142-023-01201-1