Abstract
To feed the continuously expanding world’s population, new crop varieties have been generated, which significantly contribute to the world’s food security. However, the growth of these improved plant varieties relies primarily on synthetic fertilizers, which negatively affect the environment and human health; therefore, continuous improvement is needed for sustainable agriculture. Several plants, including cereal crops, have the adaptive capability to combat adverse environmental changes by altering physiological and molecular mechanisms and modifying their root system to improve nutrient uptake efficiency. These plants operate distinct pathways at various developmental stages to optimally establish their root system. These processes include changes in the expression profile of genes, changes in phytohormone level, and microbiome-induced root system architecture (RSA) modification. Several studies have been performed to understand microbial colonization and their involvement in RSA improvement through changes in phytohormone and transcriptomic levels. This review highlights the impact of genes, phytohormones, and particularly root microbiota in influencing RSA and provides new insights resulting from recent studies on rice root as a model system and summarizes the current knowledge about biochemical and central molecular mechanisms.
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References
Abel S, Oeller PW, Theologis A (1994) Early auxin-induced genes encode short-lived nuclear proteins. Proc Natl Acad Sci 91:326–330. https://doi.org/10.1073/pnas.91.1.326
Agarwal P, Singh PC, Chaudhry V, Shirke PA, Chakrabarty D, Farooqui A, Nautiyal CS, Sane AP, Sane VA (2019) PGPR-induced OsASR6 improves plant growth and yield by altering root auxin sensitivity and the xylem structure in transgenic Arabidopsis thaliana. J Plant Physiol 240:153010. https://doi.org/10.1016/j.jplph.2019.153010
Ambreetha S, Chinnadurai C, Marimuthu P, Balachandar D (2018) Plant-associated Bacillus modulates the expression of auxin-responsive genes of rice and modifies the root architecture. Rhizosphere 5:57–66. https://doi.org/10.1016/j.rhisph.2017.12.001
Anis GB, Zhang Y, Islam A, Zhang Y, Cao Y, Wu W, Cao L, Cheng S (2019) RDWN6 XB, a major quantitative trait locus positively enhances root system architecture under nitrogen deficiency in rice. BMC Plant Biol 19:1–13. https://doi.org/10.1186/s12870-018-1620-y
Anshu A, Agarwal P, Mishra K, Yadav U, Verma I, Chauhan S, Srivastava PK, Singh PC (2022) Synergistic action of Trichoderma koningiopsis and T. asperellum mitigates salt stress in paddy. Physiol Mol Biol Plants 28:987–1004. https://doi.org/10.1007/s12298-022-01192-6
Argueso CT, Ferreira FJ, Epple P, To JP, Hutchison CE, Schaller GE, Dangl JL, Kieber JJ (2012) Two-component elements mediate interactions between cytokinin and salicylic acid in plant immunity. PLoS Genet 8:e1002448. https://doi.org/10.1371/journal.pgen.1002448
Arite T, Kameoka H, Kyozuka J (2012) Strigolactone positively controls crown root elongation in rice. J Plant Growth Regul 31:165–172. https://doi.org/10.1007/s00344-011-9228-6
Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745. https://doi.org/10.1126/science.1113373
Ashrafuzzaman M, Hossen FA, Ismail MR, Hoque A, Islam MZ, Shahidullah S, Meon S (2009) Efficiency of plant growth-promoting rhizobacteria (PGPR) for the enhancement of rice growth. Afr J Biotech 8:1247–1252
Bagautdinova ZZ, Omelyanchuk N, Tyapkin AV, Kovrizhnykh VV, Lavrekha VV, Zemlyanskaya EV (2022) Salicylic acid in root growth and development. Int J Mol Sci 23:1–26. https://doi.org/10.3390/ijms23042228
Bao F, Shen J, Brady SR, Muday GK, Asami T, Yang Z (2004) Brassinosteroids interact with auxin to promote lateral root development in Arabidopsis. Plant Physiol 4:1624–1631. https://doi.org/10.1104/pp.103.036897
Barbez E, Dünser K, Gaidora A, Lendl T, Busch W (2017) Auxin steers root cell expansion via apoplastic pH regulation in Arabidopsis thaliana. Proc Natl Acad Sci 114:E4884–E4893. https://doi.org/10.1073/pnas.1613499114
Bari R, Pant BD, Stitt M, Scheible W-R (2006) PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol 141:988–999. https://doi.org/10.1104/pp.106.079707
Batista BD, Dourado MN, Figueredo EF, Hortencio RO, Marques JP, Piotto FA, Bonatelli ML, Settles ML, Azevedo JL, Quecine MC (2021) The auxin-producing Bacillus thuringiensis RZ2MS9 promotes the growth and modifies the root architecture of tomato (Solanum lycopersicum cv. Micro-Tom). Arch Microbiol 19:1–4. https://doi.org/10.1007/s00203-021-02361-z
Bellini C, Pacurar DI, Perrone I (2014) Adventitious roots and lateral roots: similarities and differences. Annu Rev Plant Biol 65:639–666. https://doi.org/10.1146/annurev-arplant-050213-035645
Bottini R, Cassán F, Piccoli P (2004) Gibberellin production by bacteria and its involvement in plant growth promotion and yield increase. Appl Microbiol Biotechnol 65:497–503. https://doi.org/10.1007/s00253-004-1696-1
Brazelton JN, Pfeufer EE, Sweat TA, Gardener BBM, Coenen C (2008) 2,4-Diacetylphloroglucinol alters plant root development. Mol Plant Microbe Interact® 21:1349–1358. https://doi.org/10.1094/MPMI-21-10-1349
Bruno M, Kersten S, Bain JM, Jaeger M, Rosati D, Kruppa MD, Lowman DW, Rice PJ, Graves B, Ma Z (2020) Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris. Nat Microbiol 5:1516–1531. https://doi.org/10.1038/s41564-020-0780-3
Brusamarello-Santos L, Pacheco F, Aljanabi S, Monteiro R, Cruz L, Baura V, Pedrosa F, Souza E, Wassem R (2012) Differential gene expression of rice roots inoculated with the diazotroph Herbaspirillum seropedicae. Plant Soil 356:113–125. https://doi.org/10.1007/s11104-011-1044-z
Cacciari I, Lippi D, Pietrosanti T, Pietrosanti W (1989) Phytohormone-like substances produced by single and mixed diazotrophic cultures of Azospirillum and Arthrobacter. Plant Soil 115:151–153. https://doi.org/10.1007/BF02220706
Chamam A, Sanguin H, Bellvert F, Meiffren G, Comte G, Wisniewski-Dyé F, Bertrand C, Prigent-Combaret C (2013) Plant secondary metabolite profiling evidences strain-dependent effect in the Azospirillum-Oryza sativa association. Phytochemistry 87:65–77. https://doi.org/10.1016/j.phytochem.2012.11.009
Champoux M, Wang G, Sarkarung S, Mackill DJ, O’Toole JC, Huang N, McCouch SR (1995) Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular marker. Theor Appl Genet 90:969–981. https://doi.org/10.1007/BF00222910
Chen EC, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, Charron P, St-Onge C, Giorgi J, Krüger M (2018) High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. New Phytol 220:1161–1171. https://doi.org/10.1111/nph.15472
Chen R, Xu N, Yu B, Wu Q, Li X, Wang G, Huang J (2020) The WUSCHEL-related homeobox transcription factor OsWOX4 controls the primary root elongation by activating OsAUX1 in rice. Plant Sci 298(110575):1–13. https://doi.org/10.1016/j.plantsci.2020.110575
Chiu CH, Paszkowski U (2020) Receptor-like kinases sustain symbiotic scrutiny. Plant Physiol 182:1597–1612. https://doi.org/10.1104/pp.19.01341
Chiu CH, Choi J, Paszkowski U (2018) Independent signalling cues underpin arbuscular mycorrhizal symbiosis and large lateral root induction in rice. New Phytol 217:552–557. https://doi.org/10.1111/nph.14936
Clark RT, Famoso AN, Zhao K, Shaff JE, Craft EJ, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV (2013) High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell Environ 36:454–466. https://doi.org/10.1111/j.1365-3040.2012.02587
Contesto C, Desbrosses G, Lefoulon C, Béna G, Borel F, Galland M, Gamet L, Varoquaux F, Touraine B (2008) Effects of rhizobacterial ACC deaminase activity on Arabidopsis indicate that ethylene mediates local root responses to plant growth-promoting rhizobacteria. Plant Sci 175(1–2):178–189. https://doi.org/10.1016/j.plantsci.2008.01.020
Coudert Y, Périn C, Courtois B, Khong NG, Gantet P (2010) Genetic control of root development in rice, the model cereal. Trends Plant Sci 15:219–226. https://doi.org/10.1016/j.tplants.2010.01.008
Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, Frouin J, Rouan L, Goze E, Kilian A, Ahmadi N, Dingkuhn M (2013) Genome-wide association mapping of root traits in a japonica rice panel. PLoS ONE 8(11):1–18. https://doi.org/10.1371/journal.pone.0078037
Curzi M, Ribaudo C, Trinchero G, Curá J, Pagano E (2008) Changes in the content of organic and amino acids and ethylene production of rice plants in response to the inoculation with Herbaspirillum seropedicae. J Plant Interact 3:163–173. https://doi.org/10.1080/17429140802255167
Dai X, Wang Y, Yang A, Zhang W-H (2012) OsMYB2P-1, an R2R3 MYB transcription factor, is involved in the regulation of phosphate-starvation responses and root architecture in rice. Plant Physiol 159:169–183. https://doi.org/10.1104/pp.112.194217
Dai X, Wang Y, Zhang W-H (2016) OsWRKY74, a WRKY transcription factor, modulates tolerance to phosphate starvation in rice. J Exp Bot 67:947–960. https://doi.org/10.1093/jxb/erv515
Debi BR, Chhun T, Taketa S, Tsurumi S, Xia K, Miyao A, Hirochika H, Ichii M (2005) Defects in root development and gravity response in the aem1 mutant of rice are associated with reduced auxin efflux. J Plant Physiol 162:678–685. https://doi.org/10.1016/j.jplph.2004.09.012
Dennis PG, Miller AJ, Hirsch PR (2010) Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol Ecol 72:313–327. https://doi.org/10.1111/j.1574-6941.2010.00860.x
Dobbelaere S, Croonenborghs A, Thys A, Ptacek D, Okon Y, Vanderleyden J (2002) Effect of inoculation with wild type Azospirillum brasilense and A. irakense strains on development and nitrogen uptake of spring wheat and grain maize. Biol Fertil Soils 36:284–297. https://doi.org/10.1007/s00374-002-0534-9
Dodd I, Zinovkina N, Safronova V, Belimov A (2010) Rhizobacterial mediation of plant hormone status. Ann Appl Biol 157:361–379. https://doi.org/10.1111/j.1744-7348.2010.00439.x
Doni F, Fathurrahman F, Mispan MS, Suhaimi NSM, Yusoff WMW, Uphoff N (2019) Transcriptomic profiling of rice seedlings inoculated with the symbiotic fungus Trichoderma asperellum SL2. J Plant Growth Regul 38:1507–1515. https://doi.org/10.1007/s00344-019-09952-7
El Zemrany H, Czarnes S, Hallett PD, Alamercery S, Bally R, Jocteur-Monrozier L (2007) Early changes in root characteristics of maize (Zea mays) following seed inoculation with the PGPR Azospirillum lipoferum CRT1. Plant Soil 291:109–118. https://doi.org/10.1007/s11104-006-9178-0
El-Khawas H, Adachi K (1999) Identification and quantification of auxins in culture media of Azospirillum and Klebsiella and their effect on rice roots. Biol Fertil Soils 28:377–381. https://doi.org/10.1007/s003740050507
Enebe MC, Babalola OO (2019) The impact of microbes in the orchestration of plants resistance to biotic stress: a disease management approach. Appl Microbiol Biotechnol 103:9–25. https://doi.org/10.1007/s00253-018-9433-3
Ferreira Rêgo MC, Ilkiu-Borges F, Filippi MCC, de Gonçalves LA, Silva GB (2014) Morphoanatomical and biochemical changes in the roots of rice plants induced by plant growth-promoting microorganisms. J Bot 2014:818797. https://doi.org/10.1155/2014/818797
Fukao T, Yeung E, Bailey-Serres J (2011) The submergence tolerance regulator SUB1A mediates crosstalk between submergence and drought tolerance in rice. Plant Cell 23:412–427. https://doi.org/10.1105/tpc.110.080325
Galland M, Gamet L, Varoquaux F, Touraine B, Desbrosses G (2012) The ethylene pathway contributes to root hair elongation induced by the beneficial bacteria Phyllobacterium brassicacearum STM196. Plant Sci 190:74–81. https://doi.org/10.1016/j.plantsci.2012.03.008
Gamalero E, Glick BR (2015) Bacterial modulation of plant ethylene levels. Plant Physiol 169:13–22. https://doi.org/10.1104/pp.15.00284
García de Salamone IE, Hynes RK, Nelson LM (2001) Cytokinin production by plant growth promoting rhizobacteria and selected mutants. Can J Microbiol 47:404–411. https://doi.org/10.1139/w01-029
Ghosh D, Gupta A, Mohapatra S (2019) Dynamics of endogenous hormone regulation in plants by phytohormone secreting rhizobacteria under water-stress. Symbiosis 77:265–278. https://doi.org/10.1007/s13199-018-00589-w
Gray WM, Kepinski S, Rouse D, Leyser O, Estelle M (2001) Auxin regulates SCF TIR1-dependent degradation of AUX/IAA proteins. Nature 414:271–276. https://doi.org/10.1038/35104500
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
Guo Y, Wu Q, Xie Z, Yu B, Zeng R, Min Q, Huang J (2020) OsFPFL4 is involved in the root and flower development by affecting auxin levels and ROS accumulation in rice (Oryza sativa). Rice 13:1–15. https://doi.org/10.1186/s12284-019-0364-0
Gutjahr C, Casieri L, Paszkowski U (2009) Glomus intraradices induces changes in root system architecture of rice independently of common symbiosis signaling. New Phytol 182:829–837. https://doi.org/10.1111/j.1469-8137.2009.02839.x
Hanzawa E, Sasaki K, Nagai S, Obara M, Fukuta Y, Uga Y, Miyao A, Hirochika H, Higashitani A, Maekawa M (2013) Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.). Rice 6:1–11. https://doi.org/10.1186/1939-8433-6-30
Hasegawa T, Lucob-Agustin N, Yasufuku K, Kojima T, Nishiuchi S, Ogawa A, Takahashi-Nosaka M, Kano-Nakata M, Inari-Ikeda M, Sato M, Tsuji H (2021) Mutation of OUR1/OsbZIP1, which encodes a member of the basic leucine zipper transcription factor family, promotes root development in rice through repressing auxin signaling. Plant Sci 306:110861. https://doi.org/10.1016/j.plantsci.2021.110861
Hirose N, Makita N, Kojima M, Kamada-Nobusada T, Sakakibara H (2007) Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism. Plant Cell Physiol 48:523–539. https://doi.org/10.1093/pcp/pcm022
Hochholdinger F, Zimmermann R (2008) Conserved and diverse mechanisms in root development. Curr Opin Plant Biol 11:70–74. https://doi.org/10.1016/j.pbi.2007.10.002
Hochholdinger F, Park WJ, Sauer M, Woll K (2004) From weeds to crops: genetic analysis of root development in cereals. Trends Plant Sci 9:42–48. https://doi.org/10.1016/j.tplants.2003.11.003
Hou J, Zheng X, Ren R, Shi Q, Xiao H, Chen Z, Yue M, Wu Y, Hou H, Li L (2022) The histone deacetylase 1/GSK3/SHAGGY-like kinase 2/BRASSINAZOLE-RESISTANT 1 module controls lateral root formation in rice. Plant Physiol 189:858–873. https://doi.org/10.1093/plphys/kiac015
Hu L, Robert CA, Cadot S, Zhang X, Ye M, Li B, Manzo D, Chervet N, Steinger T, Van Der Heijden MG (2018) Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nat Commun 9:1–13. https://doi.org/10.1038/s41467-018-05122-7
Huang S, Liang Z, Chen S, Sun H, Fan X, Wang C, Xu G, Zhang Y (2019) A transcription factor, OsMADS57, regulates long-distance nitrate transport and root elongation. Plant Physiol 180:882–895. https://doi.org/10.1104/pp.19.00142
Ikeda A, Ueguchi-Tanaka M, Sonoda Y, Kitano H, Koshioka M, Futsuhara Y, Matsuoka M, Yamaguchi J (2001) slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8. Plant Cell 13:999–1010. https://doi.org/10.1105/tpc.13.5.999
Iqbal N, Khan NA, Ferrante A, Trivellini A, Francini A, Khan M (2017) Ethylene role in plant growth, development and senescence: interaction with other phytohormones. Front Plant Sci 8:475. https://doi.org/10.3389/fpls.2017.00475
Jain M, Tyagi AK, Khurana JP (2006) Molecular characterization and differential expression of cytokinin-responsive type-A response regulators in rice (Oryza sativa). BMC Plant Biol 6:1–11. https://doi.org/10.1186/1471-2229-6-1
Jha Y, Subramanian R, Patel S (2011) Combination of endophytic and rhizospheric plant growth promoting rhizobacteria in Oryza sativa shows higher accumulation of osmoprotectant against saline stress. Acta Physiol Plant 33:797–802. https://doi.org/10.1007/s11738-010-0604-9
Jiang W, Zhou S, Huang H, Song H, Zhang Q, Zhao Y (2020) MERISTEM ACTIVITYLESS (MAL) is involved in root development through maintenance of meristem size in rice. Plant Mol Biol 104:499–511. https://doi.org/10.1007/s11103-020-01053-4
Jing H, Strader LC (2019) Interplay of auxin and cytokinin in lateral root development. Int J Mol Sci 20:1–12. https://doi.org/10.3390/ijms20030486
Jing H, Yang X, Zhang J, Liu X, Zheng H, Dong G, Nian J, Feng J, Xia B, Qian Q (2015) Peptidyl-prolyl isomerization targets rice Aux/IAAs for proteasomal degradation during auxin signalling. Nat Commun 6:1–10. https://doi.org/10.1038/ncomms8395
Kamoshita A, Chandra Babu R, Boopathi MN, Fukai S (2008) Phenotypic and genotypic analysis of drought-resistance traits for development of rice cultivars adapted to rainfed environments. Field Crop Res 109:1–23. https://doi.org/10.1016/j.fcr.2008.06.010
Kandasamy S, Loganathan K, Muthuraj R, Duraisamy S, Seetharaman S, Thiruvengadam R, Ponnusamy B, Ramasamy S (2009) Understanding the molecular basis of plant growth promotional effect of Pseudomonas fluorescens on rice through protein profiling. Prot Sci 7:1–8. https://doi.org/10.1186/1477-5956-7-47
Khowaja FS, Norton GJ, Courtois B, Price AH (2009) Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis. BMC Genomics 10:1–14. https://doi.org/10.1186/1471-2164-10-276
Kieber JJ, Schaller GE (2018) Cytokinin signaling in plant development. Development 145:1–7. https://doi.org/10.1242/dev.149344
Kim J-Y, Kim HS, Lee SM, Park H-J, Lee S-H, Jang JS, Lee MH (2020) Plant growth promoting and disease controlling activities of Pseudomonas geniculata ANG3, Exiguobacterium acetylicum ANG40 and Burkholderia stabilis ANG51 isolated from soil. Microbiol Biotechnol Lett 48:38–47. https://doi.org/10.4014/mbl.1906.06002
Kitomi Y, Hanzawa E, Kuya N, Inoue H, Hara N, Kawai S, Kanno N, Endo M, Sugimoto K, Yamazaki T, Sakamoto S (2020) Root angle modifications by the DRO1 homolog improve rice yields in saline paddy fields. Proc Natl Acad Sci 117:21242–21250. https://doi.org/10.1073/pnas.2005911117
Klein SP, Schneider HM, Perkins AC, Brown KM, Lynch JP (2020) Multiple integrated root phenotypes are associated with improved drought tolerance. Plant Physiol 183:1011–1025. https://doi.org/10.1104/pp.20.00211
Kreuzer K, Adamczyk J, Iijima M, Wagner M, Scheu S, Bonkowski M (2006) Grazing of a common species of soil protozoa (Acanthamoeba castellanii) affects rhizosphere bacterial community composition and root architecture of rice (Oryza sativa L.). Soil Biol Biochem 38:1665–1672. https://doi.org/10.1016/j.soilbio.2005.11.027
Kudo T, Makita N, Kojima M, Tokunaga H, Sakakibara H (2012) Cytokinin activity of cis-zeatin and phenotypic alterations induced by overexpression of putative cis-zeatin-O-glucosyltransferase in rice. Plant Physiol 160:319–331. https://doi.org/10.1104/pp.112.196733
Kurakawa T, Ueda N, Maekawa M, Kobayashi K, Kojima M, Nagato Y, Sakakibara H, Kyozuka J (2007) Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature 445:652–655. https://doi.org/10.1038/nature05504
Lee HY, Chen Z, Zhang C, Yoon GM (2019) Editing of the OsACS locus alters phosphate deficiency-induced adaptive responses in rice seedlings. J Exp Bot 70:1927–1940. https://doi.org/10.1093/jxb/erz074
Li X, Zeng R, Liao H (2016) Improving crop nutrient efficiency through root architecture modifications. J Integr Plant Biol 58:193–202. https://doi.org/10.1111/jipb.12434
Li X, Chen R, Chu Y, Huang J, Jin L, Wang G, Huang J (2018a) Overexpression of RCc3 improves root system architecture and enhances salt tolerance in rice. Plant Physiol Biochem 130:566–576. https://doi.org/10.1016/j.plaphy.2018.08.008
Li X, Zhou J, Xu R-S, Meng M-Y, Yu X, Dai C-C (2018b) Auxin, cytokinin, and ethylene involved in rice N availability improvement caused by endophyte Phomopsis liquidambari. J Plant Growth Regul 37:128–143. https://doi.org/10.1007/s00344-017-9712-8
Li S-M, Zheng H-X, Zhang X-S, Sui N (2020a) Cytokinins as central regulators during plant growth and stress response. Plant Cell Rep 2:271–282. https://doi.org/10.1007/s00299-020-02612-1
Li J, Yang Y, Chai M, Ren M, Yuan J, Yang W, Dong Y, Liu B, Jian Q, Wang S (2020b) Gibberellins modulate local auxin biosynthesis and polar auxin transport by negatively affecting flavonoid biosynthesis in the root tips of rice. Plant Sci 298:1–10. https://doi.org/10.1016/j.plantsci.2020.110545
Liang C, Li A, Yu H, Li W, Liang C, Guo S, Zhang R, Chu C (2017) Melatonin regulates root architecture by modulating auxin response in rice. Front Plant Sci 8:134. https://doi.org/10.3389/fpls.2017.00134
Lorbiecke R, Sauter M (1999) Adventitious root growth and cell-cycle induction in deepwater rice. Plant Physiol 119:21–30. https://doi.org/10.1104/pp.119.1.21
Lucob-Agustin N, Kawai T, Takahashi-Nosaka M, Kano-Nakata M, Wainaina CM, Hasegawa T, Inari-Ikeda M, Sato M, Tsuji H, Yamauchi A, Inukai Y (2020) WEG1, which encodes a cell wall hydroxyproline-rich glycoprotein, is essential for parental root elongation controlling lateral root formation in rice. Physiol Plant 169:214–227. https://doi.org/10.1111/ppl.13063
Lugtenberg B, Rozen DE, Kamilova F (2017) Wars between microbes on roots and fruits. F1000Research 6:343–343. https://doi.org/10.12688/f1000research.10696.1
Lv B, Tian H, Zhang F, Liu J, Lu S, Bai M, Li C, Ding Z (2018) Brassinosteroids regulate root growth by controlling reactive oxygen species homeostasis and dual effect on ethylene synthesis in Arabidopsis. PLoS Genet 14:e1007144. https://doi.org/10.1371/journal.pgen.1007144
Lynch JP, Wojciechowski T (2015) Opportunities and challenges in the subsoil: pathways to deeper rooted crops. J Exp Bot 66:2199–2210. https://doi.org/10.1093/jxb/eru508
Ma N, Wang Y, Qiu S, Kang Z, Che S, Wang G, Huang J (2013) Overexpression of OsEXPA8, a root-specific gene, improves rice growth and root system architecture by facilitating cell extension. PLoS ONE 8:1–10. https://doi.org/10.1371/journal.pone.0075997
Mai CD, Phung NT, To HT, Gonin M, Hoang GT, Nguyen KL, Do VN, Courtois B, Gantet P (2014) Genes controlling root development in rice. Rice 7:1–11. https://doi.org/10.1186/s12284-014-0030-5
Mao C, He J, Liu L, Deng Q, Yao X, Liu C, Qiao Y, Li P, Ming F (2020) OsNAC2 integrates auxin and cytokinin pathways to modulate rice root development. Plant Biotechnol J 18:429–442. https://doi.org/10.1111/pbi.13209
Maurel C, Nacry P (2020) Root architecture and hydraulics converge for acclimation to changing water availability. Nat Plants 6:744–749. https://doi.org/10.1038/s41477-020-0684-5
Mergemann H, Sauter M (2000) Ethylene induces epidermal cell death at the site of adventitious root emergence in rice. Plant Physiol 124:609–614. https://doi.org/10.1104/pp.124.2.609
Miché L, Battistoni F, Gemmer S, Belghazi M, Reinhold-Hurek B (2006) Upregulation of jasmonate-inducible defense proteins and differential colonization of roots of Oryza sativa cultivars with the endophyte Azoarcus sp. Mol Plant Microbe Interact 19:502–511. https://doi.org/10.1094/MPMI-19-0502
Mitra D, Be GS, Khoshru B, De Los SV, Belz C, Chaudhary P, Shahri FN, Djebaili R, Adeyemi NO, El-Ballat EM, El-Esawi MA (2021) Impacts of arbuscular mycorrhizal fungi on rice growth, development, and stress management with a particular emphasis on strigolactone effects on root development. Commun Soil Sci Plant Anal 52:1591–1621. https://doi.org/10.1080/00103624.2021.1892728
Mohite B (2013) Isolation and characterization of indole acetic acid (IAA) producing bacteria from rhizospheric soil and its effect on plant growth. J Soil Sci Plant Nutr 13:638–649. https://doi.org/10.4067/S0718-95162013005000051
Neogy A, Singh Z, Mushahary KKK, Yadav SR (2020) Dynamic cytokinin signaling and function of auxin in cytokinin responsive domains during rice crown root development. Plant Cell Rep 12:1–9. https://doi.org/10.1007/s00299-020-02618-9
Ogura T, Goeschl C, Filiault D, Mirea M, Slovak R, Wolhrab B, Satbhai SB, Busch W (2019) Root system depth in Arabidopsis is shaped by EXOCYST70A3 via the dynamic modulation of auxin transport. Cell 178:400–412. https://doi.org/10.1016/j.cell.2019.06.021
Ortíz-Castro R, Contreras-Cornejo HA, Macías-Rodríguez L, López-Bucio J (2009) The role of microbial signals in plant growth and development. Plant Signal Behav 4:701–712. https://doi.org/10.4161/psb.4.8.9047
Paez-Garcia A, Motes CM, Scheible WR, Chen R, Blancaflor EB, Monteros MJ (2015) Root traits and phenotyping strategies for plant improvement. Plants 4:334–355. https://doi.org/10.3390/plants4020334
Pasternak T, Groot EP, Kazantsev FV, Teale W, Omelyanchuk N, Kovrizhnykh V, Palme K, Mironova VV (2019) Salicylic acid affects root meristem patterning via auxin distribution in a concentration-dependent manner. Plant Physiol 180:1725–1739. https://doi.org/10.1104/pp.19.00130
Pedersen O, Sauter M, Colmer TD, Nakazono M (2021) Regulation of root adaptive anatomical and morphological traits during low soil oxygen. New Phytol 229:42–49. https://doi.org/10.1111/nph.16375
Perrig D, Boiero M, Masciarelli O, Penna C, Ruiz O, Cassán F, Luna M (2007) Plant-growth-promoting compounds produced by two agronomically important strains of Azospirillum brasilense, and implications for inoculant formulation. Appl Microbiol Biotechnol 75:1143–1150. https://doi.org/10.1007/s00253-007-0909-9
Phillips DA, Fox TC, King MD, Bhuvaneswari T, Teuber LR (2004) Microbial products trigger amino acid exudation from plant roots. Plant Physiol 136:2887–2894. https://doi.org/10.1104/pp.104.044222
Plett DC, Ranathunge K, Melino VJ, Kuya N, Uga Y, Kronzucker HJ (2020) The intersection of nitrogen nutrition and water use in plants: new paths toward improved crop productivity. J Exp Bot 71:4452–4468. https://doi.org/10.1093/jxb/eraa049
Qi Y, Wang S, Shen C, Zhang S, Chen Y, Xu Y, Liu Y, Wu Y, Jiang D (2012) OsARF12, a transcription activator on auxin response gene, regulates root elongation and affects iron accumulation in rice (Oryza sativa). New Phytol 193:109–120. https://doi.org/10.1111/j.1469-8137.2011.03910.x
Qin H, Pandey BK, Li Y, Huang G, Wang J, Quan R, Zhou J, Zhou Y, Miao Y, Zhang D, Bennett MJ (2022) Orchestration of ethylene and gibberellin signals determines primary root elongation in rice. Plant Cell 34:1273–1288. https://doi.org/10.1093/plcell/koac008
Rebouillat J, Dievart A, Verdeil J-L, Escoute J, Giese G, Breitler J-C, Gantet P, Espeout S, Guiderdoni E, Périn C (2009) Molecular genetics of rice root development. Rice 2:15–34. https://doi.org/10.1007/s12284-008-9016-5
Remans R, Ramaekers L, Schelkens S, Hernandez G, Garcia A, Reyes JL, Mendez N, Toscano V, Mulling M, Galvez L (2008) Effect of Rhizobium-Azospirillum coinoculation on nitrogen fixation and yield of two contrasting Phaseolus vulgaris L. genotypes cultivated across different environments in Cuba. Plant Soil 312:25–37. https://doi.org/10.1186/s40068-017-0091-8
Rondina ABL, dos Santos Sanzovo AW, Guimarães GS, Wendling JR, Nogueira MA, Hungria M (2020) Changes in root morphological traits in soybean co-inoculated with Bradyrhizobium spp. and Azospirillum brasilense or treated with A. brasilense exudates. Biol Fertil Soils 56:537–549. https://doi.org/10.1007/s00374-020-01453-0
Sannazzaro AI, Echeverría M, Albertó EO, Ruiz OA, Menéndez AB (2007) Modulation of polyamine balance in Lotus glaber by salinity and arbuscular mycorrhiza. Plant Physiol Biochem 45:39–46. https://doi.org/10.1016/j.plaphy.2006.12.008
Sekar C, Prasad N, Sundaram M (2000) Enhancement of polygalacturonase activity during auxin induced para nodulation and endorhizosphere colonization of Azospirillum in rice roots. Indian J Exp Bot 38:80–83. http://nopr.niscair.res.in/handle/123456789/23880
Shahzad R, Khan AL, Bilal S, Waqas M, Kang S-M, Lee I-J (2017) Inoculation of abscisic acid-producing endophytic bacteria enhances salinity stress tolerance in Oryza sativa. Environ Exp Bot 136:68–77. https://doi.org/10.1016/j.envexpbot.2017.01.010
Shao Y, Lehner KR, Zhou H, Taylor I, Zhu M, Mao C, Benfey PN (2021) VAP-RELATED SUPPRESSORS OF TOO MANY MOUTHS (VST) family proteins are regulators of root system architecture. Plant Physiol 185:457–468. https://doi.org/10.1093/plphys/kiaa036
Shen C, Yue R, Sun T, Zhang L, Yang Y, Wang H (2015) OsARF16, a transcription factor regulating auxin redistribution, is required for iron deficiency response in rice (Oryza sativa L.). Plant Sci 231:148–158. https://doi.org/10.1016/j.plantsci.2014.12.003
Šimášková M, O’Brien JA, Khan M, Van Noorden G, Ötvös K, Vieten A, De Clercq I, Van Haperen JMA, Cuesta C, Hoyerová K, Vanneste S (2015) Cytokinin response factors regulate PIN-FORMED auxin transporters. Nat Commun 6:1–11. https://doi.org/10.1038/ncomms9717
Singh V, van Oosterom EJ, Jordan DR, Messina CD, Cooper M, Hammer GL (2010) Morphological and architectural development of root systems in sorghum and maize. Plant Soil 333:287–299. https://doi.org/10.1007/s11104-010-0343-0
Singh AP, Pandey BK, Mehra P, Heitz T, Giri J (2020) OsJAZ9 overexpression modulates jasmonic acid biosynthesis and potassium deficiency responses in rice. Plant Mol Biol 104:397–410. https://doi.org/10.1007/s11103-020-01047-2
Singh BK, Ramkumar MK, Dalal M, Singh A, Solanke AU, Singh NK, Sevanthi AM (2021) Allele mining for a drought responsive gene DRO1 determining root growth angle in donors of drought tolerance in rice (Oryza sativa L.). Physiol Mol Biol Plants 27:523–534. https://doi.org/10.1007/s12298-021-00950-2
Smith S, De Smet I (2012) Root system architecture: insights from Arabidopsis and cereal crops. Philos Trans R Soc B Biol Sci 367:1441–1452. https://doi.org/10.1098/rstb.2011.0234
Sreevidya V, Hernandez-Oane RJ, Gyaneshwar P, Lara-Flores M, Ladha JK, Reddy PM (2010) Changes in auxin distribution patterns during lateral root development in rice. Plant Sci 178:531–538. https://doi.org/10.1016/j.plantsci.2010.03.004
Steffens B, Rasmussen A (2016) The physiology of adventitious roots. Plant Physiol 170:603–617. https://doi.org/10.1104/pp.15.01360
Steffens B, Sauter M (2005) Epidermal cell death in rice is regulated by ethylene, gibberellin, and abscisic acid. Plant Physiol 139:713–721. https://doi.org/10.1104/pp.105.064469
Steffens B, Wang J, Sauter M (2006) Interactions between ethylene, gibberellin and abscisic acid regulate emergence and growth rate of adventitious roots in deepwater rice. Planta 223:604–612. https://doi.org/10.1007/s00425-005-0111-1
Sulieman S, Schulze J (2010) Phloem-derived γ-aminobutyric acid (GABA) is involved in upregulating nodule N2 fixation efficiency in the model legume Medicago truncatula. Plant Cell Environ 33:2162–2172. https://doi.org/10.1111/j.1365-3040.2010.02214.x
Sun J, Xu Y, Ye S, Jiang H, Chen Q, Liu F, Zhou W, Chen R, Li X, Tietz O, Wu X (2009) Arabidopsis ASA1 is important for jasmonate-mediated regulation of auxin biosynthesis and transport during lateral root formation. Plant Cell 21:1495–1511. https://doi.org/10.1105/tpc.108.064303
Suzuki G, Lucob-Agustin N, Kashihara K, Fujii Y, Inukai Y, Gomi K (2021) Rice MEDIATOR25, OsMED25, is an essential subunit for jasmonate-mediated root development and OsMYC2-mediated leaf senescence. Plant Sci 306:110853. https://doi.org/10.1016/j.plantsci.2021.110853
Tfaily MM, Cooper WT, Kostka JE, Chanton PR, Schadt CW, Hanson PJ, Iversen CM, Chanton JP (2014) Organic matter transformation in the peat column at Marcell Experimental Forest: humification and vertical stratification. J Geophys Res Biogeosci 119:661–675. https://doi.org/10.1002/2013JG002492
Timmusk S, Nicander B, Granhall U, Tillberg E (1999) Cytokinin production by Paenibacillus polymyxa. Soil Biol Biochem 31:1847–1852. https://doi.org/10.1016/s0038-0717(99)00113-3
Tiryaki I, Staswick PE (2002) An Arabidopsis mutant defective in jasmonate response is allelic to the auxin-signaling mutant axr1. Plant Physiol 130:887–894. https://doi.org/10.1104/pp.005272
Uga Y, Sugimoto K, Ogawa S, Rane J, Ishitani M, Hara N, Kitomi Y, Inukai Y, Ono K, Kanno N (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
Vacheron J, Desbrosses G, Bouffaud M-L, Touraine B, Moënne-Loccoz Y, Muller D, Legendre L, Wisniewski-Dyé F, Prigent-Combaret C (2013) Plant growth-promoting rhizobacteria and root system functioning. Front Plant Sci 4:19. https://doi.org/10.3389/fpls.2013.00356
Valette M, Rey M, Doré J, Gerin F, Wisniewski-Dyé F (2020) Identification of a small set of genes commonly regulated in rice roots in response to beneficial rhizobacteria. Physiol Mol Biol Plants 26:2537–2551. https://doi.org/10.1007/s12298-020-00911-1
Van Wees SC, Van der Ent S, Pieterse CM (2008) Plant immune responses triggered by beneficial microbes. Curr Opin Plant Biol 11:443–448. https://doi.org/10.1016/j.pbi.2008.05.005
Vargas L, de Carvalho TLG, Ferreira PCG, Baldani VLD, Baldani JI, Hemerly AS (2012) Early responses of rice (Oryza sativa L.) seedlings to inoculation with beneficial diazotrophic bacteria are dependent on plant and bacterial genotypes. Plant Soil 356:127–137. https://doi.org/10.1007/s11104-012-1274-8
Vázquez-Glaría A, Eichler-Löbermann B, Loiret FG, Ortega E, Kavka M (2021) Root-system architectures of two Cuban rice cultivars with salt stress at early development stages. Plants 10:1194. https://doi.org/10.3390/plants10061194
Venturi V, Keel C (2016) Signaling in the rhizosphere. Trends Plant Sci 21:187–198. https://doi.org/10.1016/j.tplants.2016.01.005
Verma PK, Verma S, Tripathi RD, Chakrabarty D (2020) A rice glutaredoxin regulate the expression of aquaporin genes and modulate root responses to provide arsenic tolerance. Ecotoxicol Environ Saf 195:1–11. https://doi.org/10.1016/j.ecoenv.2020.110471
Verma PK, Verma S, Tripathi RD, Pandey N, Chakrabarty D (2021) CC-type glutaredoxin, OsGrx_C7 plays a crucial role in enhancing protection against salt stress in rice. J Biotechnol 329:192–203. https://doi.org/10.1016/j.jbiotec.2021.02.008
Vives-Peris V, de Ollas C, Gómez-Cadenas A, Pérez-Clemente RM (2019) Root exudates: from plant to rhizosphere and beyond. Plant Cell Rep 39:3–17. https://doi.org/10.1007/s00299-019-02447-5
Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY (2005) Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17:2204–2216. https://doi.org/10.1105/tpc.105.033076
Wang H, Sun R, Cao Y, Pei W, Sun Y, Zhou H, Wu X, Zhang F, Luo L, Shen Q (2015) OsSIZ1, a SUMO E3 ligase gene, is involved in the regulation of the responses to phosphate and nitrogen in rice. Plant Cell Physiol 56:2381–2395. https://doi.org/10.1093/pcp/pcv162
Wang T, Li C, Wu Z, Jia Y, Wang H, Sun S, Mao C, Wang X (2017) Abscisic acid regulates auxin homeostasis in rice root tips to promote root hair elongation. Front Plant Sci 8:1121. https://doi.org/10.3389/fpls.2017.01121
Wang L, Guo M, Li Y, Ruan W, Mo X, Wu Z, Sturrock CJ, Yu H, Lu C, Peng J (2018a) LARGE ROOT ANGLE1, encoding OsPIN2, is involved in root system architecture in rice. J Exp Bot 69:385–397. https://doi.org/10.1093/jxb/erx427
Wang P, Xu X, Tang Z, Zhang W, Huang XY, Zhao F-J (2018b) OsWRKY28 regulates phosphate and arsenate accumulation, root system architecture and fertility in rice. Front Plant Sci 9:1–13. https://doi.org/10.3389/fpls.2018.01330
Wang M, Qiao J, Yu C, Chen H, Sun C, Huang L, Li C, Geisler M, Qian Q, Jiang DA, Qi Y (2019) The auxin influx carrier, OsAUX3, regulates rice root development and responses to aluminium stress. Plant, Cell Environ 42:1125–1138. https://doi.org/10.1111/pce.13478
Wang C, Li X, Caragea D, Bheemanahallia R, Jagadish SK (2020a) Root anatomy based on root cross-section image analysis with deep learning. Comput Electron Agric 175:1–13. https://doi.org/10.1016/j.compag.2020.105549
Wang R, Wang H-L, Tang R-P, Sun M-Y, Chen T-M, Duan X-C, Lu X-F, Liu D, Shi X-C, Laborda P (2020b) Pseudomonas putida represses JA-and SA-mediated defense pathways in rice and promotes an alternative defense mechanism possibly through ABA signaling. Plants 9:1–14. https://doi.org/10.3390/plants9121641
Weller DM, Landa BB, Mavrodi OV, Schroeder KL, De La Fuente L, Blouin Bankhead S, Allende Molar R, Bonsall RF, Mavrodi DV, Thomashow LS (2007) Role of 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. in the defense of plant roots. Plant Biol 9:4–20. https://doi.org/10.1055/s-2006-924473
Wing RA, Purugganan MD, Zhang Q (2018) The rice genome revolution: from an ancient grain to Green Super Rice. Nat Rev Genet 19:505–517. https://doi.org/10.1038/s41576-018-0024-z
Wu Q, Peng X, Yang M, Zhang W, Dazzo FB, Uphoff N, Jing Y, Shen S (2018) Rhizobia promote the growth of rice shoots by targeting cell signaling, division and expansion. Plant Mol Biol 97:507–523. https://doi.org/10.1007/s11103-018-0756-3
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
Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708. https://doi.org/10.1038/nature04920
Xu Y, Ge Y, Song J, Rensing C (2020) Assembly of root-associated microbial community of typical rice cultivars in different soil types. Biol Fertil Soils 56:249–260. https://doi.org/10.1007/s00374-019-01406-2
Xuan YH, Kumar V, Han X, Kim SH, Jeong JH, Kim CM, Gao Y, Han CD (2019) CBL-INTERACTING PROTEIN KINASE 9 regulates ammonium-dependent root growth downstream of IDD10 in rice (Oryza sativa). Ann Bot 124:947–960. https://doi.org/10.1093/aob/mcy242
Yamaji N, Huang CF, Nagao S, Yano M, Sato Y, Nagamura Y, Ma JF (2009) A zinc finger transcription factor ART1 regulates multiple genes implicated in aluminum tolerance in rice. Plant Cell 21:3339–3349. https://doi.org/10.1093/pcp/pcw073
Yang A, Zhang W-H (2016) A small GTPase, OsRab6a, is involved in the regulation of iron homeostasis in rice. Plant Cell Physiol 57:1271–1280. https://doi.org/10.1093/pcp/pcw073
Yang WT, Baek D, Yun D-J, Hwang WH, Park DS, Nam MH, Chung ES, Chung YS, Yi YB, Kim DH (2014) Overexpression of OsMYB4P, an R2R3-type MYB transcriptional activator, increases phosphate acquisition in rice. Plant Physiol Biochem 80:259–267. https://doi.org/10.1016/j.plaphy.2014.02.024
Yang C, Li W, Cao J, Meng F, Yu Y, Huang J, Jiang L, Liu M, Zhang Z, Chen X (2017) Activation of ethylene signaling pathways enhances disease resistance by regulating ROS and phytoalexin production in rice. Plant J 89:338–353. https://doi.org/10.1111/tpj.13388
Yano K, Yoshida S, Müller J, Singh S, Banba M, Vickers K, Markmann K, White C, Schuller B, Sato S (2008) CYCLOPS, a mediator of symbiotic intracellular accommodation. Proc Natl Acad Sci 105:20540–20545. https://doi.org/10.1073/pnas.0806858105
Yi K, Wu Z, Zhou J, Du L, Guo L, Wu Y, Wu P (2005) OsPTF1, a novel transcription factor involved in tolerance to phosphate starvation in rice. Plant Physiol 138:2087–2096. https://doi.org/10.1104/pp.105.063115
Yoon J, Cho LH, Yang W, Pasriga R, Wu Y, Hong WJ, Bureau C, Wi SJ, Zhang T, Wang R, Zhang D (2020) Homeobox transcription factor OsZHD2 promotes root meristem activity in rice by inducing ethylene biosynthesis. J Exp Bot 71:5348–5364. https://doi.org/10.1093/jxb/eraa209
Yu C, Sun C, Shen C, Wang S, Liu F, Liu Y, Chen Y, Li C, Qian Q, Aryal B, Geisler M (2015) The auxin transporter, Os AUX 1, is involved in primary root and root hair elongation and in Cd stress responses in rice (Oryza sativa L.). Plant J 83:818–830. https://doi.org/10.1111/tpj.12929
Zaheer MS, Ali HH, Iqbal MA, Erinle KO, Javed T, Iqbal J, Hashmi MIU, Mumtaz MZ, Salama EA, Kalaji HM, Wróbel J (2022) Cytokinin production by Azospirillum brasilense contributes to increase in growth, yield, antioxidant, and physiological systems of wheat (Triticum aestivum L.). Front Microbiol 13:886041. https://doi.org/10.3389/fmicb.2022.886041
Zhang H, Kim MS, Krishnamachari V, Payton P, Sun Y, Grimson M, Farag MA, Ryu CM, Allen R, Melo IS, Paré PW (2007) Rhizobacterial volatile emissions regulate auxin homeostasis and cell expansion in Arabidopsis. Planta 226:839–851. https://doi.org/10.1007/s00425-007-0530-2
Zhang R, Vivanco JM, Shen Q (2017) The unseen rhizosphere root-soil-microbe interactions for crop production. Curr Opin Microbiol 37:8–14. https://doi.org/10.1016/j.mib.2017.03.008
Zhang G, Xu N, Chen H, Wang G, Huang J (2018a) OsMADS25 regulates root system development via auxin signalling in rice. Plant J 95:1004–1022. https://doi.org/10.1111/tpj.14007
Zhang T, Li R, Xing J, Yan L, Wang R, Zhao Y (2018b) The YUCCA-auxin-WOX11 module controls crown root development in rice. Front Plant Sci 9:523. https://doi.org/10.3389/fpls.2018.00523
Zhang D, Lyu Y, Li H, Tang X, Hu R, Rengel Z, Zhang F, Whalley WR, Davies WJ, Cahill JF Jr (2020a) Neighbouring plants modify maize root foraging for phosphorus: coupling nutrients and neighbours for improved nutrient use efficiency. New Phytol 226:244–253. https://doi.org/10.1111/nph.16206
Zhang Y, Wang X, Luo Y, Zhang L, Yao Y, Han L, Chen Z, Wang L, Li Y (2020b) OsABA8ox2, an ABA catabolic gene, suppress root elongation of rice seedlings and contributes to drought response. Crop J 8:480–491. https://doi.org/10.1016/j.cj.2019.08.006
Zhao Y, Hu Y, Dai M, Huang L, Zhou D-X (2009) The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice. Plant Cell 21:736–748. https://doi.org/10.1105/tpc.108.061655
Zhao H, Duan KX, Ma B, Yin CC, Hu Y, Tao JJ, Huang YH, Cao WQ, Chen H, Yang C, Zhang ZG (2020) Histidine kinase MHZ1/OsHK1 interacts with ethylene receptors to regulate root growth in rice. Nat Commun 11:1–13. https://doi.org/10.1038/s41467-020-14313-0
Zhou Y, Dong G, Tao Y, Chen C, Yang B, Wu Y, Yang Z, Liang G, Wang B, Wang Y (2016) Mapping quantitative trait loci associated with toot traits using sequencing-based genotyping chromosome segment substitution lines derived from 9311 and Nipponbare in Rice (Oryza sativa L.). PLoS ONE 11:1–13. https://doi.org/10.1371/journal.pone.0151796
Zhu M, Hu Y, Tong A, Yan B, Lv Y, Wang S, Ma W, Cui Z, Wang X (2020) LAZY1 controls tiller angle and shoot gravitropism by regulating the expression of auxin transporters and signaling factors in rice. Plant Cell Physiol 61:2111–2125. https://doi.org/10.1093/pcp/pcaa131
Zhu Q, Tang MJ, Yang Y, Sun K, Tian LS, Lu F, Hao AY, Dai CC (2021) Endophytic fungus Phomopsis liquidambaris B3 induces rice resistance to RSRD caused by Fusarium proliferatum and promotes plant growth. J Sci Food Agric 101:4059–4075
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 (BBA) Gen Subj 1840:1676–1685. https://doi.org/10.1016/j.bbagen.2014.01.003
Zou H, Wenwen Y, Zang G, Kang Z, Zhang Z, Huang J, Wang G (2015) OsEXPB2, a β-expansin gene, is involved in rice root system architecture. Mol Breed 35:1–14. https://doi.org/10.1007/s11032-015-0203-y
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P.K.V. and N.P. thankfully acknowledged University of Lucknow and University Grants Commission (UGC), India for DSKPDF.
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Verma, P.K., Verma, S. & Pandey, N. Root system architecture in rice: impacts of genes, phytohormones and root microbiota. 3 Biotech 12, 239 (2022). https://doi.org/10.1007/s13205-022-03299-9
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DOI: https://doi.org/10.1007/s13205-022-03299-9