Abstract
In rice, moderate leaf rolling improves photosynthesis and crop yield. However, the molecular mechanisms underlying this important agronomic trait remain incompletely understood. Here, we investigated a dominant rolled leaf mutant (RL-D) developed from Nipponbare rice (WT). From the six-leaf stage, the leaves of the mutant rolled inward, and abnormal sclerenchyma tissues developed on the abaxial side of the leaf midribs. Additionally, leaf length, plant height, grain weight, and chlorophyll content were significantly greater in the mutant as compared to the WT. Genetic mapping analysis suggested that the leaf-rolling trait in the RL-D mutant was controlled by a single dominant gene, which was located in a 743-kb region on rice chromosome 3. Re-sequencing analysis showed that one gene in the mapped region encoding a protein phosphatase, Os03g0395100 (herein designated OsPP2C), had base mutations in the first exon. These mutations may have produced a truncated form of the OsPP2C protein in RL-D. Further transcriptomic analysis revealed that several biological processes, especially secondary cell wall formation and protein phosphorylation, were overrepresented among the differentially expressed genes (DEGs) between the mutant and the wild type. qRT-PCR verification also demonstrated that specific genes associated with leaf polarity and secondary cell wall formation were differentially expressed in the mutant. This study presents a novel dominant rolled-leaf germplasm that may help to improve rice leaf morphology in the future. The results also suggested that the RL-D phenotype might result from abnormal sclerenchyma tissue development, possibly regulated by OsPP2C via the dephosphorylation pathway. This may present a novel mechanism underlying leaf-rolling in rice.
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References
Abdel-Latif A, Osman G (2017) Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods 13:1
Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11(10):1–12
Anders S, Huber W (2013) Differential expression of RNA-Seq data at the gene level-the DESeq package. European Molecular Biology Laboratory (EMBL) Heidelberg Germany
Ashikari M, Jianzhong WU, Yano M, Sasaki T, Yoshimura A (1999) Rice gibberrellin-insensitive dwarf mutant gene Dwarf1 encodes the α-subunit of GTP-binding protein. Proc Natl Acad Sci USA 96(18):10284–10289
Bowman JL, Eshed Y, Baum SF (2002) Establishment of polarity in angiosperm lateral organs. Trends Genet 18(3):134–141
Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo M, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14(3):537–545
Chen QL, Xie QJ, Gao J, Wang WY, Sun B, Liu BH, Zhu HT, Peng HF, Zhao HB, Liu CH, Wang J, Zhang JL, Zhang GQ, Zhang ZM (2015) Characterization of Rolled and Erect Leaf 1 in regulating leave morphology in rice. J Exp Bot 66(19):6047
Chen SB, Tao LZ, Zeng LR, Vega-Sanchez ME, Umemura K, Wang GL (2006) A highly efficient transient protoplast system for analyzing defence gene expression and protein-protein interactions in rice. Mol Plant Pathol 7(5):417–427
Chen YL, Liang HL, Ma XL, Lou SL, Xie YY, Liu ZL, Chen LT, Liu YG (2013) An efficient rRice mutagenesis system based on suspension-cultured cells. J Integr Plant Biol 55(2):122–130
Dai MQ, Hu YF, Zhao Y, Liu HF, Zhou DX (2007) A WUSCHEL-LIKE HOMEOBOX gene represses a YABBY gene expression required for rice leaf development. Plant Physiol 144(1):380–390
Davin LB, Lewis NG (2005) Lignin primary structures and dirigent sites. Curr Opin Biotechnol 16(4):407–415
Eshed Y, Izhaki A, Baum SF, Floyd SK, Bowman J (2004) Asymmetric leaf development and blade expansion in Arabidopsis are mediated by KANADI and YABBY activities. Development 131(12):2997–3006
Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC (2006) Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr Biol 16(9):939–944
Fan LS, Hao HQ, Xue YQ, Zhang L, Song K, Ding ZJ, Botella MA, Wang HY, Lin JX (2013) Dynamic analysis of Arabidopsis AP2 σ subunit reveals a key role in clathrin-mediated endocytosis and plant development. Development 140(18):3826–3837
Fang JJ, Guo TT, Xie ZW, Chun Y, Zhao JF, Peng LX, Zafar SA, Yuan SJ, Xiao LT, Li XY (2021) The URL1-ROC5-TPL2 transcriptional repressor complex represses the ACL1 gene to modulate leaf rolling in rice. Plant Physiol 185(4):1722–1744
Fang KL, Zhao FM, Cong YF, Sang XC, Du Q, Wang DZ, Li YF, Ling YH, Yang ZL, He GH (2012) Rolling-leaf14 is a 2OG-Fe (II) oxygenase family protein that modulates rice leaf rolling by affecting secondary cell wall formation in leaves. Plant Biotechnol J 10(5):524–532
Fujii S, Toriyama K (2008) DCW11, down-regulated gene 11 in CW-type cytoplasmic male sterile rice, encoding mitochondrial protein phosphatase 2C is related to cytoplasmic male sterility. Plant Cell Physiol (japan) 9(4):633–640
Fujino K, Matsuda Y, Ozawa K, Nishimura T, Koshiba T, Fraaije MW, Sekiguchi H (2008) NARROW LEAF 7 controls leaf shape mediated by auxin in rice. Mol Genet Genom MGG 279(5):499–507
Gui JS, Shen JH, Li LG (2011) Functional characterization of evolutionarily divergent 4-coumarate: coenzyme a Ligases in rice. Plant Physiol 157(2):574–586
Guo TT, Wang DF, Fang JJ, Zhao JF, Yuan SJ, Xiao LT, Li XY (2019) Mutations in the rice OsCHR4 gene, encoding a CHD3 family chromatin remodeler, induce narrow and rolled leaves with increased cuticular wax. Int J Mol Sci 20(10):2567
Hibara KI, Obara M, Hayashida E, Abe M, Ishimaru T, Satoh H, Itoh JI, Nagato Y (2009) The ADAXIALIZED LEAF1 gene functions in leaf and embryonic pattern formation in rice. Dev Biol 334:345–354
Hu J, Zhu L, Zeng DL, Gao ZY, Guo LB, Fang YX, Zhang GH, Dong GJ, Yan MX, Liu J, Qian Q (2010) Identification and characterization of NARROW AND ROLLED LEAF 1, a novel gene regulating leaf morphology and plant architecture in rice. Plant Mol Biol 73(3):283–292
Hu XB, Zhang HJ, Li GJ, Yang YX, Zheng Z, Song FM (2009) Ectopic expression of a rice protein phosphatase 2C gene OsBIPP2C2 in tobacco improves disease resistance. Plant Cell Rep 28(6):985–995
Hunter C, Willmann MR, Wu G, Yoshikawa M, Poethig G-N, S, (2006) Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis. Development 133:2973–2981
Itoh J, Hibara K, Sato Y, Nagato Y (2008) Developmental role and auxin responsiveness of class III homeodomain leucine zipper gene family members in rice. Plant Physiol 147(4):1960–1975
Juarez MT, Kui JS, Thomas J, Heller BA, Timmermans MCP (2004) MicroRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 428(6978):84–88
Kerstetter RA, Bollman K, Taylor RA, Bomblies K, Poethig RS (2001) KANADI regulates organ polarity in Arabidopsis. Nature 411(6838):706–709
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14(4):295–311
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg LA (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1(2):174–181
Li C, Zou XH, Zhang CY, Shao QH, Liu J, Liu B, Li HY, Zhao T (2016) OsLBD3–7 overexpression induced adaxially rolled leaves in rice. PLoS One 11(6):e0156413
Li L, Shi ZY, Li L, Shen GZ, Wang XQ, An LS, Zhang JL (2010) Overexpression of ACL 1 (abaxially curled leaf 1) increased bulliform cells and induced abaxial curling of leaf blades in rice. Mol Plant 3(5):807–817
Li WQ, Zhang MJ, Gan PF, Qiao L, Yang SQ, Miao H, Wang GF, Zhang MM, Liu WT, Li HF, Shi CH, Chen KM (2017) CLD1/SRL1 modulates leaf rolling by affecting cell wall formation, epidermis integrity and water homeostasis in rice. Plant J 92(5):904–923
Li XJ, Yang YY, Yao JL, Chen GX, Li XH, Zhang QF, Wu CY (2009) FLEXIBLE CULM 1 encoding a cinnamyl-alcohol dehydrogenase controls culm mechanical strength in rice. Plant Mol Biol 69(6):685–697
Li YY, Shen A, Xiong W, Sun QL, Luo Q, Song T, Li ZL, Luan WJ (2016b) Overexpression of OsHox32 results in pleiotropic effects on plant type architecture and leaf development in rice. Rice (n y) 9(1):46
Li ZY, Mo WP, Jia LQ, Xu YC, Tang WJ, Yang WQ, Guo YL, Lin RC (2019) Rice FLUORESCENT1 is involved in the regulation of chlorophyll. Plant Cell Physiol 60(10):2307–2318
Liu HL, Xu YY, Xu ZH, Chong K (2007a) A rice YABBY gene, OsYABBY4, preferentially expresses in developing vascular tissue. Dev Genes Evol 217(9):629–637
Liu PP, Montgomery TA, Fahlgren N, Kasschau KD, Nonogaki H, Carrington JC (2007b) Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. Plant J 52:133–146
Liu XF, Li M, Liu K, Tang D, Sun MF, Li YF, Shen Y, Du GJ, Cheng ZK (2016) Semi-Rolled Leaf2 modulates rice leaf rolling by regulating abaxial side cell differentiation. J Exp Bot 67(8):2139–2150
Liang JY, Guo SY, Sun B, Liu Q, Chen XH, Peng HF, Zhang ZM, Xie QJ (2018) Constitutive expression of REL1 confers the rice response to drought stress and abscisic acid. Rice (n y) 11(1):59
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt Method. Methods 25(4):402–408
Mallory AC, Bartel DP, Bartel B (2005) MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17:1360–1375
Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang GL, Zamore PD, Barton MK, Bartel DP (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region. EMBO J 23(16):3356–3364
Mao XZ, Cai T, Olyarchuk JG, Wei LP (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21(19):3787–3793
Matsumoto H, Yasui Y, Kumamaru T, Hirano HY (2018) Characterization of a half-pipe-like leaf1 mutant that exhibits a curled leaf phenotype. Genes Genet Syst 92(6):287–291
Muthayya S, Sugimoto JD, Montgomery S, Maberly GF (2014) An overview of global rice production, supply, trade, and consumption. Ann N Y Acad Sci 1324:7–14
Shi ZY, Wang J, Wan XS, Shen GZ, Wang XQ, Zhang JL (2007) Over-expression of rice OsAGO7 gene induces upward curling of the leaf blade that enhanced erect-leaf habit. Planta 226(1):99–108
Tanaka K, Murata K, Yamazaki M, Onosato K, Miyao A, Hirochika H (2003) Three distinct rice cellulose synthase catalytic subunit genes required for cellulose synthesis in the secondary wall. Plant Physiol 133(1):73–83
Tonnessen BW, Manosalva P, Lang JM, Baraoidan M, Bordeos A, Mauleon R, Oard J, Hulbert S, Leung H, Leach JE (2015) Rice phenylalanine ammonia-lyase gene OsPAL4 is associated with broad spectrum disease resistance. Plant Mol Biol 87(3):273–286
Toriba T, Harada K, Takamura A, Nakamura H, Ichikawa H, Suzaki T, Hirano HY (2007) Molecular characterization the YABBY gene family in Oryza sativa and expression analysis of OsYABBY1. Mol Genet Genomics 277(5):457–468
Tougane K, Komatsu K, Bhyan SB, Sakata Y, Ishizaki K, Yamato KT, Kohchi T, Takezawa D (2010) Evolutionarily conserved regulatory mechanisms of abscisic acid signaling in land plants:characterization of ABSCISIC ACID INSENSITIVE1-like type 2C protein phosphatase in the liverwort Marchantia polymorpha. Plant Physiol 152(3):1529–1543
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(28):511–515
Umbrasaite J, Schweighofer A, Kazanaviciute V, Magyar Z, Ayatollahi Z, Unterwurzacher V, Choopayak C, Boniecka J, Murray JA, Bogre L, Meskiene I (2010) MAPK Phosphatase AP2C3 Induces Ectopic Proliferation of Epidermal Cells Leading to Stomata Development in Arabidopsis. PLoS One 5(12):e15357
Waites R, Selvadurai HR, Oliver IR, Hudson A (1998) The PHANTASTICA gene encodes a MYB transcription factor involved in growth and dorsoventrality of lateral organs in Antirrhinum. Cell 93(5):779–789
Wang XL, Wang FH, Chen HQ, Liang XY, Huang YM, Yi JC (2017) Comparative genomic hybridization and transcriptome sequencing reveal that two genes, OsI_14279 (LOC_Os03g62620) and OsI_10794 (LOC_Os03g14950) regulate the mutation in the γ-rl rice mutant. Physiol Mol Biol Plants 23(4):745–754
Wang YH, Xue YB, Li JY (2005) Towards molecular breeding and improvement of rice in China. Trends Plant Sci 10(12):610–614
Wu J, Mizuno H, Hayashi-Tsugane M, Ito Y, Chiden Y, Fujisawa M, Katagiri S, Saji S, Yoshiki S, Karasawa W, Yoshihara R, Hayashi A, Kobayashi H, Ito K, Hamada M, Okamoto M, Ikeno M, Ichikawa Y, Katayose Y, Yano M, Matsumoto T, Sasaki T (2003) Physical maps and recombination frequency of six rice chromosomes. Plant J 36(5):720–730
Wu RH, Li BS, He S, Wassmann F, Yu CH, Qin GJ, Schreiber L, Qu LJ, Gu HY (2011) CFL1, a WW domain protein, regulates cuticle development by modulating the function of HDG1, a class IV homeodomain transcription factor, in rice and Arabidopsis. Plant Cell 23(9):3392–3411
Xiang JJ, Zhang GH, Qian Q, Xue HW (2012) Semi-rolled leaf1 encodes a putative glycosylphosphatidylinositol- anchored protein and modulates rice leaf rolling by regulating the formation of bulliform cells. Plant Physiol 159(4):1488–1500
Xu PZ, Ali A, Han BL, Wu XJ (2018) Current advances in molecular basis and mechanisms regulating leaf morphology in rice. Front Plant Sci 9:1528
Xu SB, Tao YF, Yang ZQ, Chu JY (2002) A simple and rapid methods used for silver staining and gel preservation. Hereditas 24:335–336
Xu Y, Wang YH, Long QZ, Huang JX, Wang YL, Zhou KN, Zheng M, Sun J, Chen H, Chen SH, Jiang L, Wang CM, Wan JM (2014) Overexpression of OsZHD1, a zinc finger homeodomain class homeobox transcription factor, induces abaxially curled and drooping leaf in rice. Planta 239(4):803–816
Yang JW, Fu JX, Li J, Cheng XL, Li F, Dong JF, Liu ZL, Zhuang CX (2014) A novel co-immunoprecipitation protocol based on protoplast transient gene expression for studying protein-protein interactions in rice. Plant Mol Biol Rep 32:153–161
Yang SQ, Li WQ, Miao H, Gan PF, Qiao L, Chang YL, Shi CH, Chen KM (2016) REL2, a gene encoding an unknown function protein which contains DUF630 and DUF632 domains controls leaf rolling in rice. Rice (n y) 9(1):37
Yi JC, Liu LN, Cao YP, Li JZ, Mei MT (2013) Cloning, characterization and expression of OsFMO(t) in rice encoding a flavin monooxygenase. J Genet 92(3):471–480
You J, Zong W, Hu HH, Li XH, Xiao JH, Xiong LZ (2014) A STRESS-RESPONSIVE NAC1-regulated protein phosphatase gene rice Protein Phosphatase18 modulates drought and oxidative stress tolerance through abscisic acid-independent reactive oxygen species scavenging in rice. Plant Physiol 166(4):2100–2114
Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11(2):R14
Zhang GH, Hou X, Wang L, Xu J, Chen J, Fu X, Shen NW, Nian JQ, Jiang ZZ, Hu J, Zhu L, Rao YC, Shi YF, Ren DY, Dong GJ, Gao ZY, Guo LB, Qian Q, Luan S (2021) PHOTO-SENSITIVE LEAF ROLLING 1 encodes a polygalacturonase that modifies cell wall structure and drought tolerance in rice. New Phytol 229:890–901
Zhang GH, Xu Q, Zhu XD, Qian Q, Xue HW (2009) SHALLOT-LIKE1 is a KANADI transcription factor that modulates rice leaf rolling by regulating leaf abaxial cell development. Plant Cell 21:719–735
Zhao SS, Zhao L, Liu FX, Wu YZ, Zhu ZF, Sun CQ, Tan LB (2016) NARROW AND ROLLED LEAF 2 regulates leaf shape, male fertility, and seed size in rice. J Integr Plant Biol 58(12):983–996
Zou LP, Sun XH, Zhang ZG, Liu P, Wu JX, Tian CJ, Qiu JL, Lu TG (2011) Leaf rolling controlled by the homeodomain Leucine Zipper Class IV gene Roc5 in rice. Plant Physiol 156(3):1589–1602
Acknowledgements
We thank Dr. Yuanling Chen at South China Agricultural University for providing rice seeds of Rolled Leaf-Dominant (RL-D) mutant.
Funding
This work was supported by the National Natural Science Foundation of China (Nos. 30671279 and 31071070), the Guangdong Basic and Applied Basic Research Foundation (No. 2020A1515010906), and the Special Fund for Scientific Innovation Strategy-construction of High Level Academy of Agriculture Science (No. R2019PY-JX001).
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XMG and FHW carried out the experiment and prepared the figures and tables. JCY designed the research, analyzed the data, and wrote the manuscript. HMC, XLL, and SCZ contributed to plant materials management and data evaluation. JLZ contributed for critically analyzing the data and reading this manuscript. All authors approved the final version of manuscript.
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• This study investigated the dominant rolled-leaf (RL-D) rice mutant and presented a novel dominant rolled-leaf germplasm that may help to improve rice leaf morphology. The results also suggested that the RL-D phenotype might result from abnormal sclerenchyma tissues, possibly regulated by a protein phosphatase encoding gene OsPP2C via the dephosphorylation pathway.
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Gong, X., Wang, F., Chen, H. et al. Genetic Mapping and Transcriptomic Analysis Revealed the Molecular Mechanism Underlying Leaf-Rolling and a Candidate Protein Phosphatase Gene for the Rolled Leaf-Dominant (RL-D) Mutant in Rice. Plant Mol Biol Rep 40, 256–270 (2022). https://doi.org/10.1007/s11105-021-01318-2
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DOI: https://doi.org/10.1007/s11105-021-01318-2