Abstract
Rice is an important food crop, and the leaf angle is regulated by phytohormonal pathway and the non-phytohormonal pathway, which is an important agronomic trait for plant type formation and yield formation. Studies have shown that OsOFP8 was involved in the Brassinosteroid (BR) response pathway and positively regulated the rice leaf angle. In order to further explore the transcriptional response of OsOFP8 in related metabolic pathways that regulate leaf development during rice growth. Comparative transcriptomic analysis of gene expression in leaves of OsOFP8-overexpressed (OE) and OsOFP8-RNA-interference (RNAi) transgenic seedlings and Zhonghua (japonica cv. ZH11) were performed using RNA sequencing (RNA-Seq). And 73,913,197, 92,056,850 and 64,179,231 clean reads were obtained for each sample. A total of 952 differentially expressed genes (DEGs) were compared between AZH11 versus OE8 and AZH11 versus RNAi8. The Gene Ontology functional classification and the Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis showed that plant hormone signal transduction, pentose and glucuronate interconversions, plant interaction and diterpenoid biosynthesis and other metabolic processes are involved in the regulation of leaf angle during leaf development in rice. The expression patterns of 8 DEGs, including the gene OsPP108/OsSIPP2C1 and LOC_Os03g06330, which are involved in plant hormone functions, the gene OsCML10 involved in signal transduction mechanisms in the plant-pathogen interaction pathway, and the gene OSIPK involved in cell wall/membrane/envelope biogenesis, might be related to the leaf angle by quantitative real-time PCR analysis were consistent with those of RNA-Seq. These results may provide transcriptomic guidance for further elucidating the regulation of OsOFP8 on rice leaf development, and may provide reference for further verifying that OsOFP8 regulates leaf angle through plant hormones and other pathways.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: NCBI BioProject repository under the accession PRJNA778464.
Abbreviations
- OFPs:
-
OVATE family proteins
- OE:
-
Overexpression
- RNAi:
-
RNA-interference
- RNA-Seq:
-
RNA sequencing
- DEGs:
-
Differentially expressed genes
- GO:
-
Gene Ontology
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- qRT-PCR:
-
Quantitative real-time PCR
- ZH11:
-
Zhonghua
- BR/BL:
-
Brassinosteroid/Brassinolide
- IAA:
-
Indole-3-aceticacid
- GA:
-
Gibberellin
- Pfam:
-
Protein family
- COG:
-
Clusters of Orthologous Groups of proteins
- KO:
-
KEGG Ortholog database
References
Asano T, Hakata M, Nakamura H, Aoki N, Komatsu S, Ichikawa H et al (2011) Functional characterisation of OsCPK21, a calcium-dependent protein kinase that confers salt tolerance in rice. Plant Mol Biol 75:179–191. https://doi.org/10.1007/s11103-010-9717-1
Bender KW, Snedden WA (2013) Calmodulin-related proteins step out from the shadow of their namesake. Plant Physiol 163:486–495. https://doi.org/10.1104/pp.113.221069
Boonburapong B, Buaboocha T (2007) Genome-wide identification and analyses of the rice calmodulin and related potential calcium sensor proteins. BMC Plant Biol 7:1–17. https://doi.org/10.1186/1471-2229-7-4
da Maia LC, Cadore PRB, Benitez LC, Danielowski R, Braga EJB, Fagundes PRR et al (2016) Transcriptome profiling of rice seedlings under cold stress. Funct Plant Biol 44:419–429. https://doi.org/10.1071/FP16239
Deng G, Bi F, Liu J, He W, Li C, Dong T et al (2021) Transcriptome and metabolome profiling provide insights into molecular mechanism of pseudostem elongation in banana. BMC Plant Biol 21:125. https://doi.org/10.1186/s12870-021-02899-6
Faralli M, Lawson T (2020) Natural genetic variation in photosynthesis: an untapped resource to increase crop yield potential. Plant J 101:518–528. https://doi.org/10.1111/tpj.14568
He J, Liu Y, Yuan D, Duan M, Liu Y, Shen Z et al (2020) An R2R3 MYB transcription factor confers brown planthopper resistance by regulating the phenylalanine ammonia-lyase pathway in rice. Proc Natl Acad Sci U S A 117:271–277. https://doi.org/10.1073/pnas.1902771116
Ito Y, Kurata N (2006) Identification and characterization of cytokinin-signalling gene families in rice. Gene 382:57–65. https://doi.org/10.1016/j.gene.2006.06.020
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M et al (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484. https://doi.org/10.1093/nar/gkm882
Khush GS (2005) What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol Biol 2005(59):1–6. https://doi.org/10.1007/s11103-005-2159-5
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360. https://doi.org/10.1038/nmeth.3317
Liu J, Van EJ, Cong B, Tanksley SD (2002) A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc Natl Acad Sci USA 99:13302–13306. https://doi.org/10.1073/pnas.162485999
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8
Luo X, Liu J, Zhao J, Dai L, Chen Y, Zhang L et al (2018) Rapid mapping of candidate genes for cold tolerance in Oryza rufipogon Griff. by QTL-seq of seedlings. J Integr Agric 17:265–275. https://doi.org/10.1016/S2095-3119(17)61712-X
Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21:3787–3793. https://doi.org/10.1093/bioinformatics/bti430
Ning J, Zhang B, Wang N, Zhou Y, Xiong LZ (2011) Increased leaf angle1, a Raf-like MAPKKK that interacts with a nuclear protein family, regulates mechanical tissue formation in the Lamina joint of rice. Plant Cell 23:4334–4347. https://doi.org/10.1105/tpc.111.093419
Qian W, Wu C, Fu Y, Hu G, He Z, Liu W (2017) Novel rice mutants overexpressing the brassinosteroid catabolic gene CYP734A4. Plant Mol Biol 93:197–208. https://doi.org/10.1007/s11103-016-0558-4
Song Q, Zhang G, Zhu X (2013) Optimal crop canopy architecture to maximise canopy photosynthetic CO2 uptake under elevated CO2-a theoretical study using a mechanistic model of canopy photosynthesis. Funct Plant Biol 40:108–124. https://doi.org/10.1071/FP12056
Sun S, Wang D, Li J, Lei Y, Li G, Cai W et al (2021) Transcriptome analysis reveals photoperiod-associated genes expressed in rice anthers. Front Plant Sci 12:621561. https://doi.org/10.3389/fpls.2021.621561
Tai Y, Wei C, Yang H, Zhang L, Chen Q, Deng W et al (2015) Transcriptomic and phytochemical analysis of the biosynthesis of characteristic constituents in tea (Camellia sinensis) compared with oil tea (Camellia oleifera). BMC Plant Biol 15:190. https://doi.org/10.1186/s12870-015-0574-6
Tente E, Ereful N, Rodriguez AC, Grant P, O’Sullivan DM, Boyd LA et al (2021) Reprogramming of the wheat transcriptome in response to infection with Claviceps purpurea, the causal agent of ergot. BMC Plant Biol 21:316. https://doi.org/10.1186/s12870-021-03086-3
Waititu JK, Zhang X, Chen T, Zhang C, Zhao Y, Wang H (2021) Transcriptome analysis of tolerant and susceptible maize genotypes reveals novel insights about the molecular mechanisms underlying drought responses in leaves. Int J Mol Sci 22:6980. https://doi.org/10.3390/ijms22136980
Wang J, Hu J, Qian Q, Xue H (2013) LC2 and OsVIL2 promote rice flowering by photoperoid-induced epigenetic silencing of OsLF. Mol Plant 6:514–527. https://doi.org/10.1093/mp/sss096
Wu X, Tang D, Li M, Wang K, Cheng Z (2013) Loose Plant Architecture1, an INDETERMINATE DOMAIN protein involved in shoot gravitropism, regulates plant architecture in rice. Plant Physiol 161:317–329. https://doi.org/10.1104/pp.112.208496
Xie X, Chen Z, Zhang B, Guan H, Zheng Y, Lan T et al (2020) Transcriptome analysis of xa5-mediated resistance to bacterial leaf streak in rice (Oryza sativa L.). Sci Rep 10:19439. https://doi.org/10.1038/s41598-020-74515-w
Xu J, Wang L, Qian Q, Zhang G (2013) Research advance in molecule regulation mechanism of leaf morphogenesis in rice (Oryza sativa L.). Acta Agron Sin 39:767–774 (in Chinese with English abstract)
Yang S, Chen W, Zhang L (1988) Trends in breeding rice forideotype. Chin J Rice Sci. https://doi.org/10.16819/j.1001-7216.1988.03.005
Yang C, Shen W, He Y, Tian Z, Li J (2016) OVATE family protein 8 positively mediates brassinosteroid signaling through interacting with the GSK3-like kinase in rice. PLoS Genet 12:e1006118. https://doi.org/10.1371/journal.pgen.1006118
Yoon DH, Lee SS, Park HJ, Lyu JI, Chong WS, Liu JR et al (2016) Overexpression of OsCYP19-4 increases tolerance to cold stress and enhances grain yield in rice (Oryza sativa). J Exp Bot 67:69–82. https://doi.org/10.1093/jxb/erv421
Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:R14. https://doi.org/10.1186/gb-2010-11-2-r14
Yu H, Jiang W, Liu Q, Zhang H, Piao M, Chen Z et al (2015) Expression pattern and subcellular localization of the ovate protein family in rice. PLoS ONE 10:e0118966. https://doi.org/10.1371/journal.pone.0118966
Yuan L (1997) Super high yield breeding of hybrid rice. Hybrid Rice 6:4–9. https://doi.org/10.16267/j.cnki.1005-3956.1997.06.001 (in Chinese with English abstract)
Zhao S, Hu J, Guo L, Qian Q, Xue H (2010) Rice leaf inclination2, a VIN3-like protein, regulates leaf angle through modulating cell division of the collar. Cell Res 20:935–947. https://doi.org/10.1038/cr.2010.109
Zhou L, Xiao L, Xue H (2017) Dynamic cytology and transcriptional regulation of rice lamina joint development. Plant Physiol 174:1728–1746. https://doi.org/10.1104/pp.17.00413
Zhou H, He Y, Zhu Y, Li M, Song S, Bo W et al (2020) Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars. BMC Plant Biol 20:240. https://doi.org/10.1186/s12870-020-02450-z
Acknowledgements
We thank the Beijing Biomarker Technologies Co, LTD (China) for excellent technical help in bioinformatics analysis.
Funding
This work was supported by the National Natural Science Foundation of China (31970523).
Author information
Authors and Affiliations
Contributions
Hongjuan Chen performed the experiments and wrote the manuscript. Yao wan, Kaichong Teng, Binghuan Liu, Neng Zhao and Kaizun Xu provided assistance on the experimental analysis. Jianxiong L designed the experiments. All authors contributed to the article and approved the submitted version.
Corresponding author
Ethics declarations
Conflict of interest
We declare that there is no conflict of interest regarding the publication of this article.
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
Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Chen, H., Wan, Y., Teng, K. et al. The role of OsOFP8 gene in regulating rice leaf angle. J. Plant Biochem. Biotechnol. 32, 304–318 (2023). https://doi.org/10.1007/s13562-022-00806-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13562-022-00806-0