Skip to main content
Log in

Metabolomic analysis of rice brittle culm mutants reveals each mutant- specific metabolic pattern in each organ

  • Original Article
  • Published:
Metabolomics Aims and scope Submit manuscript



Plant cell walls play an important role in providing physical strength and defence against abiotic stress. Rice brittle culm (bc) mutants are a strength-decreased mutant because of abnormal cell walls, and it has been reported that the causative genes of bc mutants affect cell wall composition. However, the metabolic alterations in each organ of bc mutants have remained unknown.


To evaluate the metabolic changes in rice bc mutants, comparative analysis of the primary metabolites was conducted.


The primary metabolites in leaves, internodes, and nodes of rice bc mutants and wild-type control were measured using CE- and LC-MS/MS. Multivariate analyses using metabolomic data was performed.


We found that mutations in each bc mutant had different effects on metabolism. For example, higher oxalate content was observed in bc3 and bc1 bc3 mutants, suggesting that surplus carbon that was not used for cell wall components might be used for oxalate synthesis. In addition, common metabolic alterations such as a decrease of sugar nucleotides in nodes were found in bc1 and Bc6, in which the causative genes are involved in cellulose accumulation.


These results suggest that metabolic analysis of the bc mutants could elucidate the functions of causative gene and improve the cell wall components for livestock feed or bioethanol production.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others



Dihydroxyacetone phosphate












Glutathione (reduced)


Glutathione disulphide








Principal component
















Taichung 65


Tricarboxylic acid
















  • Adachi, S., Tanaka, Y., Miyagi, A., Kashima, M., Tezuka, A., Toya, Y., Kobayashi, S., Ohkubo, S., Shimizu, H., Kawai-Yamada, M., Sage, R. F., Nagano, A. J., & Yamori, W. (2019). High-yielding rice Takanari has superior photosynthetic response to a commercial rice Koshihikari under fluctuating light. Journal of Experimental Botany, 70, 5287–5297.

    Article  CAS  Google Scholar 

  • Aohara, T., Kotake, T., Kaneko, Y., Takatsuji, H., Tsumuraya, Y., & Kawasaki, S. (2009). Rice BRITTLE CULM5 (BRITTLE NODE) is involved in secondary cell wall formation in the sclerenchyma tissue of nodes. Plant, Cell and Physiology, 50, 1886–1897.

    Article  CAS  Google Scholar 

  • Barros, J., Escamilla-Trevino, L., Song, L., Rao, X., Serrani-Yarce, J., Palacios, M., Engle, N., Choudhury, F., Tschaplinski, T., Venables, B., Mittler, R., & Dixon, R. (2019). 4-Coumarate 3-hydroxylase in the lignin biosynthesis pathway is a cytosolic ascorbate peroxidase. Nature Communications, 10, 1994.

    Article  Google Scholar 

  • Brown, D. M., Zeef, L. A. H., Ellis, J., Goodacre, R., & Turner, S. R. (2005). Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. The Plant Cell, 17, 2281–2295.

    Article  CAS  Google Scholar 

  • Carpita, N., & McCann, M. (2015). Characterizing visible and invisible cell wall mutant phenotypes. Journal of Experimental Botany, 66, 4145–4163.

    Article  CAS  Google Scholar 

  • Franceschi, V., & Nakata, P. (2005). Calcium oxalate in plants: Formation and function. Annual Review of Plant Biology, 56, 41–71.

    Article  CAS  Google Scholar 

  • Halliwell, B. (1978). Lignin synthesis: The generation of hydrogen peroxide and superoxide by horseradish peroxidase and its stimulation by manganese (II) and phenols. Planta, 140, 81–88.

    Article  CAS  Google Scholar 

  • Hirano, K., Kotake, T., Kamihara, K., Tsuna, K., Aohara, T., Kaneko, Y., Takatsuji, H., Tsumuraya, Y., & Kawasaki, S. (2010). Rice BRITTLE CULM3 (BC3) encodes a classical dynamin OsDRP2B essential for proper secondary cell wall synthesis. Planta, 232, 95–108.

    Article  CAS  Google Scholar 

  • Honda, S., Ohkubo, S., San, N. S., Nakkasame, A., Tomisawa, K., Katsura, K., Ookawa, T., Nagano, A. J., & Adachi, S. (2021). Maintaining higher leaf photosynthesis after heading stage could promote biomass accumulation in rice. Scientific Reports, 11, 7579.

    Article  CAS  Google Scholar 

  • Ito, J., Herter, T., Baidoo, E., Lao, J., Vega-Sanchez, M., Smith-Moritz, M., Adams, P., Keasling, J., Usabel, B., Petzold, C., & Heazlewood, J. (2014). Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry. Analytical Biochemistry, 448, 14–22.

    Article  CAS  Google Scholar 

  • Kokubo, A., Kuraishi, S., & Sakurai, N. (1989). Culm strength of barley. Plant Physiology, 91, 876–882.

    Article  CAS  Google Scholar 

  • Kokubo, A., Sakurai, N., Kuraishi, S., & Takeda, K. (1991). Culm brittleness of barley (Hordeum vulgare L.) mutants is caused by smaller number of cellulose molecules in cell wall. Plant Physiology, 97, 509–514.

    Article  CAS  Google Scholar 

  • Kotake, T., Aohara, T., Hirano, K., Sato, A., Kaneko, Y., Tsumuraya, Y., Takatsuji, H., & Kawasaki, S. (2011). Rice Brittle culm 6 encodes a dominant-negative form of CesA protein that perturbs cellulose synthesis in secondary cell walls. Journal of Experimental Botany, 62, 2053–2062.

    Article  CAS  Google Scholar 

  • Li, Y., Qian, Q., Zhou, Y., Yan, M., Sun, L., Zhang, M., Fu, Z., Wang, Y., Han, B., Pan, X., Chen, M., & Li, J. (2003). Brittle culm 1, which encodes a COBRA-like protein, affects the mechanical properties of rice plants. The Plant Cell, 15, 2020–2031.

    Article  CAS  Google Scholar 

  • Miyagi, A., Kawai-Yamada, M., Uchimiya, M., Ojima, N., Suzuki, K., & Uchimiya, H. (2013a). Metabolome analysis of food-chain between plants and insects. Metabolomics, 9, 1254–1261.

    Article  CAS  Google Scholar 

  • Miyagi, A., Noguchi, K., Tokida, T., Usui, Y., Nakamura, H., Sakai, H., Hasegawa, T., & Kawai-Yamada, M. (2019). Oxalate contents in leaves of two rice cultivars grown at a free-air CO2 enrichment (FACE) site. Plant Production Science, 22, 407–411.

    Article  CAS  Google Scholar 

  • Miyagi, A., Takahashi, H., Takahara, K., Hirabayashi, T., Nishimura, Y., Tezuka, T., Kawai-Yamada, M., & Uchimiya, H. (2010). Principal component and hierarchical clustering analysis of metabolites in destructive weeds; polygonaceous plants. Metabolomics, 6, 146–155.

    Article  CAS  Google Scholar 

  • Miyagi, A., Uchimiya, M., Kawai-Yamada, M., & Uchimiya, H. (2013b). An antagonist treatment in combination with tracer experiments revealed isocitrate pathway dominant to oxalate biosynthesis in Rumex obtusifolius L. Metabolomics, 9, 590–598.

    Article  CAS  Google Scholar 

  • Noguchi, K., Tsunoda, T., Miyagi, A., Kawai-Yamada, M., Sugiura, D., Miyazawa, S.-I., Tokida, T., Usui, Y., Nakamura, H., Sakai, H., & Hasegawa, T. (2018). Effects of elevated atmospheric CO2 on respiratory rates in mature leaves of two rice cultivars grown at a free-air CO2 enrichment site and analyses of the underlying mechanisms. Plant and Cell Physiology, 59, 637–649.

    Article  CAS  Google Scholar 

  • Ohkubo, S., Tanaka, Y., Yamori, W., & Adachi, S. (2020). Rice cultivar Takanari has higher photosynthetic performance under fluctuating light than Koshihikari, especially under limited nitrogen supply and elevated CO2. Frontiers in Plant Science, 11, 1308.

    Article  Google Scholar 

  • Ookawa, T., Aoba, R., Yamamoto, T., Ueda, T., Takai, T., Fukuoka, S., Ando, T., Adachi, S., Matsuoka, M., Ebitani, T., Kato, Y., Mulsanti, I., Kishii, M., Reynolds, M., Piñera, F., Kotake, T., Kawasaki, S., Motobayashi, T., & Hirasawa, T. (2016). Precise estimation of genomic regions controlling lodging resistance using a set of reciprocal chromosome segment substitution lines in rice. Scientific Reports, 6, 30572.

    Article  CAS  Google Scholar 

  • Sanchez, A., & Khush, G. (1994). Chromosomal location of some marker genes in rice using the primary trisomics. The Journal of Heredity, 85, 297–300.

    Article  Google Scholar 

  • Sato-Izawa, K., Nakamura, S., & Matsumoto, T. (2020). Mutation of rice bc1 gene affects internode elongation and induces delayed cell wall deposition in developing internodes. Plant Signaling & Behavior, 15, e1749786.

    Article  Google Scholar 

  • Sharma, U., Brillouet, J., Scalbert, A., & Monties, B. (1986). Studies on a brittle stem mutant of rice, Oryza sativa L.; characterization of lignin fractions, associated phenolic acids and polysaccharides from rice stem. Agronomie, 6, 265–271.

    Article  Google Scholar 

  • Sindhu, A., Langewisch, T., Olek, A., Multani, D., McCann, M., Vermerris, W., Cartita, N., & Johal, G. (2007). Maize brittle stalk2 encodes a COBRA-like protein expressed in early organ development but required for tissue flexibility at maturity. Plant Physiology, 145, 1444–1459.

    Article  CAS  Google Scholar 

  • Song, X., Liu, L., Jiang, Y., Zhang, B., Gao, Y., Liu, X., Lin, Q., Ling, H., & Zhou, Y. (2013). Disruption of secondary wall cellulose biosynthesis alters cadmium translocation and tolerance in rice plants. Molecular Plant, 6, 768–780.

    Article  CAS  Google Scholar 

  • Takahashi, M., Kinoshita, T., & Takeda, K. (1968). Character expressions and causal genes of some mutants in rice plant: (Genetical studies on rice plant, XXXIII). Journal of the Faculty of Agriculture, Hokkaido University, 55, 496–512.

    Google Scholar 

  • Takenaka, Y., Watanabe, Y., Schuetz, M., Unda, F., Hill, J., Phookaew, P., Yoneda, A., Mansfield, S., Samuels, L., Ohtani, M., & Demura, T. (2018). Patterned deposition of xylan and lignin is independent from that of the secondary wall cellulose of arabidopsis xylem vessels. The Plant Cell, 30, 2663–2676.

    Article  CAS  Google Scholar 

  • 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 Physiology, 133, 73–83.

    Article  CAS  Google Scholar 

  • Vaughan, P., & Butt, V. (1970). The action of o-dihydric phenols in the hydroxylation of p-coumaric acid by a phenolase from leaves of spinach beet (Beta vulgaris L.). Biochemical Journal, 119, 89–94.

    Article  CAS  Google Scholar 

  • Xiong, G., Li, R., Qian, Q., Song, X., Liu, X., Yu, Y., Zeng, D., Wan, J., Li, J., & Zhou, Y. (2010). The rice dynamin-related protein DRP2B mediates membrane trafficking, and thereby plays a critical role in secondary cell wall cellulose biosynthesis. The Plant Journal, 64, 56–70.

    CAS  Google Scholar 

  • Yan, C., Yan, S., Zeng, X., Zhang, Z., & Gu, M. (2007). Fine mapping and isolation of Bc7(t), allelic to OsCesA4. Journal of Genetics and Genomics, 34, 1019–1027.

    Article  CAS  Google Scholar 

  • Zhang, B., Deng, L., Qian, Q., Xiong, G., Zeng, D., Li, R., Guo, L., Li, J., & Zhou, Y. (2009). A missense mutation in the transmembrane domain of CESA4 affects protein abundance in the plasma membrane and results in abnormal cell wall biosynthesis in rice. Plant Molecular Biology, 71, 509–524.

    Article  CAS  Google Scholar 

  • Zhang, M., Zhang, B., Qian, Q., Yu, Y., Li, R., Zhang, J., Liu, X., Zeng, D., Li, J., & Zhou, Y. (2010). Brittle Culm 12, a dual-targeting kinesin-4 protein, controls cell-cycle progression and wall properties in rice. The Plant Journal, 63, 312–328.

    Article  CAS  Google Scholar 

  • Zhong, R., Burk, D., Morrison, W., & Ye, Z. (2002). A Kinesin-like protein is essential for oriented deposition of cellulose microfibrils and cell wall strength. The Plant Cell, 14, 3101–3117.

    Article  CAS  Google Scholar 

  • Zhong, R., Burk, D., Morrison, W., & Ye, Z. (2004). Fragile fiber 3, an Arabidopsis gene encoding a type II inositol polyphosphate 5-phosphatase, is required for secondary wall synthesis and actin organization in fiber cells. The Plant Cell, 16, 3242–3259.

    Article  CAS  Google Scholar 

  • Zhong, R., Pena, M., Zhou, G., Nairn, C., Wood-Jones, A., Richardson, E., Morrison, W., Darvill, A., York, W., & Ye, Z. (2005). Arabidopsis fragile fiber 8, which encodes a putative glucuronyltransferase, is essential for normal secondary wall synthesis. The Plant Cell, 17, 3390–3408.

    Article  CAS  Google Scholar 

Download references


We are grateful to Dr. Shinji Kawasaki (NIAS) for providing the rice bc mutant seeds. We thank Ms. Tomoe Nishimoto (Saitama University) for technical assistance. The present study was supported by MEXT Kakenhi Grant Number 18K14386 and 22K05435, Japan.

Author information

Authors and Affiliations



A.M. and K.M. wrote the manuscript. A.M., K.M., S.O., S.A., T.O., T.K. and M.K.-Y. designed research. A.M., K.M., S.O., S.A., T.I. and T.O. performed experiments. A.M., K.M., T.I., M.Y., T.K. and M.K.-Y. analysed data. All authors contributed to approve the manuscript.

Corresponding authors

Correspondence to Atsuko Miyagi or Maki Kawai-Yamada.

Ethics declarations

Competing interests

The authors of this manuscript have no competing interests; they do not have any other interests that influence the results and discussion of this paper.

Research involving human and/or animal participants

This article does not contain any studies with human participants or animals performed by any of the authors.

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.

Supplementary file1 (PDF 2602 kb)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) 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.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Miyagi, A., Mori, K., Ishikawa, T. et al. Metabolomic analysis of rice brittle culm mutants reveals each mutant- specific metabolic pattern in each organ. Metabolomics 18, 95 (2022).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: