Open Access Open Badges Research article

Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid

Wen-Chang Chi1, Yun-An Chen12, Yu-Chywan Hsiung1, Shih-Feng Fu3, Chang-Hung Chou4, Ngoc Nam Trinh1, Ying-Chih Chen1 and Hao-Jen Huang1*

Author Affiliations

1 Department of Life Sciences, National Cheng Kung University, No. 1 University Rd. 701, Tainan, Taiwan, ROC

2 Department of Biological Sciences, National Sun Yat-Sen University, No. 70, Lienhai Rd. 80424, Kaohsiung, Taiwan, ROC

3 Department of Biology, National Changhua University of Education, No. 1, Jin-De Road, Changhua City 500, Taiwan, ROC

4 Graduate Institute of Ecology and Evolutionary Biology, College of Life Sciences, China Medical University, 91, Hsueh-Shih Road, Taichung 404, Taiwan, ROC

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BMC Genomics 2013, 14:351  doi:10.1186/1471-2164-14-351

Published: 25 May 2013



Autotoxicity plays an important role in regulating crop yield and quality. To help characterize the autotoxicity mechanism of rice, we performed a large-scale, transcriptomic analysis of the rice root response to ferulic acid, an autotoxin from rice straw.


Root growth rate was decreased and reactive oxygen species, calcium content and lipoxygenase activity were increased with increasing ferulic acid concentration in roots. Transcriptome analysis revealed more transcripts responsive to short ferulic-acid exposure (1- and 3-h treatments, 1,204 genes) than long exposure (24 h, 176 genes). Induced genes were involved in cell wall formation, chemical detoxification, secondary metabolism, signal transduction, and abiotic stress response. Genes associated with signaling and biosynthesis for ethylene and jasmonic acid were upregulated with ferulic acid. Ferulic acid upregulated ATP-binding cassette and amino acid/auxin permease transporters as well as genes encoding signaling components such as leucine-rich repeat VIII and receptor-like cytoplasmic kinases VII protein kinases, APETALA2/ethylene response factor, WRKY, MYB and Zinc-finger protein expressed in inflorescence meristem transcription factors.


The results of a transcriptome analysis suggest the molecular mechanisms of plants in response to FA, including toxicity, detoxicification and signaling machinery. FA may have a significant effect on inhibiting rice root elongation through modulating ET and JA hormone homeostasis. FA-induced gene expression of AAAP transporters may contribute to detoxicification of the autotoxin. Moreover, the WRKY and Myb TFs and LRR-VIII and SD-2b kinases might regulate downstream genes under FA stress but not general allelochemical stress. This comprehensive description of gene expression information could greatly facilitate our understanding of the mechanisms of autotoxicity in plants.

Allelochemical; Ferulic acid; Microarray; Protein kinase; Rice; Autotoxicity