title: Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.forename: Wen-Chang
authors.initials: WC
authors.lastname: Chi
authors.forename: Yun-An
authors.initials: YA
authors.lastname: Chen
authors.forename: Yu-Chywan
authors.initials: YC
authors.lastname: Hsiung
authors.forename: Shih-Feng
authors.initials: SF
authors.lastname: Fu
authors.forename: Chang-Hung
authors.initials: CH
authors.lastname: Chou
authors.forename: Ngoc Nam
authors.initials: NN
authors.lastname: Trinh
authors.forename: Ying-Chih
authors.initials: YC
authors.lastname: Chen
authors.affiliation: Department of Life Sciences, National Cheng Kung University, No, 1 University Rd, 701, Tainan, Taiwan, ROC. haojen@mail.ncku.edu.tw.
authors.forename: Hao-Jen
authors.initials: HJ
authors.lastname: Huang
mesh_terms: D002118:Calcium / Q000378:metabolism; D002473:Cell Wall / Q000378:metabolism; D003373:Coumaric Acids / Q000494:pharmacology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015227:Lipid Peroxidation / Q000187:drug effects; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000187:drug effects* / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010937:Plant Growth Regulators / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000187:drug effects* / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D011134:Polysaccharides / Q000378:metabolism; D017382:Reactive Oxygen Species / Q000378:metabolism; D015398:Signal Transduction; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D003373:Coumaric Acids; D026901:Membrane Transport Proteins; D010937:Plant Growth Regulators; D011134:Polysaccharides; D017382:Reactive Oxygen Species; C004999:ferulic acid; D002118:Calcium