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.

Mercury (Hg) is a serious environmental pollution threat to the planet. The accumulation of Hg in plants disrupts many cellular-level functions and inhibits growth and development, but the mechanism is not fully understood. To gain more insight into the cellular response to Hg, we performed a large-scale analysis of the rice transcriptome during Hg stress. Genes induced with short-term exposure represented functional categories of cell-wall formation, chemical detoxification, secondary metabolism, signal transduction and abiotic stress response. Moreover, Hg stress upregulated several genes involved in aromatic amino acids (Phe and Trp) and increased the level of free Phe and Trp content. Exogenous application of Phe and Trp to rice roots enhanced tolerance to Hg and effectively reduced Hg-induced production of reactive oxygen species. Hg induced calcium accumulation and activated mitogen-activated protein kinase. Further characterization of the Hg-responsive genes we identified may be helpful for better understanding the mechanisms of Hg in plants.

Salt-affected soil induces detrimental influences on paddy rice (Oryza sativa L.) growth and ameliorating the influences could be done with organic amendments, such as animal manure and biochar. The aims of the current study are: (1) to examine the interactive effects of biochar and cow manure on rice growth and on selected properties of salt-affected soil, and (2) to identify potential mechanisms related to the amendments. Saline-sodic soil was used for a net house experiment with two experimental factors: biochar (no-biochar, rice-husk, and -straw biochar) and cow manure (with and without cow manure). Without the manure, addition of both rice-hush and – straw biochar significantly increased rice growth, whereas a combination of individual biochar with manure did not show a positive synergistic effect. The interactive effect of two factors was not significant on available P and exchangeable K concentrations, but the main effects of the two factors were significant. Biochar addition resulted in higher soil cation exchange capacity (CEC) (28.8 to 29.0 cmol_c kg⁻¹) than the control (25.6 cmol_c kg⁻¹), but manure addition did not. Improved nutrient availabilities such as P and K, as well as CEC are among the potential mechanisms accounting for the enhanced rice growth with biochar.