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Plants suffer from oxygen deficiency (hypoxia) and energy starvation under flooding conditions. Higher plants have evolved complex adaptive mechanisms to flooding that are induced by changes in the cellular redox state and phytohormones. Previously, we showed that the transcript levels of respiratory burst oxidase homolog I (AtRBOH I) in Arabidopsis increase under hypoxic stress. In this study, we used two independent Atrboh I-knockout lines to assess the molecular function of AtRBOH I in hypoxic signaling pathways. Under submergence conditions, the Atrboh I-knockout lines had a reduced survival rate and lower chlorophyll contents than those of wild type. The patterns of AtRBOH I expression were analyzed by fusing its promoter to the GUS reporter. These expression analyses indicated that AtRBOH I expression was activated by hypoxia, but this induction was reduced by the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Quantitative RT-PCR analyses showed that the transcript levels of hypoxia-inducible genes (AtHRE1, AtADH1, AtLDH, and AtSUS1) were reduced in AtRBOH I-knockout lines under hypoxic conditions. The transcript levels of AtSUS1 were lower in AtRBOH I-knockout lines than in wild type in the hypoxia combined with NPA treatment. Hypoxic conditions increased the transcript levels of the auxin-responsive genes At1g19840, At3g23030, and At5g19140, and hypoxia combined with NPA resulted in increased transcript levels of the ethylene biosynthetic genes AtACS7 and AtACS8. Together, these results show that AtRBOH I regulates the expression of genes involved in ethylene biosynthesis and down-stream of hypoxia signaling, and that there is some interplay between hypoxia signaling and auxin-mediated signaling pathways under hypoxic stress.

Additional file 1: Table S1. The primer sequence used for quantitative RT-PCR in this study.

Cultivating rice in wet or water direct seeding systems is simple and time and labor efficient. Rice (Oryza sativa) seeds are a unique cereal that can germinate not only when submerged, but also in anoxic conditions. Many complicated hormone signals interact in submerged seed germination. Ethylene is involved in rice coleoptile elongation, but little is known regarding the role of auxin signaling under submergence. This study demonstrated that the coleoptile is shorter and curlier when submerged with 2,3,5-triiodobenzoic acid (TIBA). In transcriptomic analysis, 3448 of the 31,860 genes were upregulated, and 4360 genes were downregulated with submergence and TIBA treatment. The Gene Ontology function classification results demonstrated that upregulated differentially expressed genes (DEGs) were mainly involved in redox, stress, and signal transduction, whereas the down-regulated DEGs were mainly involved in RNA transcription, stress, and development. Furthermore, auxin signaling involved in the carbohydrate metabolism pathway was demonstrated while using transcriptomic analysis and confirmed in a quantitative real-time polymerase chain reaction. In addition, the transcript levels of development-related genes and mitochondria-electron- transport-related genes were regulated by auxin signaling under submergence. Auxin signaling was not only involved in regulating rice coleoptile elongation and development, but also regulated secondary metabolism, carbohydrate metabolism, and mitochondria electron transport under submergence. Our results presented that auxin signaling plays an important role during rice coleoptile elongation upon the submergence condition and improving the advance of research of direct rice seeding system.

Background Flooding due to global climate change is a serious problem that frequently decreases crop yields. Rice fields in flood-prone areas often experience full or partial submergence. Submergence has an adverse effect on internal oxygen availability, sugar status and survival. Complete submergence imposes severe pressure on plants, principally because the excess water in their surroundings deprives them of certain basic resources such as oxygen, carbon dioxide and light for photosynthesis. To better understand the mechanisms involved under different levels of flooding, it is necessary to further observe physiological responses and to identify the Rboh genes involved and determine how they are regulated during submergence. Results In this study, significant physiological changes were observed in plant height, leaf sheath elongation and chlorophyll a, b and total content under partial and full submergence treatments. Senescence-regulating genes were severely affected under full submergence. Additionally, intracellular oxidative homeostasis was disrupted by overproduction of H2O2 and O2−, which affected cell viability and antioxidant enzyme activity, under different levels of submergence. Quantitative RT-PCR analyses revealed that complex regulation of Rboh genes is involved under different levels of submergence. Conclusion Our results demonstrated that the effect of physiological and the transcript levels of OsRboh genes were presented different responses to different levels of submergence in rice seedlings. There have different mechanism in intracellular to response different levels of submergence. Finally we discuss effects of the regulation of OsRboh expression and ROS production which was important to maintain homeostasis to help rice seedlings face different levels of submergence. Electronic supplementary material The online version of this article (doi:10.1186/s12284-016-0074-9) contains supplementary material, which is available to authorized users.