title: Comparative Digital Gene Expression Analysis of the Arabidopsis Response to Volatiles Emitted by Bacillus amyloliquefaciens.
abstract: Some plant growth-promoting rhizobacteria (PGPR) regulated plant growth and elicited plant basal immunity by volatiles. The response mechanism to the Bacillus amyloliquefaciens volatiles in plant has not been well studied. We conducted global gene expression profiling in Arabidopsis after treatment with Bacillus amyloliquefaciens FZB42 volatiles by Illumina Digital Gene Expression (DGE) profiling of different growth stages (seedling and mature) and tissues (leaves and roots). Compared with the control, 1,507 and 820 differentially expressed genes (DEGs) were identified in leaves and roots at the seedling stage, respectively, while 1,512 and 367 DEGs were identified in leaves and roots at the mature stage. Seventeen genes with different regulatory patterns were validated using quantitative RT-PCR. Numerous DEGs were enriched for plant hormones, cell wall modifications, and protection against stress situations, which suggests that volatiles have effects on plant growth and immunity. Moreover, analyzes of transcriptome difference in tissues and growth stage using DGE profiling showed that the plant response might be tissue-specific and/or growth stage-specific. Thus, genes encoding flavonoid biosynthesis were downregulated in leaves and upregulated in roots, thereby indicating tissue-specific responses to volatiles. Genes related to photosynthesis were downregulated at the seedling stage and upregulated at the mature stage, respectively, thereby suggesting growth period-specific responses. In addition, the emission of bacterial volatiles significantly induced killing of cells of other organism pathway with up-regulated genes in leaves and the other three pathways (defense response to nematode, cell morphogenesis involved in differentiation and trichoblast differentiation) with up-regulated genes were significantly enriched in roots. Interestingly, some important alterations in the expression of growth-related genes, metabolic pathways, defense response to biotic stress and hormone-related genes were firstly founded response to FZB42 volatiles.
authors: Gaolan Station of Agricultural and Ecological Experiment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China.|Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Lanzhou, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Hai-Ting
authors: HT
authors: Hao
authors: Gaolan Station of Agricultural and Ecological Experiment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China.|Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Lanzhou, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Xia
authors: X
authors: Zhao
authors: Gaolan Station of Agricultural and Ecological Experiment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China.|Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Lanzhou, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Qian-Han
authors: QH
authors: Shang
authors: Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Yun
authors: Y
authors: Wang
authors: Gaolan Station of Agricultural and Ecological Experiment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China.|Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Lanzhou, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Zhi-Hong
authors: ZH
authors: Guo
authors: Gaolan Station of Agricultural and Ecological Experiment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China.|Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Lanzhou, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Yu-Bao
authors: YB
authors: Zhang
authors: Gaolan Station of Agricultural and Ecological Experiment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China.|Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Lanzhou, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Zhong-Kui
authors: ZK
authors: Xie
authors: Gaolan Station of Agricultural and Ecological Experiment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China.|Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Lanzhou, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Ruo-Yu
authors: RY
authors: Wang
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D000069977:Bacillus amyloliquefaciens / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010940:Plant Proteins / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D036226:Seedlings / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome; D055549:Volatile Organic Compounds / Q000494:pharmacology*
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant; D055549:Volatile Organic Compounds