Project description:Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination. Methods: After 3-day imbibition, sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads. Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. Candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function. Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.
Project description:Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination. Methods: After 3-day imbibition, WT and sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads. Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. There are 6230 candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function. Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.
Project description:Root exudates play an important role in plant-microbe interaction. The transcriptional profilings of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 in response to maize root exudates under static condition, were investigated by an Illumina RNA-seq for understanding the regulatory roles of the root exudates. 4 treatments, including 2 blank control (24 h and 48 h-post inoculation, named as 5 and 15, respectively), and 2 treatments with maize root exudates (24 h and 48 h-post inoculation, named as 7 and 17, respectively)
Project description:Plant pathogenic bacteria disseminate and survive through transmission to and by seeds of hosts and non-hosts plants. To investigate the interaction between xanthomonads and developing seeds of Medicago truncatula, plants at the M-oM-,M-^Bower bud stage were spray inoculated until runoff with xanthomonads suspensions. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed on seeds to characterize the molecular dialogue between Xanthomonas campestris pv. campestris in an incompatible situation with M. truncatula seeds and Xanthomonas alfalfae pv. alfalfae in a compatible situation at two developmental time points (16 and 32 days atfter pollination (DAP). Six-condition experiment, 16dap_Mock versus 16dap_Xaa, 16dap_Mock versus 16dap_Xcc, 32dap_Mock versus 32dap_Xaa, 32dap_Mock versus 32dap_Xcc. Biological replicates: 6 controls (16dap_Mock, 32dap_Mock), 12 treatments (16dap_Xaa, 16dap_Xcc, 32dap_Xaa, 32dap_Xcc), independently grown and harvested. One replicate per array.