Transcriptome analysis of sweet1 seeds upon treatments during germination

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. Overall design: Seed transcript profiles in sweet1 under glucose, ABA and ABA+glucose treatments in 30 hours after imbibition.