Daytime soybean transcriptome fluctuations during water deficit stress

Abstract

BackgroundSince drought can seriously affect plant growth and development and little is known about how the oscillations of gene expression during the drought stress-acclimation response in soybean is affected, we applied Illumina technology to sequence 36 cDNA libraries synthesized from control and drought-stressed soybean plants to verify the dynamic changes in gene expression during a 24-h time course. Cycling variables were measured from the expression data to determine the putative circadian rhythm regulation of gene expression.ResultsWe identified 4866 genes differentially expressed in soybean plants in response to water deficit. Of these genes, 3715 were differentially expressed during the light period, from which approximately 9.55 % were observed in both light and darkness. We found 887 genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes, 35.52 % exhibited expression oscillations in a 24 h period. This number increased to 39.23 % when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Such differences in plants under stress were primarily observed in ZT0 (early morning) to ZT8 (late day) and also from ZT4 to ZT12. Stress-related pathways were triggered in response to water deficit primarily during midday, when more genes were up-regulated compared to early morning. Additionally, genes known to be involved in secondary metabolism and hormone signaling were also expressed in the dark period.ConclusionsGene expression networks can be dynamically shaped to acclimate plant metabolism under environmental stressful conditions. We have identified putative cycling genes that are expressed in soybean leaves under normal developmental conditions and genes whose expression oscillates under conditions of water deficit. These results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1731-x) contains supplementary material, which is available to authorized users.

Molecular, physiological, and agronomical characterization, in greenhouse and in field conditions, of soybean plants genetically modified with AtGolS2 gene for drought tolerance

“…In soybean submitted to water deficit, Marcolino and co-workers (2014) described a diurnal oscillation and expression induction for GmGols-like gene. Gene exp r e s s i o n q u a n t i f i c a t i o n f o r s o y b e a n G o l S (Glyma19g40680) confirmed the expression induction in plants submitted to water deficit (Rodrigues et al 2015). These reports corroborates data obtained here, as in water deficit conditions, AtGolS2 gene was highly expressed in event 2Ia4 (Fig.…”

“…In soybean, submitted to water deficit, Marcolino and co-workers (2014) described a diurnal oscillation and induced expression for GmGolslike gene. Gene expression quantification for soybean GolS (Glyma19g40680) confirmed the expression induction in plants submitted to water deficit (Rodrigues et al 2015).…”

Tinkering Cis Motifs Jigsaw Puzzle Led to Root-Specific Drought-Inducible Novel Synthetic Promoters

“…Prior to designing synthetic promoter against drought stress, we had to select appropriate cis motifs. Cis motif families were identified among drought-responsive soybean genes revealed through transcriptome analysis previously [41,42]. Initially, differentially expressed genes (DEGs) were identified in the early and late morning periods (ZT0 and ZT4).…”

The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species

“…PcircRNA_finder required rRNA À /RNase R þ RNA-Seq using paired-end sequencing for identification of circular RNAs in plants (Chen et al, 2016). Thus, we collected all available rRNA À /RNase R þ RNA-Seq for species mentioned in this study, which included Arabidopsis thaliana (Liu et al, 2017;Lu et al, 2017;Ye et al, 2015), Oryza sativa (Lu et al, 2015;Ye et al, 2017a, b), Solanum lycopersicum (Yin et al, 2018), Zea mays (Chen et al, 2018) and Glycine max (Rodrigues et al, 2015). The raw sequence data from SRA archives was first converted to FASTQ using fastq-dump (2.5.7) in SRA Toolkit (https://github.com/ncbi/sratoolkit) and then lowquality reads were filtered out using ht2-filter (1.92.1) from highthroughput quality control (HTQC) package (Yang et al, 2013).…”

“…However, the raw RNA-Seq dataset from that study was not deposited in SRA. Thus, we used another study in soybean (Rodrigues et al, 2015) for circular RNAs identification using PcircRNA_finder. We only detected 27 overlapped circular RNAs between two studies.…”