Transcriptomic reprogramming in soybean seedlings under salt stress

Abstract

To obtain a comprehensive understanding of transcriptomic reprogramming under salt stress, we performed whole-transcriptome sequencing on the leaf and root of soybean seedlings subjected to salt treatment in a time-course experiment (0, 1, 2, 4, 24, and 48 hr). This time series dataset enabled us to identify important hubs and connections of gene expressions. We highlighted the analysis on phytohormone signaling pathways and their possible crosstalks. Differential expressions were also found among those genes involved in carbon and nitrogen metabolism. In general, the salt-treated seedlings slowed down their photosynthetic functions and ramped up sugar catabolism to provide extra energy for survival. Primary nitrogen assimilation was shut down whereas nitrogen resources were redistributed. Overall, the results from the transcriptomic analyses indicate that the plant uses a multipronged approach to overcome salt stress, with both fast-acting, immediate physiological responses, and longer term reactions that may involve metabolic adjustment.

Polyamines and legumes: Joint stories of stress, nitrogen fixation and environment

“…Several studies using "omics" techniques have revealed that salinity modulates the expression of genes involved in PAs metabolism. Using transcriptomic, Liu et al, (2019) (Liu et al, 2019) confirmed previous results (Xing et al, 2007) showing the occurrence of the alternative pathway for GABA accumulation, that is the expression of PAs oxidase in the PAs degradation pathway, in G. max plants exposed to saline stress. The same phenomenon had been reported previously for V. faba plants grown under hypoxia (Yang et al, 2013).…”

Analysis of Soybean Long Non-Coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts

“…We also investigated lncRNA transcriptional responses with respect to time by making use of previously published RNA-Seq datasets corresponding to timed salt treatment of two of our in-house soybean germplasms, C08 (Liu et al, 2018) and W05 (Xie et al, 2019). In a previous study from our group, it was shown that sodium ion started to accumulate in root tissues within the first hour of salt treatment, while it was detected in leaf tissues after 24 h of salt treatment (Liu et al, 2018). In accordance with these observations, we mainly focused on lncRNAs that tended to be induced either at early time points (e.g.…”

The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte

“…To unveil the interrelationships among high-salt-stress responsive genes, we performed the weighted gene co-expression networks analysis (WGCNA) (Liu et al, 2019) with all 3875 DE unigenes from varying degrees of salt stress (Table S7 ). The co-expression network was built and DE unigenes were classified into five modules with hierarchical clustering.…”

“…Transcriptome sequencing has been widely adopted to explore the gene expression dynamics in response to salt stress from different species (Bushman, Amundsen, Warnke, Robins, & Johnson, 2016; Liu et al, 2019; Mutwakil et al, 2017; Qiu et al, 2017). However, the transcriptome studies in high salt tolerance from halophyte are relative limited and most of them mainly focus on dicotyledonous halophytes (Lee et al, 2013; Subudhi & Baisakh, 2011; Y.…”

“…Zhang et al, 2008). Moreover, although the genome-wide transcriptome reprogramming under salt stress has been reported (Liu et al, 2019), the reprogramming under different salinity stress conditions remains unexplored. In addition, alternative splicing (AS) is one important post-transcriptional regulation that plays critical roles in eukaryotic pre-mRNA processing and contributes to diversifying the transcriptome and proteome (Deng & Cao, 2017).…”