Integrated Physiological, Transcriptomic, and Metabolomic Analyses Revealed Molecular Mechanism for Salt Resistance in Soybean Roots

Abstract

Salinity stress is a threat to yield in many crops, including soybean (Glycine max L.). In this study, three soybean cultivars (JD19, LH3, and LD2) with different salt resistance were used to analyze salt tolerance mechanisms using physiology, transcriptomic, metabolomic, and bioinformatic methods. Physiological studies showed that salt-tolerant cultivars JD19 and LH3 had less root growth inhibition, higher antioxidant enzyme activities, lower ROS accumulation, and lower Na+ and Cl- contents than salt-susceptible cultivar LD2 under 100 mM NaCl treatment. Comparative transcriptome analysis showed that compared with LD2, salt stress increased the expression of antioxidant metabolism, stress response metabolism, glycine, serine and threonine metabolism, auxin response protein, transcription, and translation-related genes in JD19 and LH3. The comparison of metabolite profiles indicated that amino acid metabolism and the TCA cycle were important metabolic pathways of soybean in response to salt stress. In the further validation analysis of the above two pathways, it was found that compared with LD2, JD19, and LH3 had higher nitrogen absorption and assimilation rate, more amino acid accumulation, and faster TCA cycle activity under salt stress, which helped them better adapt to salt stress. Taken together, this study provides valuable information for better understanding the molecular mechanism underlying salt tolerance of soybean and also proposes new ideas and methods for cultivating stress-tolerant soybean.

Integrated metabolomic and transcriptomic analysis reveals the role of phenylpropanoid biosynthesis pathway in tomato roots during salt stress

“…In the present study, based on the morphological and physiological responses of S. lycopersicum to salt stress, metabolomic and transcriptomic approaches were used to analyze the DEGs and DAMs of S. lycopersicum roots during various stages of salt stress and to identify significantly enriched KEGG pathways, mainly "biosynthesis of secondary metabolites", "plant hormone signal transduction", and "phenylpropanoid biosynthesis". This is consistent with the results of former works that used a multiomics approach to analyze the response mechanisms and metabolic processes of S. alopecuroides, B. vulgaris, and B. napus roots to salt stress (Liu et al, 2020;Zhu et al, 2021;Wang et al, 2022b), but also differs somewhat from the results of studies on the molecular mechanisms of salt tolerance in G. max roots (Jin et al, 2021).…”

“…Since the effective response capacity of plants under salt stress depends on the roots ( Deolu-Ajayi et al., 2019 ; Nakamura et al., 2020 ). A combined metabolome and transcriptome analysis have been carried out in G. max ( Jin et al., 2021 ), S. alopecuroides ( Zhu et al., 2021 ), B. vulgaris ( Liu et al., 2020 ), and B. napus ( Wang et al., 2022b ) roots to reveal the molecular mechanisms underlying their salt tolerance. In the present study, based on the morphological and physiological responses of S. lycopersicum to salt stress, metabolomic and transcriptomic approaches were used to analyze the DEGs and DAMs of S. lycopersicum roots during various stages of salt stress and to identify significantly enriched KEGG pathways, mainly “biosynthesis of secondary metabolites”, “plant hormone signal transduction”, and “phenylpropanoid biosynthesis”.…”

“…This means that the effective response capacity of plants under salt stress depends on the roots ( Yang and Guo, 2018 ; Deolu-Ajayi et al., 2019 ; Nakamura et al., 2020 ). In recent years, the results of studies that integrated physiological, transcriptional, and metabolic analyses to reveal the molecular mechanisms of salt tolerance in soybean ( Glycine max ) roots have demonstrated that salt tolerant varieties have higher rates of nitrogen (N) uptake and assimilation, an increased amino acid accumulation and more rapid tricarboxylic acid cycle activity in response to salt stress, which contributes to their improved adaptation under salt stress ( Jin et al., 2021 ). The findings of combined transcriptional and metabolic analyses to reveal the effects of the phenylpropanoid biosynthesis pathway during salt resistance of fabaceae ( Sophora alopecuroides ) suggest that lignans and flavonoids are probably engaged in the scavenging of ROS from S. alopecuroides roots, mitigating the damage induced by salt stress ( Zhu et al., 2021 ).…”

Weighted gene co-expression network analysis revealed the key pathways and hub genes of potassium regulating cotton root adaptation to salt stress

“…The researchers suggest that maintaining the TCA cycle helps plants survive stress conditions such as high temperature (Li et al, 2016), drought (Li et al, 2017b) and salt stress (Che-Othman et al, 2020). Salt-tolerant soybean varieties have higher amino acid accumulation rate and faster TCA cycle activity (Jin et al, 2021). Some scholars also pointed out that wild soybean (Li et al, 2017a) promoted its energy metabolism and intermediate metabolite levels under saltalkali stress by increasing TCA cycle activity, thus enhancing salt tolerance.…”

Possible melatonin-induced salt stress tolerance pathway in Phaseolus vulgaris L. using transcriptomic and metabolomic analyses

“…Previous studies have used integrated transcriptomic and metabolomic analysis to examine abiotic stress in plants. It was found that isoflavones were differentially expressed under drought stress in soybean and isoflavones played an important role in the regulation of ROS [ 22 ]. In tobacco, it was reported that increased polyphenol content may protect against low temperature stress [ 23 ].…”