Comparative Proteomic Analysis of Tolerant and Sensitive Varieties Reveals That Phenylpropanoid Biosynthesis Contributes to Salt Tolerance in Mulberry

Exploring the Genetic Basis of Calonectria spp. Resistance in Eucalypts

Selecting high-quality varieties with disease resistance by artificial crossbreeding is the most fundamental way to address the damage caused by Calonectria spp. in eucalypt plantations. However, understanding the mechanism of disease-resistant heterosis occurrence in eucalypts is crucial for successful crossbreeding. Two eucalypt hybrids, the susceptible EC333 (H1522 × unknown) and the resistant EC338 (W1767 × P9060), were screened through infection with Calonectria isolates, a pathogen that causes eucalypt leaf blight. RNA-Seq was performed on the susceptible hybrid, the disease-resistant hybrid, and their parents. The gene differential expression analysis showed that there were 3912 differentially expressed genes between EC333 and EC338, with 1631 up-regulated and 2281 down-regulated genes. The expression trends of the differential gene sets in P9060 and EC338 were similar. However, the expression trend of W1767 was opposite that of EC338. The similarity of the expression and the advantage of stress resistance in E. pellita suggested that genes with significant differences in expression likely relate to disease resistance. A GSEA based on GO annotations revealed that the carbohydrate binding pathway genes were differentially expressed between EC338 and EC333. The gene pathways that were differentially expressed between EC338 and EC333 revealed by the GSEA based on KEGG annotations were the sesquiterpenoid and triterpenoid biosynthesis pathways. The alternative splicing analysis demonstrated that an AS event between EC338 and EC333 occurred in LOC104426602. According to our SNP analysis, EC338 had 626 more high-impact mutation loci than the male parent P9060 and 396 more than the female parent W1767; W1767 had 259 more mutation loci in the downstream region than EC338, while P9060 had 3107 fewer mutation loci in the downstream region than EC338. Additionally, EC338 had 9631 more mutation loci in the exon region than EC333. Modules were found via WGCNA that were strongly and oppositely correlated with EC338 and EC333, such as module MEsaddlebrown, likely associated with leaf blight resistance. The present study provides a detailed explanation of the genetic basis of eucalypt leaf blight resistance, providing the foundation for exploring genes related to this phenomenon.

Molecular analysis of the reactions in Salicornia europaea to varying NaCl concentrations at various stages of development to better exploit its potential as a new crop plant

Freshwater scarcity demands exploration of alternative resources like saline water and soils. Understanding the molecular mechanisms behind NaCl regulation in potential crop plants becomes increasingly important for promoting saline agriculture. This study investigated the euhalophyte Salicornia europaea, analyzing its gene expression, yield, and total phenolic compounds under hydroponic cultivation. We employed five salinity levels (0, 7.5, 15, 22.5, and 30 g/L NaCl) across five harvests at 15-day intervals, capturing plant development. Notably, this design deviated from conventional gene expression studies by recording organ-specific responses (shoots and roots) in plants adapted to long-term salinity treatments at various developmental stages. The highest fresh mass of S. europaea was observed four months after germination in 15 g/L NaCl. Identifying a reliable set of reference genes for normalizing gene expression data was crucial due to comparisons across shoots, roots, developmental stages, and salinity levels. A set of housekeeping genes - ubiquitin c (SeUBC), actin (SeActin) and dnaJ-like protein (SeDNAJ) - was identified for this purpose. Interestingly, plants grown without NaCl (0 g/L) displayed upregulation of certain genes associated with a NaCl deficiency related nutritional deprivation. These genes encode a tonoplast Na+/H+-antiporter (SeNHX1), a vacuolar H+-ATPase (SeVHA-A), two H+-PPases (SeVP1, SeVP2), a hkt1-like transporter (SeHKT), a vinorine synthase (SeVinS), a peroxidase (SePerox), and a plasma membrane Na+/H+-antiporter (SeSOS1). Other genes encoding an amino acid permease (SeAAP) and a proline transporter (SeProT) demonstrated marginal or dispersing salinity influence, suggesting their nuanced regulation during plants development. Notably, osmoregulatory genes (SeOsmP, SeProT) were upregulated in mature plants, highlighting their role in salinity adaptation. This study reveals distinct regulatory mechanisms in S. europaea for coping with varying salinity levels. Identifying and understanding physiological reactions and sodium responsive key genes further elucidate the relationship between sodium tolerance and the obligate sodium requirement as a nutrient in euhalophytes.

Transcriptomics Combined with Physiology and Metabolomics Reveals the Mechanism of Tolerance to Lead Toxicity in Maize Seedling

Lead (Pb) exposure can induce molecular changes in plants, disrupt metabolites, and impact plant growth. Therefore, it is essential to comprehend the molecular mechanisms involved in Pb tolerance in plants to evaluate the long-term environmental consequences of Pb exposure. This research focused on maize as the test subject to study variations in biomass, root traits, genes, and metabolites under hydroponic conditions under Pb conditions. The findings indicate that high Pb stress significantly disrupts plant growth and development, leading to a reduction in catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) activities by 17.12, 5.78, and 19.38%, respectively. Conversely, Pb stress led to increase malondialdehyde (MDA) contents, ultimately impacting the growth of maize. The non-targeted metabolomics analysis identified 393 metabolites categorized into 12 groups, primarily consisting of organic acids and derivatives, organ heterocyclic compounds, lipids and lipid-like molecules and benzenoids. Further analysis indicated that Pb stress induced an accumulation of 174 metabolites mainly enriched in seven metabolic pathways, for example phenylpropanoid biosynthesis and flavonoid biosynthesis. Transcriptome analysis revealed 1933 shared differentially expressed genes (DEGs), with 1356 upregulated and 577 downregulated genes across all Pb treatments. Additionally, an integrated analysis identified several DEGs and differentially accumulated metabolites (DAMs), including peroxidase, alpha-trehalose, and D-glucose 6-phosphate, which were linked to cell wall biosynthesis. These findings imply the significance of this pathway in Pb detoxification. This comprehensive investigation, employing multiple methodologies, provides a detailed molecular-level insight into maize's response to Pb stress.

Response Mechanisms of Zelkova schneideriana Leaves to Varying Levels of Calcium Stress

Calcium stress can negatively impact plant growth, prompting plants to respond by mitigating this effect. However, the specific mechanisms underlying this response remain unclear. In this study, we used non-targeted metabolomics and transcriptomics to investigate the response mechanisms of Zelkova schneideriana leaves under varying degrees of calcium stress. Results revealed that calcium stress led to wilt in young leaves. When calcium stress exceeds the tolerance threshold of the leaf, it results in wilting of mature leaves, rupture of chloroplasts in palisade tissue, and extensive wrinkling and breakage of leaf cells. Transcriptomic analysis indicated that calcium stress inhibited photosynthesis by suppressing the expression of genes related to photosynthetic system II and electron transport. Leaf cells activate phenylpropanoid biosynthesis, flavonoid biosynthesis, and Vitamin B6 metabolism to resist calcium stress. When calcium accumulation gradually surpassed the tolerance threshold of the cells, this results in failure of conventional anti-calcium stress mechanisms, leading to cell death. Furthermore, excessive calcium stress inhibits the expression of CNGC and anti-pathogen genes. The results of the metabolomics study showed that five key metabolites increased in response to calcium stress, which may play an important role in countering calcium stress. This study provides insights into the response of Z. schneideriana leaves to different levels of calcium stress, which could provide a theoretical basis for cultivating Z. schneideriana in karst areas and enhance our understanding of plant responses to calcium stress.

Grafting seedling rootstock strengthens tolerance to drought stress in polyploid mulberry (Morus alba L.)

The economically adaptable mulberry (Morus alba L.) has a long history of grafting in China, yet the physiological mechanisms and advantages in drought tolerance remain unexplored. In our study, we investigated the responses of self-rooted 2X (diploid), 3X (triploid), and 4X (tetraploid) plants, as well as polyploid plants grafted onto diploid seedling rootstocks (2X/2X, 3X/2X, and 4X/2X) under drought stress. We found that self-rooted diploid plants exhibited the most severe phenotypic damage, lowest water retention, photosynthetic capacity, and the least effective osmotic stress adjustment compared to tetraploid and triploid plants. However, grafted diploid and triploid plants showed effective mitigation of drought-induced damage, with higher relative water content and improved soil water retention. Grafted plants also improved the photosystem response to drought stress through elevated photosynthetic potential, closed stomatal aperture, and faster recovery of chlorophyll biosynthesis in the leaves. Additionally, grafted plants altered osmotic protective compound levels, including starch, soluble sugar, and proline content, thereby enhancing drought resistance. Absolute quantification PCR indicated that the expression levels of proline synthesis-related genes in grafted plants were not influenced after drought stress, whereas they were significantly increased in self-rooted plants. Consequently, our findings support that self-rooted triploid and tetraploid mulberries exhibited superior drought resistance compared to diploid plants. Moreover, grafting onto seedling rootstocks enhanced tolerance against drought stress in diploid and triploid mulberry, but not in tetraploid. Our study provides valuable insights for a comprehensive analysis of physiological effects in response to drought stress between stem-roots and seedling rootstocks.

Metabolomics combined with physiology and transcriptomics reveal key metabolic pathway responses in apple plants exposure to different selenium concentrations

Selenium (Se) can be absorbed by plants, thereby affects plant physiological activity, interferes gene expression, alters metabolite content and influences plant growth. However, the molecular mechanism underlying the plant response to Se remains unclear. In this study, apple plants were exposed to Se at concentrations of 0, 3, 6, 9, 12, 24, and 48 μM. Low concentrations of Se promoted plant growth, while high Se concentrations (≥24 μM) reduced photosynthesis, disturbed carbon and nitrogen metabolism, damaged the antioxidant system, and ultimately inhibited plant growth. The transcriptome and metabolome revealed that Se mainly affected three pathways, namely the 'biosynthesis of amino acids', 'starch and sucrose metabolism', and 'phenylpropanoid biosynthesis' pathways. 9 μM Se improved the synthesis, catabolism and utilization of amino acids and sugars, ultimately promoted plant growth. However, 24 μM Se up-regulated the related genes expression of PK, GPT, P5CS, SUS, SPS and CYP98A, and accumulated a large number of osmoregulation substances, such as citric acid, L-proline, D-sucrose and chlorogenic acid in the roots, ultimately affected the balance between plant growth and defense. In conclusion, this study reveals new insights into the key metabolic pathway in apple plants responses to Se.

Integration of Physiological, Transcriptomic, and Metabolomic Analyses Reveal Molecular Mechanisms of Salt Stress in Maclura tricuspidata

Salt stress is a universal abiotic stress that severely affects plant growth and development. Understanding the mechanisms of Maclura tricuspidate's adaptation to salt stress is crucial for developing salt-tolerant plant varieties. This article discusses the integration of physiology, transcriptome, and metabolome to investigate the mechanism of salt adaptation in M. tricuspidata under salt stress conditions. Overall, the antioxidant enzyme system (SOD and POD) of M. tricuspidata exhibited higher activities compared with the control, while the content of soluble sugar and concentrations of chlorophyll a and b were maintained during salt stress. KEGG analysis revealed that deferentially expressed genes were primarily involved in plant hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, alkaloids, and MAPK signaling pathways. Differential metabolites were enriched in amino acid metabolism, the biosynthesis of plant hormones, butanoate, and 2-oxocarboxylic acid metabolism. Interestingly, glycine, serine, and threonine metabolism were found to be important both in the metabolome and transcriptome-metabolome correlation analyses, suggesting their essential role in enhancing the salt tolerance of M. tricuspidata. Collectively, our study not only revealed the molecular mechanism of salt tolerance in M. tricuspidata, but also provided a new perspective for future salt-tolerant breeding and improvement in salt land for this species.

Exogenous Brassinosteroid Enhances Zinc tolerance by activating the Phenylpropanoid Biosynthesis pathway in Citrullus lanatus L

Zinc (Zn) is an important element in plants, but over-accumulation of Zn is harmful. The phytohormone brassinosteroids (BRs) play a key role in regulating plant growth, development, and response to stress. However, the role of BRs in watermelon (Citrullus lanatus L.) under Zn stress, one of the most important horticultural crops, remains largely unknown. In this study, we revealed that 24-epibrassinolide (EBR), a bioactive BR enhanced Zn tolerance in watermelon plants, which was related to the EBR-induced increase in the fresh weight, chlorophyll content, and net photosynthetic rate (Pn) and decrease in the content of hydrogen peroxide (H₂O₂), malondialdehyde (MDA), and Zn in watermelon leaves. Through RNA deep sequencing (RNA-seq), 350 different expressed genes (DEG) were found to be involved in the response to Zn stress after EBR treatment, including 175 up-regulated DEGs and 175 down-regulated DEGs. The up-regulated DEGs were significantly enriched in 'phenylpropanoid biosynthesis' pathway (map00940) using KEGG enrichment analysis. The gene expression levels of PAL, 4CL, CCR, and CCoAOMT, key genes involved in phenylpropanoid pathway, were significantly induced after EBR treatment. In addition, compared with Zn stress alone, EBR treatment significantly promoted the activities of PAL, 4CL, and POD by 30.90%, 20.69%, and 47.28%, respectively, and increased the content of total phenolic compounds, total flavonoids, and lignin by 23.02%, 40.37%, and 29.26%, respectively. The present research indicates that EBR plays an active role in strengthening Zn tolerance, thus providing new insights into the mechanism of BRs enhancing heavy metal tolerance.

Integrated Transcriptomic and Metabolomic Analyses Uncover the Differential Mechanism in Saline-Alkaline Tolerance between Indica and Japonica Rice at the Seedling Stage

Saline-alkaline stress is one of the major damages that severely affects rice (Oryza sativa L.) growth and grain yield; however, the mechanism of the tolerance remains largely unknown in rice. Herein, we comparatively investigated the transcriptome and metabolome of two contrasting rice subspecies genotypes, Luohui 9 (abbreviation for Chao2R under study, O. sativa ssp. indica, saline-alkaline-sensitive) and RPY geng (O. sativa ssp. japonica, saline-alkaline-tolerant), to identify the main pathways and important factors related to saline-alkaline tolerance. Transcriptome analysis showed that 68 genes involved in fatty acid, amino acid (such as phenylalanine and tryptophan), phenylpropanoid biosynthesis, energy metabolism (such as Glycolysis and TCA cycle), as well as signal transduction (such as hormone and MAPK signaling) were identified to be specifically upregulated in RPY geng under saline-alkaline conditions, implying that a series of cascade changes from these genes promotes saline-alkaline stress tolerance. The transcriptome changes observed in RPY geng were in high accordance with the specifically accumulation of metabolites, consisting mainly of 14 phenolic acids, 8 alkaloids, and 19 lipids based on the combination analysis of transcriptome and metabolome. Moreover, some genes involved in signal transduction as hub genes, such as PR5, FLS2, BRI1, and NAC, may participate in the saline-alkaline stress response of RPY geng by modulating key genes involved in fatty acid, phenylpropanoid biosynthesis, amino acid metabolism, and glycolysis metabolic pathways based on the gene co-expression network analysis. The present research results not only provide important insights for understanding the mechanism underlying of rice saline-alkaline tolerance at the transcriptome and metabolome levels but also provide key candidate target genes for further enhancing rice saline-alkaline stress tolerance.

Identification of the inducible activity in the promoter of the soybean BBI-DII gene exposed to abiotic stress or abscisic acid

The expression of the soybean Bowman-Birk proteinase isoinhibitor DII (BBI-DII) gene and the inducible activity of its promoter were studied under salt, drought, low temperature, and abscisic acid (ABA) exposure conditions. The BBI-DII gene was induced by salt, drought, low temperature, and ABA, and the relative expression levels were 103.09-, 107.01-, 17.25- and 27.24-fold, respectively, compared with the untreated control. The putative promoter, designated BP1 (- 1255 to + 872 bp), located 5'-upstream of the BBI-DII gene was cloned. The expression of the GUS gene in pCAM-BP1 transgenic tobacco plants was highest at 5 h after treatment with salt, drought, low temperature and ABA, especially under salt and drought. Using histochemical staining and fluorescence analysis of GUS, BP1 activity under salt and drought conditions after 5 h was 1.03 and 1.07-fold, respectively, compared with that of the CaMV35S promoter. Based on a 5' deletion analysis, the segment (+ 41 to + 474 bp) was the basal region that responded to salt and drought, whereas the segment (- 820 to + 41 bp) was the area that responded to increased salt and drought activity. The BP2 (- 820 to + 872) activities were 0.98- and 1.02-fold compared with that of BP1 under salt and drought conditions and was 435 bp shorter than BP1. The salt- and drought-inducible activities of the BP2 promoter in the roots, stems, and leaves of transgenic tobacco plants were stable. Taken together, BP2 is more suitable than the BP1 promoter for the study and molecular breeding of stress-resistant soybean plants.

Evaluation of salinity resistance and combining ability analysis in the seedlings of mulberry hybrids (Morus alba L.)

Soil salinization has become one of the major abiotic stresses influencing food security and maintenance of sustainable eco-environment. Highly salt-tolerant germplasm in mulberry, an important perennial woody plant, could restore the ecology and increase the agricultural income. Studies on the salt tolerance of mulberry are limited. Therefore, the aim of this study was to estimate the genetic variation and develop a reliable and effective evaluation of salt tolerance in 14 F1 mulberry hybrids that were directionally constructed using nine genotypes, including two females and seven males. A salt stress test was performed using 0.3%, 0.6%, and 0.9% (w/v) NaCl to investigate four morphological indexes of the growth rate: the shoot height (SHR), leaf number (LNR), leaf area (LAR), and the total weight of the whole plant after defoliation (BI) in the seedlings of the 14 combinations. The most suitable concentration for evaluating salt tolerance was identified as 0.9% NaCl based on the changes in the salt tolerance coefficient (STC). Comprehensive evaluation (D) values were obtained using principal components and membership functions based on four morphological indexes and their STCs, grouped into three principal component indexes cumulatively contributing to approximately 88.90% of the total variance. Two highly salt-tolerant, three moderately salt-tolerant, five salt-sensitive, and four highly salt-sensitive genotypes were screened. Anshen × Xinghainei and Anshen × Xinghaiwai had the highest D values. The analyses of combining ability further showed that the variances for LNR, LAR, and BI were elevated significantly with the increasing NaCl concentrations. Anshen × Xinghainei from two superior parents (female: Anshen, male: Xinghainei) with relatively higher general combing abilities for SHR, LAR, and BI was the best hybrid combination under high salinity stress, and presented the best specific combining ability for BI. Of all the traits tested, LAR and BI were greatly affected by additive effects and might be the two most reliable indexes. These traits show higher correlation with the salt tolerance of mulberry germplasm at the seedling stage. These results may enrich the mulberry resources by breeding and screening for elite germplasms with high salt tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01304-w.

Screening and Verification of Photosynthesis and Chloroplast-Related Genes in Mulberry by Comparative RNA-Seq and Virus-Induced Gene Silencing

Photosynthesis is one of the most important factors in mulberry growth and production. To study the photosynthetic regulatory network of mulberry we sequenced the transcriptomes of two high-yielding (E1 and E2) and one low-yielding (H32) mulberry genotypes at two-time points (10:00 and 12:00). Re-annotation of the mulberry genome based on the transcriptome sequencing data identified 22,664 high-quality protein-coding genes with a BUSCO-assessed completeness of 93.4%. A total of 6587 differentially expressed genes (DEGs) were obtained in the transcriptome analysis. Functional annotation and enrichment revealed 142 out of 6587 genes involved in the photosynthetic pathway and chloroplast development. Moreover, 3 out of 142 genes were further examined using the VIGS technique; the leaves of MaCLA1- and MaTHIC-silenced plants were markedly yellowed or even white, and the leaves of MaPKP2-silenced plants showed a wrinkled appearance. The expression levels of the ensiled plants were reduced, and the levels of chlorophyll b and total chlorophyll were lower than those of the control plants. Co-expression analysis showed that MaCLA1 was co-expressed with CHUP1 and YSL3; MaTHIC was co-expressed with MaHSP70, MaFLN1, and MaEMB2794; MaPKP2 was mainly co-expressed with GH9B7, GH3.1, and EDA9. Protein interaction network prediction revealed that MaCLA1 was associated with RPE, TRA2, GPS1, and DXR proteins; MaTHIC was associated with TH1, PUR5, BIO2, and THI1; MaPKP2 was associated with ENOC, LOS2, and PGI1. This study offers a useful resource for further investigation of the molecular mechanisms involved in mulberry photosynthesis and preliminary insight into the regulatory network of photosynthesis.

Transcriptomic Insights Into Root Development and Overwintering Transcriptional Memory of Brassica rapa L. Grown in the Field

As the only overwintering oil crop in the north area of China, living through winter is the primary feature of winter rapeseed. Roots are the only survival organ during prolonged cold exposure during winter to guarantee flowering in spring. However, little is known about its root development and overwintering memory mechanism. In this study, root collar tissues (including the shoot apical meristem) of three winter rapeseed varieties with different cold resistance, i.e., Longyou-7 (strong cold tolerance), Tianyou-4 (middle cold tolerance), and Lenox (cold-sensitive), were sampled in the pre-winter period (S1), overwintering periods (S2-S5), and re-greening stage (S6), and were used to identify the root development and overwintering memory mechanisms and seek candidate overwintering memory genes by measuring root collar diameter and RNA sequencing. The results showed that the S1-S2 stages were the significant developmental stages of the roots as root collar diameter increased slowly in the S3-S5 stages, and the roots developed fast in the strong cold resistance variety than in the weak cold resistance variety. Subsequently, the RNA-seq analysis revealed that a total of 37,905, 45,102, and 39,276 differentially expressed genes (DEGs), compared to the S1 stage, were identified in Longyou-7, Tianyou-4, and Lenox, respectively. The function enrichment analysis showed that most of the DEGs are significantly involved in phenylpropanoid biosynthesis, plant hormone signal transduction, MAPK signaling pathway, starch and sucrose metabolism, photosynthesis, amino sugar and nucleotide sugar metabolism, and spliceosome, ribosome, proteasome, and protein processing in endoplasmic reticulum pathways. Furthermore, the phenylpropanoid biosynthesis and plant hormone signal transduction pathways were related to the difference in root development of the three varieties, DEGs involved in photosynthesis and carbohydrate metabolism processes may participate in overwintering memory of Longyou-7 and Tianyou-4, and the spliceosome pathway may contribute to the super winter resistance of Longyou-7. The transcription factor enrichment analysis showed that the WRKY family made up the majority in different stages and may play an important regulatory role in root development and overwintering memory. These results provide a comprehensive insight into winter rapeseed's complex overwintering memory mechanisms. The identified candidate overwintering memory genes may also serve as important genetic resources for breeding to further improve the cold resistance of winter rapeseed.

Effects of Mixed Decomposition of Pinus sylvestris var. mongolica and Morus alba Litter on Microbial Diversity

Pinus sylvestris var. mongolica is widely planted in China as a windbreak and sand fixation tree. To improve the current situation of large-scale declines of forested areas planted as P. sylvestris var. mongolica monocultures, we investigated the biological and microbial effects of stand establishment using mixed tree species. The interactions during the mixed decomposition of the litter and leaves of different tree species are an important indicator in determining the relationships among species. In this experiment, a method of simulating the mixed decomposition of P. sylvestris var. mongolica and Morus alba litter under P. sylvestris var. mongolica forest was used to determine the total C, total N, and total P contents in the leaf litter, and the microbial structures were determined by using Illumina MiSeq high-throughput sequencing. It was found that with samples with different proportions of P. sylvestris var. mongolica and M. alba litters, the decomposition rate of P. sylvestris var. mongolica × M. alba litter was significantly higher than that of the pure P. sylvestris var. mongolica forest, and the microbial community and composition diversity of litter in a pure P. sylvestris var. mongolica forest could be significantly improved. The possibility of using M. alba as a mixed tree species to address the declines of pure P. sylvestris var. mongolica forest was verified to provide guidance for pure P. sylvestris var. mongolica forests by introducing tree species with coordinated interspecific relationships and creating a mixed forest.

Multiomics Analyses of Two Sorghum Cultivars Reveal the Molecular Mechanism of Salt Tolerance

Sorghum [Sorghum bicolor (L.) Moench] is one of the most important cereal crops and contains many health-promoting substances. Sorghum has high tolerance to abiotic stress and contains a variety of flavonoids compounds. Flavonoids are produced by the phenylpropanoid pathway and performed a wide range of functions in plants resistance to biotic and abiotic stress. A multiomics analysis of two sorghum cultivars (HN and GZ) under different salt treatments time (0, 24, 48, and 72) was performed. A total of 45 genes, 58 secondary metabolites, and 246 proteins were recognized with significant differential abundances in different comparison models. The common differentially expressed genes (DEGs) were allocated to the "flavonoid biosynthesis" and "phenylpropanoid biosynthesis" pathways. The most enriched pathways of the common differentially accumulating metabolites (DAMs) were "flavonoid biosynthesis," followed by "phenylpropanoid biosynthesis" and "arginine and proline metabolism." The common differentially expressed proteins (DEPs) were mainly distributed in "phenylpropanoid biosynthesis," "biosynthesis of cofactors," and "RNA transport." Furthermore, considerable differences were observed in the accumulation of low molecular weight nonenzymatic antioxidants and the activity of antioxidant enzymes. Collectively, the results of our study support the idea that flavonoid biological pathways may play an important physiological role in the ability of sorghum to withstand salt stress.

Integrated physiological and comparative proteomics analysis of contrasting genotypes of pearl millet reveals underlying salt-responsive mechanisms

Salinity stress poses a significant risk to plant development and agricultural yield. Therefore, elucidation of stress-response mechanisms has become essential to identify salt-tolerance genes in plants. In the present study, two genotypes of pearl millet (Pennisetum glaucum L.) with contrasting tolerance for salinity exhibited differential morpho-physiological and proteomic responses under 150 mM NaCl. The genotype IC 325825 was shown to withstand the stress better than IP 17224. The salt-tolerance potential of IC 325825 was associated with its ability to maintain intracellular osmotic, ionic, and redox homeostasis and membrane integrity under stress. The IC 325825 genotype exhibited a higher abundance of C4 photosynthesis enzymes, efficient enzymatic and non-enzymatic antioxidant system, and lower Na⁺ /K⁺ ratio compared with IP 17224. Comparative proteomics analysis revealed greater metabolic perturbation in IP 17224 under salinity, in contrast to IC 325825 that harbored pro-active stress-responsive machinery, allowing its survival and better adaptability under salt stress. The differentially abundant proteins were in silico characterized for their functions, subcellular-localization, associated pathways, and protein-protein interaction. These proteins were mainly involved in photosynthesis/response to light stimulus, carbohydrate and energy metabolism, and stress responses. Proteomics data were validated through expression profiling of the selected genes, revealing a poor correlation between protein abundance and their relative transcript levels. This study has provided novel insights into salt adaptive mechanisms in P. glaucum, demonstrating the power of proteomics-based approaches. The critical proteins identified in the present study could be further explored as potential objects for engineering stress tolerance in salt-sensitive major crops.

Salt stress proteins in plants: An overview

Salinity stress is considered the most devastating abiotic stress for crop productivity. Accumulating different types of soluble proteins has evolved as a vital strategy that plays a central regulatory role in the growth and development of plants subjected to salt stress. In the last two decades, efforts have been undertaken to critically examine the genome structure and functions of the transcriptome in plants subjected to salinity stress. Although genomics and transcriptomics studies indicate physiological and biochemical alterations in plants, it do not reflect changes in the amount and type of proteins corresponding to gene expression at the transcriptome level. In addition, proteins are a more reliable determinant of salt tolerance than simple gene expression as they play major roles in shaping physiological traits in salt-tolerant phenotypes. However, little information is available on salt stress-responsive proteins and their possible modes of action in conferring salinity stress tolerance. In addition, a complete proteome profile under normal or stress conditions has not been established yet for any model plant species. Similarly, a complete set of low abundant and key stress regulatory proteins in plants has not been identified. Furthermore, insufficient information on post-translational modifications in salt stress regulatory proteins is available. Therefore, in recent past, studies focused on exploring changes in protein expression under salt stress, which will complement genomic, transcriptomic, and physiological studies in understanding mechanism of salt tolerance in plants. This review focused on recent studies on proteome profiling in plants subjected to salinity stress, and provide synthesis of updated literature about how salinity regulates various salt stress proteins involved in the plant salt tolerance mechanism. This review also highlights the recent reports on regulation of salt stress proteins using transgenic approaches with enhanced salt stress tolerance in crops.

Integrated de novo Analysis of Transcriptional and Metabolic Variations in Salt-Treated Solenostemma argel Desert Plants

Solenostemma argel (Delile) Hayne is a desert plant that survives harsh environmental conditions with several vital medicinal properties. Salt stress is a major constraint limiting agricultural production around the globe. However, response mechanisms behind the adaptation of S. argel plants to salt stress are still poorly understood. In the current study, we applied an omics approach to explore how this plant adapts to salt stress by integrating transcriptomic and metabolomic changes in the roots and leaves of S. argel plants under salt stress. De novo assembly of transcriptome produced 57,796 unigenes represented by 165,147 transcripts/isoforms. A total of 730 differentially expressed genes (DEGs) were identified in the roots (396 and 334 were up- and down-regulated, respectively). In the leaves, 927 DEGs were identified (601 and 326 were up- and down-regulated, respectively). Gene ontology and Kyoto Encyclopedia of Genes And Genomes pathway enrichment analyses revealed that several defense-related biological processes, such as response to osmotic and oxidative stress, hormonal signal transduction, mitogen-activated protein kinase signaling, and phenylpropanoid biosynthesis pathways are the potential mechanisms involved in the tolerance of S. argel plants to salt stress. Furthermore, liquid chromatography-tandem mass spectrometry was used to detect the metabolic variations of the leaves and roots of S. argel under control and salt stress. 45 and 56 critical metabolites showed changes in their levels in the stressed roots and leaves, respectively; there were 20 metabolites in common between the roots and leaves. Differentially accumulated metabolites included amino acids, polyamines, hydroxycinnamic acids, monolignols, flavonoids, and saccharides that improve antioxidant ability and osmotic adjustment of S. argel plants under salt stress. The results present insights into potential salt response mechanisms in S. argel desert plants and increase the knowledge in order to generate more tolerant crops to salt stress.