Ionomic and transcriptomic analyses of two cotton cultivars (Gossypium hirsutum L.) provide insights into the ion balance mechanism of cotton under salt stress

Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops

The deployment of omics technologies has obtained an incredible boost over the past few decades with the advances in next-generation sequencing (NGS) technologies, innovative bioinformatics tools, and the deluge of available biological information. The major omics technologies in the limelight are genomics, transcriptomics, proteomics, metabolomics, and phenomics. These biotechnological advances have modernized crop breeding and opened new horizons for developing crop varieties with improved traits. The genomes of several crop species are sequenced, and a huge number of genes associated with crucial economic traits have been identified. These identified genes not only provide insights into the understanding of regulatory mechanisms of crop traits but also decipher practical grounds to assist in the molecular breeding of crops. This review discusses the potential of omics technologies for the acquisition of biological information and mining of the genes associated with important agronomic traits in important food and fiber crops, such as wheat, rice, maize, potato, tomato, cassava, and cotton. Different functional genomics approaches for the validation of these important genes are also highlighted. Furthermore, a list of genes discovered by employing omics approaches is being represented as potential targets for genetic modifications by the latest genome engineering methods for the development of climate-resilient crops that would in turn provide great impetus to secure global food security.

Improving the monitoring of root zone soil salinity under vegetation cover conditions by combining canopy spectral information and crop growth parameters

Soil salinization is one of the main causes of land degradation in arid and semi-arid areas. Timely and accurate monitoring of soil salinity in different areas is a prerequisite for amelioration. Hyperspectral technology has been widely used in soil salinity monitoring due to its high efficiency and rapidity. However, vegetation cover is an inevitable interference in the direct acquisition of soil spectra during crop growth period, which greatly limits the monitoring of soil salinity by remote sensing. Due to high soil salinity could lead to difficulty in plants' water absorption, and inhibit plant dry matter accumulation, a method for monitoring root zone soil salinity by combining vegetation canopy spectral information and crop aboveground growth parameters was proposed in this study. The canopy spectral information was acquired by a spectroradiometer, and then variable importance in projection (VIP), competitive adaptive reweighted sampling (CARS), and random frog algorithm (RFA) were used to extract the salinity spectral features in cotton canopy spectrum. The extracted features were then used to estimate root zone soil salinity in cotton field by combining with cotton plant height, aboveground biomass, and shoot water content. The results showed that there was a negative correlation between plant height/aboveground biomass/shoot water content and soil salinity in 0-20, 0-40, and 0-60 cm soil layers at different growth stages of cotton. Spectral feature selection by the three methods all improved the prediction accuracy of soil salinity, especially CARS. The prediction accuracy based on the combination of spectral features and cotton growth parameters was significantly higher than that based on only spectral features, with R² increasing by 10.01%, 18.35%, and 29.90% for the 0-20, 0-40, and 0-60 cm soil layer, respectively. The model constructed based on the first derivative spectral preprocessing, spectral feature selection by CARS, cotton plant height, and shoot water content had the highest accuracy for each soil layer, with R² of 0.715,0.769, and 0.742 for the 0-20, 0-40, 0-60 cm soil layer, respectively. Therefore, the method by combining cotton canopy hyperspectral data and plant growth parameters could significantly improve the prediction accuracy of root zone soil salinity under vegetation cover conditions. This is of great significance for the amelioration of saline soil in salinized farmlands arid areas.

Genomic Dynamics and Functional Insights under Salt Stress in Gossypium hirsutum L

The changing climate is intensifying salt stress globally. Salt stress is a menace to cotton crop quality and yield. The seedling, germination, and emergence phases are more prone to the effects of salt stress than other stages. Higher levels of salt can lead to delayed flowering, a reduced number of fruiting positions, shedding of fruits, decreased boll weight, and yellowing of fiber, all of which have an adverse effect on the yield and quality of the seed cotton. However, sensitivity toward salt stress is dependent on the salt type, cotton growth phase, and genotype. As the threat of salt stress continues to grow, it is crucial to gain a comprehensive understanding of the mechanisms underlying salt tolerance in plants and to identify potential avenues for enhancing the salt tolerance of cotton. The emergence of marker-assisted selection, in conjunction with next-generation sequencing technologies, has streamlined cotton breeding efforts. This review begins by providing an overview of the causes of salt stress in cotton, as well as the underlying theory of salt tolerance. Subsequently, it summarizes the breeding methods that utilize marker-assisted selection, genomic selection, and techniques for identifying elite salt-tolerant markers in wild species or mutated materials. Finally, novel cotton breeding possibilities based on the approaches stated above are presented and debated.

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

Soil salinization is one of the main abiotic stresses affecting cotton yield and planting area. Potassium application has been proven to be an important strategy to reduce salt damage in agricultural production. However, the mechanism of potassium regulating the salt adaptability of cotton has not been fully elucidated. In the present research, the appropriate potassium application rate for alleviating salt damage of cotton based on different K⁺/Na⁺ ratios we screened, and a gene co-expression network based on weighted gene co-expression network analysis (WGCNA) using the transcriptome data sets treated with CK (0 mM NaCl), S (150 mM NaCl), and SK8 (150 mM NaCl + 9.38 mM K₂SO₄) was constructed. In this study, four key modules that are highly related to potassium regulation of cotton salt tolerance were identified, and the mitogen-activated protein kinase (MAPK) signaling pathway, tricarboxylic acid (TCA) cycle and glutathione metabolism pathway were identified as the key biological processes and metabolic pathways for potassium to improve cotton root salt adaptability. In addition, 21 hub genes and 120 key candidate genes were identified in this study, suggesting that they may play an important role in the enhancement of salt adaptability of cotton by potassium. The key modules, key biological pathways and hub genes discovered in this study will provide a new understanding of the molecular mechanism of potassium enhancing salinity adaptability in cotton, and lay a theoretical foundation for the improvement and innovation of high-quality cotton germplasm.

Integrated Transcriptome and Metabolome Analysis of Rice Leaves Response to High Saline-Alkali Stress

Rice (Oryza sativa) is one of the most important crops grown worldwide, and saline-alkali stress seriously affects the yield and quality of rice. It is imperative to elucidate the molecular mechanisms underlying rice response to saline-alkali stress. In this study, we conducted an integrated analysis of the transcriptome and metabolome to elucidate the effects of long-term saline-alkali stress on rice. High saline-alkali stress (pH > 9.5) induced significant changes in gene expression and metabolites, including 9347 differentially expressed genes (DEGs) and 693 differentially accumulated metabolites (DAMs). Among the DAMs, lipids and amino acids accumulation were greatly enhanced. The pathways of the ABC transporter, amino acid biosynthesis and metabolism, glyoxylate and dicarboxylate metabolism, glutathione metabolism, TCA cycle, and linoleic acid metabolism, etc., were significantly enriched with DEGs and DAMs. These results suggest that the metabolites and pathways play important roles in rice's response to high saline-alkali stress. Our study deepens the understanding of mechanisms response to saline-alkali stress and provides references for molecular design breeding of saline-alkali resistant rice.

Trehalose alleviates salt tolerance by improving photosynthetic performance and maintaining mineral ion homeostasis in tomato plants

Trehalose (Tre), which was an osmoprotective or stabilizing molecule, played a protective role against different abiotic stresses in plants and showed remarkable perspectives in salt stress. In this study, the potential role of Tre in improving the resistance to salt stress in tomato plants was investigated. Tomato plants (Micro Tom) were treated with Hoagland nutrient solution (CK), 10 mM Tre (T), 150 mM sodium chloride (NaCl, S), and 10 mM Tre+150 mM NaCl (S+T) for 5 days. Our results showed that foliar application of Tre alleviated the inhibition of tomato plant growth under salt stress. In addition, salt stress decreased the values of net photosynthetic rate (Pn, 85.99%), stomata conductance (gs, 57.3%), and transpiration rate (Tr, 47.97%), but increased that of intercellular carbon dioxide concentration (Ci, 26.25%). However, exogenous application of Tre significantly increased photosynthetic efficiency, increased the activity of Calvin cycle enzymes [ribulose diphosphate carboxylase/oxygenase (Rubisco), fructose-1,6-bisphosphate aldolase (FBA), fructose-1, 6-bisphosphatase (FBPase), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and transketolase (TK)], up-regulated the expression of genes encoding enzymes, induced stomatal opening, and alleviated salt-induced damage to the chloroplast membrane and structure. In the saline environment, photosynthetic electron transport was restricted, resulting the J-I-P phase to decrease. At the same time, the absorption, capture, and transport energies per excited cross-section and per active reaction center decreased, and the dissipation energy increased. Conversely, Tre reversed these values and enhanced the photosystem response to salt stress by protecting the photosynthetic electron transport system. In addition, foliage application with Tre significantly increased the potassium to sodium transport selectivity ratio (S _K-Na ) by 16.08%, and increased the levels of other ions to varying degrees. Principal component analysis (PCA) analysis showed that exogenous Tre could change the distribution of elements in different organs and affect the expressions of SlSOS1, SlNHX, SlHKT1.1, SlVHA, and SlHA-A at the transcriptional level under salt stress, thereby maintaining ion homeostasis. This study demonstrated that Tre was involved in the process of mitigating salt stress toxicity in tomato plants and provided specific insights into the effectiveness of Tre in mediating salt tolerance.

Transcriptome and Metabolome Analysis of Upland Cotton (Gossypium hirsutum) Seed Pretreatment with MgSO4 in Response to Salinity Stress

Upland cotton (Gossypium hirsutum) is a salt-tolerant crop that can withstand high salinity levels without showing signs of harm to the plant. However, the plant is more prone to salinity stress at the germination stage and a poor germination as well as poor crop stand lead to a weak productivity. It is possible to obtain a comprehensive picture of the cotton seedling germination and establishment against salt stress by examining dynamic changes in the transcriptomic and metabolomic profiles. The reported study employed a pretreatment of cotton seeds by soaking them in 0.2% Magnesium Sulphate (MgSO₄) solution at room temperature for 4, 8, and 12 h. The analysis of variance based on the studied traits emergence rate, above and underground plant parts' fresh weight measured, displayed significant differences of the three treatments compared with the control. A total of 28,801 and 264 differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were discovered to code for biological processes such as response to salt stress, cellular response to salt stress, abscisic acid receptor PYR/PYL, regulation of seed growth and germination, and auxin-activated signaling pathways. A large amount of ethylene-responsive transcription factors (ERF) was identified (1235) as differentially expressed, followed by bHLH (252), WRKY (96), MYB (202), GATA (81), RABA (64), DIVARICATA (28), and MADs-box (26) in treated seedling samples. Functional enrichment analysis revealed the significant roles in the hormones and signal transduction, carbohydrates metabolism, and biosynthesis of amino acids, promoting salt stress tolerance. Our results indicated positive effects of MgSO₄ at 4 h treatment on seedling germination and growth, seemingly by activating certain growth-regulating enzymes (auxins, gibberellins, jasmonates, abscisic acid, and salicylic acid) and metabolites (phenolic acids, flavonoids, and akaloids). Such pretreatment of MgSO₄ on seeds would be beneficial in future cotton management under saline conditions to enhance good crop stand and productivity.

Comparative Ionomics and Metabolic Responses and Adaptive Strategies of Cotton to Salt and Alkali Stress

Soil salinization and alkalization severely inhibit agriculture. However, the response mechanisms of cotton to salt stress or alkali stress are unclear. Ionomics and metabolomics were used to investigate salt and alkali stresses in cotton roots and leaves. Compared with the control, salt-treated and alkali-treated cotton plants showed 51.8 and 53.0% decreases in biomass, respectively. Under salt stress, the concentration of N decreased in roots but increased in leaves, and the concentrations of P and K increased in roots but decreased in leaves. Salt stress inhibited Ca, B, N, and Fe uptake and Mg, K, P, S, and Cu transport, but promoted Mo, Mn, Zn, Mg, K, P, S, and Cu uptake and Mo, Mn, Zn, B, N, and Fe transport. Under alkali stress, the concentrations of N and P in roots and leaves decreased, while the concentrations of K in roots and leaves increased. Alkali stress inhibited P, Ca, S, N, Fe, and Zn uptake and N, P, Mg and B transport, but promoted K, Mn, Cu, Mo, Mg, and B uptake and K, Mn, Cu, Mo, Fe, and Zn transport. Under salt stress in the leaves, 93 metabolites increased, mainly organic acids, amino acids, and sugars, increased in abundance, while 6 decreased. In the roots, 72 metabolites increased, mainly amino acids, organic acids, and sugars, while 18 decreased. Under alkali stress, in the leaves, 96 metabolites increased, including organic acids, amino acids, and sugars, 83 metabolites decreased, including organic acids, amino acids, and sugars; In the roots, 108 metabolites increased, including organic acids, amino acids, and sugars. 83 metabolites decreased, including organic acids and amino acids. Under salt stress, cotton adapts to osmotic stress through the accumulation of organic acids, amino acids and sugars, while under alkali stress, osmoregulation was achieved via inorganic ion accumulation. Under salt stress, significant metabolic pathways in the leaves and roots were associated with amino acid and organic acid metabolism, sugar metabolism was mainly used as a source of energy, while under alkali stress, the pathways in the leaves were related to amino acid and linoleic acid metabolism, β-Oxidation, TCA cycle, and glycolysis were enhanced to provide the energy needed for life activities. Enhancing organic acid accumulation and metabolism in the roots is the key response mechanism of cotton to alkalinity.

Trehalose Alleviated Salt Stress in Tomato by Regulating ROS Metabolism, Photosynthesis, Osmolyte Synthesis, and Trehalose Metabolic Pathways

Trehalose plays a critical role in plant response to salinity but the involved regulatory mechanisms remain obscure. Here, this study explored the mechanism of exogenous trehalose-induced salt tolerance in tomato plants by the hydroponic test method. Our results indicated that 10 mM trehalose displayed remarkable plant biomass by improving growth physiology, which were supported by the results of chlorophyll fluorescence and rapid light-response curve. In the salinity environment, trehalose + NaCl treatment could greatly inhibit the decrease of malondialdehyde level, and it increases the contents of other osmotic substances, carbohydrates, K⁺, and K⁺/Na⁺ ratio. Meanwhile, trehalose still had similar effects after recovery from salt stress. Furthermore, trehalose pretreatment promoted trehalose metabolism; significantly increased the enzymatic activity of the trehalose metabolic pathway, including trehalose-6-phosphate synthase (TPS), trehalose-6-phosphate phosphatase (TPP), and trehalase (TRE); and upregulated the expression of SlTPS1, SlTPS5, SlTPS7, SlTPPJ, SlTPPH, and SlTRE under saline conditions. However, the transcriptional levels of SlTPS1, SlTPS5, and SlTPS7 genes and the activity of TPS enzyme were reversed after recovery. In addition, we found that hydrogen peroxide (H₂O₂) and superoxide anion (O₂ ^-) were accumulated in tomato leaves because of salt stress, but these parameters were all recovered by foliar-applied trehalose, and its visualization degree was correspondingly reduced. Antioxidant enzyme activities (SOD, POD, and CAT) and related gene expression (SlCu/Zn-SOD, SlFe-SOD, SlMn-SOD, SlPOD, and SlCAT) in salt-stressed tomato leaves were also elevated by trehalose to counteract salt stress. Collectively, exogenous trehalose appeared to be the effective treatment in counteracting the negative effects of salt stress.

Ion homeostasis and Na+ transport-related gene expression in two cotton (Gossypium hirsutum L.) varieties under saline, alkaline and saline-alkaline stresses

The sensitivity of cotton to salt stress depends on the genotypes and salt types. Understanding the mechanism of ion homeostasis under different salt stresses is necessary to improve cotton performance under saline conditions. A pot experiment using three salt stresses saline stress (NaCl+Na2SO4), alkaline stress (Na2CO3+NaHCO3), and saline-alkaline stress (NaCl+Na2SO4+Na2CO3+NaHCO3) and two cotton varieties (salt-tolerant variety L24 and salt-sensitive variety G1) was conducted. The growth, ion concentrations, and Na+ transport-related gene expression in the cotton varieties were determined. The inhibitory effects of saline-alkaline stress on cotton growth were greater than that of either saline stress or alkaline stress alone. The root/shoot ratio under alkaline stress was significantly lower than that under saline stress. The salt-tolerant cotton variety had lower Na and higher K concentrations in the leaves, stems and roots than the salt-sensitive variety under different salt stresses. For the salt-sensitive cotton variety, saline stress significantly inhibited the absorption of P and the transport of P, K, and Mg, while alkaline stress and saline-alkaline stress significantly inhibited the uptake and transport of P, K, Ca, Mg, and Zn. Most of the elements in the salt-tolerant variety accumulated in the leaves and stems under different salt stresses. This indicated that the salt-tolerant variety had a stronger ion transport capacity than the salt-sensitive variety under saline conditions. Under alkaline stress and salt-alkaline stress, the relative expression levels of the genes GhSOS1, GhNHX1 and GhAKT1 in the salt-tolerant variety were significantly higher than that in the salt-sensitive variety. These results suggest that this salt-tolerant variety of cotton has an internal mechanism to maintain ionic homeostasis.

Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants

Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.

IRONing out stress problems in crops: a homeostatic perspective

Iron (Fe) is essential for plant growth and therefore plays a key role in influencing crop productivity worldwide. Apart from its central role in chlorophyll biosynthesis and oxidative phosphorylation (electron transfer), it is an important constituent of many enzymes involved in primary metabolism. Fe has different accessibilities to the roots in the rhizosphere depending upon whether it is ferrous (soluble) or ferric (insoluble) oxidation stages, which in turn, determine two kinds of Fe uptake strategies employed by the plants. The reduction strategy is exclusively found in non-graminaceous plants wherein the ferrous Fe²⁺ is absorbed and translocated from the soil through specialized transporters. In contrast, the chelation strategy (widespread in graminaceous plants) relies on the formation of Fe (III)-chelate complex as the necessary requirement of Fe uptake. Once inside the cell, Fe is translocated, compartmentalized and stored through a common set of physiological processes involving many transporters and enzymes whose functions are controlled by underlying genetic components, so that a fine balance of Fe homeostasis is maintained. Recently, molecular and mechanistic aspects of the process involving the role of transcription factors, signaling components, and cis-acting elements have been obtained, which has enabled a much better understanding of its ecophysiology. This mini-review summarizes recent developments in our understanding of Fe transport in higher plants with particular emphasis on crops in the context of major agronomically important abiotic stresses. It also highlights outstanding questions on the regulation of Fe homeostasis and lists potentially useful genes/regulatory pathways that may be useful for subsequent crop improvement under the stresses discussed through either conventional or transgenic approaches.

Application of compound material alleviates saline and alkaline stress in cotton leaves through regulation of the transcriptome

BACKGROUND

Soil salinization and alkalinization are the main factors that affect the agricultural productivity. Evaluating the persistence of the compound material applied in field soils is an important part of the regulation of the responses of cotton to saline and alkaline stresses.

RESULT

To determine the molecular effects of compound material on the cotton's responses to saline stress and alkaline stress, cotton was planted in the salinized soil (NaCl 8 g kg^- 1) and alkalized soil (Na₂CO₃ 8 g kg^- 1) after application of the compound material, and ion content, physiological characteristics, and transcription of new cotton leaves at flowering and boll-forming stage were analyzed. The results showed that compared with saline stress, alkaline stress increased the contents of Na⁺, K⁺, SOD, and MDA in leaves. The application of the compound material reduced the content of Na⁺ but increased the K⁺/Na⁺ ratio, the activities of SOD, POD, and CAT, and REC. Transcriptome analysis revealed that after the application of the compound material, the Na⁺/H⁺ exchanger gene in cotton leaves was down-regulated, while the K⁺ transporter, K⁺ channel, and POD genes were up-regulated. Besides, the down-regulation of genes related to lignin synthesis in phenylalanine biosynthesis pathway had a close relationship with the ion content and physiological characteristics in leaves. The quantitative analysis with PCR proved the reliability of the results of RNA sequencing.

CONCLUSION

These findings suggest that the compound material alleviated saline stress and alkaline stress on cotton leaves by regulating candidate genes in key biological pathways, which improves our understanding of the molecular mechanism of the compound material regulating the responses of cotton to saline stress and alkaline stress.