A Glycine max sodium/hydrogen exchanger enhances salt tolerance through maintaining higher Na+ efflux rate and K+/Na+ ratio in Arabidopsis

Integrated transcriptomics and metabolomics elucidate additive inhibitory effects of combined salinity-waterlogging stress on soybean growth and metabolic adaptations

Salinity and waterlogging are major abiotic stresses constraining soybean productivity, with their combined effects often surpassing individual impacts. However, the nature of these combined effects-whether additive, synergistic, or antagonistic-remains unclear. In this study, we quantitatively demonstrated that combined salinity-waterlogging stress exerts additive inhibitory effects on soybean (Glycine max L. cv. Qihuang 34) growth, surpassing individual stresses without reaching synergistic severity. Physiological analysis revealed additive inhibition, as reflected by a 38.8 % reduction in leaf area, 36.8 % decrease in dry matter accumulation, and a 63.4 % decline in net photosynthetic rate under combined stress conditions, closely aligning with theoretical additive predictions (e.g., observed vs. predicted values: 38.8 % vs. 40.8 % for leaf area; 36.8 % vs. 37.7 % for biomass). Integrated transcriptomic and metabolomic analysis identified hypoxia-induced ATP depletion as a key driver, disrupting Na+/K+ homeostasis (277.9 % increase in Na+/K+ ratio) despite upregulation of key ion transporters (SOS1: +84.3 %, NHX1a: +54.0 % and NHX1b: +68.7 %). Additive activation of flavonoid biosynthesis genes (CHI, CHR) and metabolites (prunin, chalcone 2'-O-glucoside) mitigated oxidative damage through cumulative metabolite accumulation rather than synergistic interactions. Downregulation of photosynthesis-related genes (e.g., PsbO, PsaA) and ATP synthesis collapse explained energy deficits. Crucially, cutin/suberine biosynthesis emerged as a novel adaptive signature under combined stress. This study provides mechanistic insights into additive salt-waterlogging interactions, identifying targets for stress-resilient soybean breeding.

GmAKT1-mediated K+ absorption positively modulates soybean salt tolerance by GmCBL9-GmCIPK6 complex

Soybean is one of the most important crops in the world. However, salt stress poses a major challenge to soybean growth and productivity. Therefore, unravelling the complex mechanisms governing salt tolerance in soybean is imperative for molecular breeding of salt-tolerant varieties to improve yield. Maintaining intracellular Na+/K+ homeostasis is one of the key factors for plant salt tolerance. Although some salt tolerance mechanisms involving Na+ exclusion have been well identified in plants, few studies have been conducted on how K+ influx controls soybean salt tolerance. Here, we characterized the function of soybean K+ channel gene GmAKT1 and identified GmCBL9-GmCIPK6 complex, which modulated GmAKT1-mediated K+ uptake under salt stress. Functional studies found that soybean lines GmAKT1 overexpressing increased K+ content and promoted salt tolerance, while CRISPR/Cas9-mediated disruption of GmAKT1 soybean lines decreased the K+ content and showed salt sensitivity. Furthermore, we identified that GmCIPK6 interacted with GmAKT1 and GmCBL9 interacted with GmCIPK6. In addition, Mn2+-Phos-tag assays proved that GmCIPK6 could phosphorylate GmAKT1. This collaborative activation of the GmCBL9-GmCIPK6-GmAKT1 module promoted K+ influx and enhanced soybean salt tolerance. Our findings reveal a new molecular mechanism in soybeans under salt stress and provide insights for cultivating new salt-tolerant soybean varieties by molecular breeding.

Molecular Regulatory Network of Soybean Responses to Abiotic Stress

Global climate change exacerbates the impact of environmental stressors such as drought, salinity and extreme temperatures on crop growth and grain yield, endangering the sustainability of the food supply. Soybean (Glycine Max [L.] Merr.) is an important legume crop and plays a crucial role in the global food supply chain and food security, and contributes the substantial protein content relative to other crops. However, soybean yield stability is critically dependent on the plant's adaptive responses to abiotic stress factors, particularly drought, salinity and temperature extremes, which primarily impact its growth and productivity. Recently, various molecular techniques, including genetic engineering, transcriptomics, transcription factor analysis, CRISPR/Cas9, and conventional methods, have been employed to elucidate the molecular mechanisms of soybean responses to environmental stresses for the breeding of tolerant cultivars of soybean. This review summarises recent advances in dissecting the genetic factors and networks that contribute to soybean abiotic stress tolerance through diverse strategies. We also discuss future challenges and opportunities for the development of climate-resilient soybean varieties. Consequently, the updated review will serve as a comprehensive guideline for researchers investigating the genetic mechanism of abiotic stress in soybean.

The origins and spread of the opium poppy (Papaver somniferum L.) revealed by genomics and seed morphometrics

The opium poppy (Papaver somniferum L.) is one of the most important plants in human history. It is the main source of opiates used as analgesic medicines or psychotropic drugs, the latter related to addiction problems, illegal trafficking and geopolitical issues. Poppyseed is also used in cooking. The prehistoric origins, domestication and cultivation spread of the opium poppy remain unresolved. Traditionally, Papaver setigerum has been considered the wild ancestor with early cultivation presumed to have occurred in the Western Mediterranean region, where setigerum is autochthonous. Other theories suggest that somniferum may have been introduced by Southwest Asian early farmers as a weed. To investigate these hypotheses, we analysed 190 accessions from 15 Papaver species using genotype-by-sequencing and geometric morphometric (GMM) techniques. Our analysis revealed that setigerum is the only taxa genetically close to somniferum and can be better described as a subspecies. The domesticated plants are, however, distinct from setigerum. Additionally, GMM analysis of seeds also revealed morphological differences between setigerum and somniferum. Some phenotypically wild setigerum accessions exhibited intermediate genetic features, suggesting introgression events. Two major populations were found in somniferum and, to some extent, these correspond to differences in seed form. These two populations may reflect recent attempts to breed varieties rich in opiates, as opposed to varieties used for poppyseed production. This study supports the idea that opium poppy cultivation began in the Western Mediterranean, with setigerum as the wild progenitor, although some wild varieties are likely to be feral forms, which can confound domestication studies.This article is part of the theme issue 'Unravelling domestication: multi-disciplinary perspectives on human and non-human relationships in the past, present and future'.

Genome-Wide Identification of the Cation/Proton Antiporter (CPA) Gene Family and Expression Pattern Analysis Under Salt Stress in Winter Rapeseed (Brassica rapa L.)

The CPA gene family regulates ionic balance and pH homeostasis in cells, significantly contributing to plant stress tolerance. In this study, a total of 63 BrCPA gene family members were identified in the whole genome of Brassica rapa L. (B. rapa), and the three subfamily members were BrNHX (9), BrKEA (15), and BrCHX (39), respectively. The members of the BrCPA gene family encoded 303-1259 amino acids, with molecular weights in the range of 32,860.39~139,884.73 kDa, distributed on 10 chromosomes, and contained 17 conserved motifs, BrNHX and BraKEA, and the BrCPA gene family members had the same molecular weights on 10 chromosomes and contain 17 conserved motifs. The BrNHX and BraKEA subfamilies have more exons than the BrCHX subfamily. An analysis of promoter cis-acting elements in the BrCPA gene showed that members of this gene family contain TC-rich, LTR, MBS, and ARE stress response elements. In addition, transcriptome analysis revealed the expression of CPA genes in B. rapa under salt stress. The selected genes were verified by RT-qPCR. By detecting the Na+ and K+ flow rates in the root and chloroplast cells of salt-tolerant and salt-sensitive varieties after salt treatment, it was found that the rate of Na+ and K+ efflux from the root and chloroplast cells of salt-sensitive varieties was significantly higher than that of salt-tolerant varieties. This investigation marks the first systematic identification of the CPA gene family in B. rapa. This study further explores its expression patterns and the efflux rates of Na+ and K+ across salt-tolerant varieties, providing a theoretical basis for understanding the role of the CPA gene family in the salt stress response of B. rapa.

Growth and physiological characteristics of forage bermudagrass in response to salt stress

BACKGROUND

Bermudagrass (Cynodon dactylon) has a long history as an excellent forage grass, and salt stress will inhibit its growth and development. In order to minimize the damage, it is necessary to continuously develop innovative technologies and management strategies.

RESULTS

This study evaluated the salt tolerance of new Bermudagrass strains 'FB2019R101' and 'FB2019R105' compared to commercial varieties 'Wrangler' and 'A12359' under simulated soil salinity conditions through seawater irrigation. Through correlation analysis of growth, physiological, and nutritional indicators, and principal component analysis, core indicators and weights for salt tolerance evaluation were identified. The salt-tolerant varieties were 'FB2019R101' and 'FB2019R105'. Under salinity stress, the plants of Bermudagrass varieties with salt tolerance suffered less damage as a whole, which could better regulate the osmotic balance inside and outside cells, accumulate more nutrients and have stronger ability to resist salt damage. The expression level of salt-tolerant variety CdCINV1, CdSPS1, CdSUS5, and CdSWEET6 was up-regulated under salt stress. CdCINV1, CdSPS1, CdSUS5 can promote the transformation of sucrose into glucose and fructose in Bermudagrass under salt stress, and CdSWEET6 can promote the accumulation of fructose.

CONCLUSIONS

'FB2019R101' and 'FB2019R105' exhibited higher salt tolerance, with minimal impact on their biomass, physiological, and nutritional indicators under salt stress. The comprehensive evaluation revealed a salt tolerance ranking of 'FB2019R105' > 'FB2019R101' > 'Wrangler' > 'A12359'. This study provides significant reference for the bioremediation of coastal saline soils and promotes research on the application of Bermudagrass under salt stress conditions. CdCINV1, CdSPS1, CdSUS5, and CdSWEET6 can improve the salt tolerance of plants by regulating the changes of carbohydrates.

Enhancing Soybean Salt Tolerance with GSNO and Silicon: A Comprehensive Physiological, Biochemical, and Genetic Study

Soil salinity is a major global challenge affecting agricultural productivity and food security. This study explores innovative strategies to improve salt tolerance in soybean (Glycine max), a crucial crop in the global food supply. This study investigates the synergistic effects of S-nitroso glutathione (GSNO) and silicon on enhancing salt tolerance in soybean (Glycine max). Two soybean cultivars, Seonpung (salt-tolerant) and Cheongja (salt-sensitive), were analyzed for various physiological, biochemical, and genetic traits under salt stress. The results showed that the combined GSNO and Si treatment significantly improved several key traits, including plant height, relative water content, root development, nodule numbers, chlorophyll content, and stomatal aperture, under both control and salt stress conditions. Additionally, this treatment optimized ion homeostasis by enhancing the Na/K ratio and Ca content, while reducing damage markers such as electrolyte leakage, malondialdehyde, and hydrogen peroxide. The stress-responsive compounds, including proline, ascorbate peroxidase, and water-soluble proteins, were elevated under stress conditions, indicating improved tolerance. Gene expression analysis revealed significant upregulation of genes such as GmNHX1, GmSOS2, and GmAKT1, associated with salt stress response, while GmNIP2.1, GmNIP2.2, and GmLBR were downregulated in both varieties. Notably, the salt-sensitive variety Cheongja exhibited higher electrolyte leakage and oxidative damage compared to the salt-tolerant Seonpung. These findings suggest that the combination of GSNO and silicon enhances salt tolerance in soybean by improving physiological resilience, ion homeostasis, and stress-responsive gene expression.

Evaluation of drought and salinity tolerance potentials of different soybean genotypes based upon physiological, biochemical, and genetic indicators

The present study has evaluated different soybean genotypes to understand the salt and drought tolerance mechanisms based on physiological traits (photosynthesis, stomatal conductance, chlorophyll, and cell membrane stability), antioxidant enzymes (superoxide dismutase, catalase, and peroxidase), reactive oxygen species (H2O2 and O2 •-), osmolytes (glycine betaine, proline, and Na+/K+), plant water relations (relative water content, water potential, and solute potential) and expression of related genes (GmCAT1, GmPOD1, GmSOD, GmP5CS, GmNHX1, GmAKT1, GmDREB1, and GmARF1). The experiment was conducted in a two-factorial arrangement using randomized complete block design (RCBD) with genotypes as one factor and salt, drought, and control treatments as the other factor. All physiological traits, relative water content, and water potential decreased significantly in all soybean genotypes due to individual and combined treatments of drought and salt stress, with significantly less decrease in soybean genotypes G4620RX, DM45X61, and NARC-21. Besides that, the activity of antioxidant enzymes, production of ROS, accumulation of osmolytes, solute potential, and Na+/K+ ratio were increased significantly in all soybean genotypes under salt and water deficit conditions. As a whole, the soybean genotypes G4620RX, DM45X61, and NARC-21 showed the maximum enzymatic activity with less increase in ROS and Na+/K+ in addition to a high accumulation of osmolytes and an increase in solute potential. Correspondingly, the genotypes exhibiting high physiological and biochemical tolerance to drought and salt stresses showed the high expression of genes imparting the stress tolerance. Moreover, correlation, heatmap, and principal component analysis further confirmed the varying physiological and biochemical responses of all soybean genotypes under individual and combined applications of drought and salinity stresses. Overall, the present study confirmed that plants opt for the integrated physiological, biochemical, and genetic approaches to counteract the harmful effects of environmental stresses.

CRISPR-Cas9-mediated editing of GmARM improves resistance to multiple stresses in soybean

The growth and development of soybean plants can be affected by both abiotic and biotic stressors, such as saline-alkali stress and Phytophthora root rot. In this study, we identified a stress-related gene-GmARM-whose promoter contained several hormone-response and stress-regulatory elements, including ABRE, TCA element, STRE, and MBS. qRT-PCR analysis showed that the expression of GmARM was the highest in seeds at 55 days after flowering. Furthermore, this gene was upregulated after exposure to saline-alkali stress and Phytophthora root rot infection at the seedling stage. Thus, we generated GmARM mutants using the CRISPR-Cas9 system to understand the role of this gene in stress response. T3 plants showed significantly improved salt tolerance, alkali resistance, and disease resistance, with a significantly higher survival rate than the wildtype plants. Moreover, mutations in GmARM affected the expression of related stress-resistance genes, indicating that GmARM mutants achieved multiple stress tolerance. Therefore, this study provides a foundation for further exploration of the genes involved in resistance to multiple stresses in soybean that can be used for breeding multiple stress-resistance soybean varieties.

Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits

Actinidia arguta, the most widely distributed Actinidia species and the second cultivated species in the genus, can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit, rapid softening, and excellent cold tolerance. Adaptive evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still unclear. Here, we generated a chromosome-scale genome assembly of an autotetraploid male A. arguta accession. The genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 pseudo-chromosomes. Resequencing and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups, Southern and Northern, which first diverged 12.9 million years ago. A. arguta underwent two prominent expansions and one demographic bottleneck from the mid-Pleistocene climate transition to the late Pleistocene. Population genomics studies using paleoclimate data enabled us to discern the evolution of the species' adaptation to different historical environments. Three genes (AaCEL1, AaPME1, and AaDOF1) related to flesh softening were identified by multi-omics analysis, and their ability to accelerate flesh softening was verified through transient expression assays. A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome (Chr3) or autosomal chromosomes showed biased expression during stamen or carpel development. This chromosome-level assembly of the autotetraploid A. arguta genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of A. arguta.

Weighted gene co-expression network analysis reveals hub genes regulating response to salt stress in peanut

Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. However, soil salinization becomes one of the main limiting factors of peanut production. Therefore, developing salt-tolerant varieties and understanding the molecular mechanisms of salt tolerance is important to protect peanut yield in saline areas. In this study, we selected four peanut varieties with contrasting response to salt challenges with T1 and T2 being tolerance and S1 and S2 being susceptible. High-throughput RNA sequencing resulted in more than 314.63 Gb of clean data from 48 samples. We identified 12,057 new genes, 7,971of which have functional annotations. KEGG pathway enrichment analysis of uniquely expressed genes in salt-tolerant peanut revealed that upregulated genes in the root are involved in the MAPK signaling pathway, fatty acid degradation, glycolysis/gluconeogenesis, and upregulated genes in the shoot were involved in plant hormone signal transduction and the MAPK signaling pathway. Na+ content, K+ content, K+/ Na+, and dry mass were measured in root and shoot tissues, and two gene co-expression networks were constructed based on weighted gene co-expression network analysis (WGCNA) in root and shoot. In this study, four key modules that are highly related to peanut salt tolerance in root and shoot were identified, plant hormone signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, flavonoid biosynthesis, carbon metabolism were identified as the key biological processes and metabolic pathways for improving peanut salt tolerance. The hub genes include genes encoding ion transport (such as HAK8, CNGCs, NHX, NCL1) protein, aquaporin protein, CIPK11 (CBL-interacting serine/threonine-protein kinase 11), LEA5 (late embryogenesis abundant protein), POD3 (peroxidase 3), transcription factor, and MAPKKK3. There were some new salt-tolerant genes identified in peanut, including cytochrome P450, vinorine synthase, sugar transport protein 13, NPF 4.5, IAA14, zinc finger CCCH domain-containing protein 62, beta-amylase, fatty acyl-CoA reductase 3, MLO-like protein 6, G-type lectin S-receptor-like serine/threonine-protein kinase, and kinesin-like protein KIN-7B. The identification of key modules, biological pathways, and hub genes in this study enhances our understanding of the molecular mechanisms underlying salt tolerance in peanuts. This knowledge lays a theoretical foundation for improving and innovating salt-tolerant peanut germplasm.

Zinc Oxide Nanoparticles Alleviate Salt Stress in Cotton (Gossypium hirsutum L.) by Adjusting Na+/K+ Ratio and Antioxidative Ability

Soil salinization poses a threat to the sustainability of agricultural production and has become a global issue. Cotton is an important cash crop and plays an important role in economic development. Salt stress has been harming the yield and quality of many crops, including cotton, for many years. In recent years, soil salinization has been increasing. It is crucial to study the mechanism of cotton salt tolerance and explore diversified materials and methods to alleviate the salt stress of cotton for the development of the cotton industry. Nanoparticles (NPs) are an effective means to alleviate salt stress. In this study, zinc oxide NPs (ZnO NPs) were sprayed on cotton leaves with the aim of investigating the intrinsic mechanism of NPs to alleviate salt stress in cotton. The results show that the foliar spraying of ZnO NPs significantly alleviated the negative effects of salt stress on hydroponic cotton seedlings, including the improvement of above-ground and root dry and fresh weight, leaf area, seedling height, and stem diameter. In addition, ZnO NPs can significantly improve the salt-induced oxidative stress by reducing the levels of MDA, H2O2, and O2- and increasing the activities of major antioxidant enzymes, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). Furthermore, RNA-seq showed that the foliar spraying of ZnO NPs could induce the expressions of CNGC, NHX2, AHA3, HAK17, and other genes, and reduce the expression of SKOR, combined with the CBL-CIPK pathway, which alleviated the toxic effect of excessive Na+ and reduced the loss of excessive K+ so that the Na+/K+ ratio was stabilized. In summary, our results indicate that the foliar application of ZnO NPs can alleviate high salt stress in cotton by adjusting the Na+/K+ ratio and regulating antioxidative ability. This provides a new strategy for alleviating the salt stress of cotton and other crops, which is conducive to the development of agriculture.

Analysis of Genetic Diversity in Adzuki Beans (Vigna angularis): Insights into Environmental Adaptation and Early Breeding Strategies for Yield Improvement

Adzuki beans are widely cultivated in East Asia and are one of the earliest domesticated crops. In order to gain a deeper understanding of the genetic diversity and domestication history of adzuki beans, we conducted Genotyping by Sequencing (GBS) analysis on 366 landraces originating from Korea, China, and Japan, resulting in 6586 single-nucleotide polymorphisms (SNPs). Population structure analysis divided these 366 landraces into three subpopulations. These three subpopulations exhibited distinctive distributions, suggesting that they underwent extended domestication processes in their respective regions of origin. Phenotypic variance analysis of the three subpopulations indicated that the Korean-domesticated subpopulation exhibited significantly higher 100-seed weights, the Japanese-domesticated subpopulation showed significantly higher numbers of grains per pod, and the Chinese-domesticated subpopulation displayed significantly higher numbers of pods per plant. We speculate that these differences in yield-related traits may be attributed to varying emphases placed by early breeders in these regions on the selection of traits related to yield. A large number of genes related to biotic/abiotic stress resistance and defense were found in most quantitative trait locus (QTL) for yield-related traits using genome-wide association studies (GWAS). Genomic sliding window analysis of Tajima's D and a genetic differentiation coefficient (Fst) revealed distinct domestication selection signatures and genotype variations on these QTLs within each subpopulation. These findings indicate that each subpopulation would have been subjected to varied biotic/abiotic stress events in different origins, of which these stress events have caused balancing selection differences in the QTL of each subpopulation. In these balancing selections, plants tend to select genotypes with strong resistance under biotic/abiotic stress, but reduce the frequency of high-yield genotypes to varying degrees. These biotic/abiotic stressors impact crop yield and may even lead to selection purging, resulting in the loss of several high-yielding genotypes among landraces. However, this also fuels the flow of crop germplasms. Overall, balancing selection appears to have a more significant impact on the three yield-related traits compared to breeder-driven domestication selection. These findings are crucial for understanding the impact of domestication selection history on landraces and yield-related traits, aiding in the improvement of adzuki bean varieties.

Genome-Wide Analysis of Cation/Proton Antiporter Family in Soybean (Glycine max) and Functional Analysis of GmCHX20a on Salt Response

Monovalent cation proton antiporters (CPAs) play crucial roles in ion and pH homeostasis, which is essential for plant development and environmental adaptation, including salt tolerance. Here, 68 CPA genes were identified in soybean, phylogenetically dividing into 11 Na+/H+ exchangers (NHXs), 12 K+ efflux antiporters (KEAs), and 45 cation/H+ exchangers (CHXs). The GmCPA genes are unevenly distributed across the 20 chromosomes and might expand largely due to segmental duplication in soybean. The GmCPA family underwent purifying selection rather than neutral or positive selections. The cis-element analysis and the publicly available transcriptome data indicated that GmCPAs are involved in development and various environmental adaptations, especially for salt tolerance. Based on the RNA-seq data, twelve of the chosen GmCPA genes were confirmed for their differentially expression under salt or osmotic stresses using qRT-PCR. Among them, GmCHX20a was selected due to its high induction under salt stress for the exploration of its biological function on salt responses by ectopic expressing in Arabidopsis. The results suggest that the overexpression of GmCHX20a increases the sensitivity to salt stress by altering the redox system. Overall, this study provides comprehensive insights into the CPA family in soybean and has the potential to supply new candidate genes to develop salt-tolerant soybean varieties.

Analysis of N6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sugar beet (Beta vulgaris)

Salinity is an important environmental factor in crop growth and development. N6-methyladenosine (m6A) is an essential epigenetic modification that regulates plant-environment interaction. Sugar beet is a major sugar-yielding crop that has a certain tolerance to salt, but the dynamic response elicited by the m6A modification of transcripts under salt stress remains unknown. In this study, sugar beet was exposed to 300 mM NaCl to investigate its physiological response to high salinity and transcriptome-wide m6A modification profile. After the salt treatment, 7737 significantly modified m6A sites and 4981 differentially expressed genes (DEGs) were identified. Among the 312 m6A-modified DEGs, 113 hypomethylated DEGs were up-regulated and 99 hypermethylated DEGs were down-regulated, indicating a negative correlation between m6A modification and gene expression. Well-known salt tolerance genes (e.g., sodium/hydrogen exchanger 1, choline monooxygenase, and nucleoredoxin 2) and phospholipid signaling pathway genes (phosphoinositol-specific phospholipase C, phospholipase D, diacylglycerol kinase 1, etc.) were also among the m6A-modified genes. Further analysis showed that m6A modification may regulate salt-tolerant related gene expression by controlling mRNA stability. Therefore, changes in m6A modification may negatively regulate the expression of the salt-resistant genes in sugar beet, at least in part by modulating the stability of the mRNA via demethylase BvAlkbh10B. These findings could provide a better understanding of the epigenetic mechanisms of salt tolerance in sugar beets and uncover new candidate genes for improving the production of sugar beets planted in high-salinity soil.

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.

Twenty years of mining salt tolerance genes in soybean

Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01383-3.

Integrated GWAS and transcriptomic analysis reveal the candidate salt-responding genes regulating Na+/K+ balance in barley (Hordeum vulgare L.)

Salt stress is one of the main abiotic stresses affecting crop yield and quality. Barley has strong salt tolerance, however, the underlying genetic basis is not fully clear, especially in the seedling stage. This study examined the ionic changes in barley core germplasms under the control and salt conditions. Genome-wide association study (GWAS) analysis revealed 54 significant SNPs from a pool of 25,342 SNPs distributed in 7 chromosomes (Chr) of the Illumina Barley 50K SNP array. These SNPs are associated with ion homeostasis traits, sodium (Na⁺) and potassium (K⁺) content, and Na⁺/K⁺ ratio representing five genomic regions on Chr 2, 4, 5, 6, and 7 in the leaves of worldwide barley accessions. And there are 3 SNP peaks located on the Chr 4, 6, and 7, which could be the "hot spots" regions for mining and identifying candidate genes for salt tolerance. Furthermore, 616 unique candidate genes were screened surrounding the significant SNPs, which are associated with transport proteins, protein kinases, binding proteins, and other proteins of unknown function. Meanwhile, transcriptomic analysis (RNA-Seq) was carried out to compare the salt-tolerant (CM72) and salt-sensitive (Gairdner) genotypes subjected to salt stress. And there was a greater accumulation of differentially expressed genes(DEGs) in Gairdner compared to CM72, mainly enriched in metabolic pathway, biosynthesis of secondary metabolites, photosynthesis, signal transduction,emphasizing the different transcriptional response in both genotypes following salt exposure. Combined GWAS and RNA-Seq analysis revealed 5 promising salt-responding genes (PGK2, BASS3, SINAT2, AQP, and SYT3) from the hot spot regions, which were verified between the salt-tolerant and salt-sensitive varieties by qRT-PCR. In all, these results provide candidate SNPs and genes responsible for salinity responding in barley, and a new idea for studying such genetic basis in similar crops.

Characterization of hexokinase gene family members in Glycine max and functional analysis of GmHXK2 under salt stress

Hexokinase (HXK) is a bifunctional enzyme involved in carbohydrate metabolism and sugar signal sensing. HXK gene family has been extensively discussed in many species, while the detailed investigations of the family in Glycine max have yet to be reported. In this study, 17 GmHXK genes (GmHXKs) were identified in the G. max genome and the features of their encoded proteins, conserved domains, gene structures, and cis-acting elements were systematically characterized. The GmHXK2 gene isolated from G. max was firstly constructed into plant expression vector pMDC83 and then transformed with Agrobacterium tumefaciens into Arabidopsis thaliana. The expression of integrated protein was analyzed by Western Blotting. Subcellular localization analysis showed that the GmHXK2 was located on both vacuolar and cell membrane. Under salt stress, seedlings growth was significantly improved in Arabidopsis overexpressing GmHXK2 gene. Furthermore, physiological indicators and expression of salt stress responsive genes involved in K⁺ and Na⁺ homeostasis were significantly lower in GmHXK2-silenced soybean seedlings obtained by virus-induced gene silencing (VIGS) technique under salt stress compared with the control plants. Our study showed that GmHXK2 gene played an important role in resisting salt stress, which suggested potential value for the genetic improvement of abiotic resistant crops.

Transcriptomic and functional characterization reveals CsHAK5;3 as a key player in K+ homeostasis in grafted cucumbers under saline conditions

Grafting can improve the salt tolerance of many crops. However, critical genes in scions responsive to rootstock under salt stress remain a mystery. We found that pumpkin rootstock decreased the content of Na⁺ by 70.24 %, increased the content of K⁺ by 25.9 %, and increased the K⁺/Na⁺ ratio by 366.0 % in cucumber scion leaves. RNA-seq analysis showed that ion transport-related genes were the key genes involved in salt stress tolerance in grafted cucumber. The identification and analysis of the expression of K⁺ transporter proteins in cucumber and pumpkin revealed six and five HAK5 members, respectively. The expression of CsHAK5;3 in cucumber was elevated in different graft combinations under salt stress and most notably in cucumber scion/pumpkin rootstock. CsHAK5;3 was localized to the plasma membrane, and a yeast complementation assay revealed that it can transport K⁺. CsHAK5;3 knockout in hairy root mutants decreased the K⁺ content of leaves (45.6 %) and roots (50.3 %), increased the Na⁺ content of leaves (29.3 %) and roots (34.8 %), and decreased the K⁺/Na⁺ ratio of the leaves (57.9 %) and roots (62.9 %) in cucumber. However, CsHAK5;3 overexpression in hairy roots increased the K⁺ content of the leaves (31.2 %) and roots (38.3 %), decreased the Na⁺ content of leaves (17.2 %) and roots (14.3 %), and increased the K⁺/Na⁺ ratio of leaves (58.9 %) and roots (61.6 %) in cucumber. In conclusion, CsHAK5;3 in cucumber can mediate K⁺ transport and is one of the key target pumpkin genes that enhance salt tolerance of cucumber grafted.

Unfolding molecular switches for salt stress resilience in soybean: recent advances and prospects for salt-tolerant smart plant production

The increasing sodium salts (NaCl, NaHCO3, NaSO4 etc.) in agricultural soil is a serious global concern for sustainable agricultural production and food security. Soybean is an important food crop, and their cultivation is severely challenged by high salt concentration in soils. Classical transgenic and innovative breeding technologies are immediately needed to engineer salt tolerant soybean plants. Additionally, unfolding the molecular switches and the key components of the soybean salt tolerance network are crucial for soybean salt tolerance improvement. Here we review our understandings of the core salt stress response mechanism in soybean. Recent findings described that salt stress sensing, signalling, ionic homeostasis (Na⁺/K⁺) and osmotic stress adjustment might be important in regulating the soybean salinity stress response. We also evaluated the importance of antiporters and transporters such as Arabidopsis K⁺ Transporter 1 (AKT1) potassium channel and the impact of epigenetic modification on soybean salt tolerance. We also review key phytohormones, and osmo-protectants and their role in salt tolerance in soybean. In addition, we discuss the progress of omics technologies for identifying salt stress responsive molecular switches and their targeted engineering for salt tolerance in soybean. This review summarizes recent progress in soybean salt stress functional genomics and way forward for molecular breeding for developing salt-tolerant soybean plant.

Tobacco leaf tissue rapidly detoxifies direct salt loads without activation of calcium and SOS signaling

Salt stress is a major abiotic stress, responsible for declining agricultural productivity. Roots are regarded as hubs for salt detoxification, however, leaf salt concentrations may exceed those of roots. How mature leaves manage acute sodium chloride (NaCl) stress is mostly unknown. To analyze the mechanisms for NaCl redistribution in leaves, salt was infiltrated into intact tobacco leaves. It initiated pronounced osmotically-driven leaf movements. Leaf downward movement caused by hydro-passive turgor loss reached a maximum within 2 h. Salt-driven cellular water release was accompanied by a transient change in membrane depolarization but not an increase in cytosolic calcium ion (Ca²⁺ ) level. Nonetheless, only half an hour later, the leaves had completely regained turgor. This recovery phase was characterized by an increase in mesophyll cell plasma membrane hydrogen ion (H⁺ ) pumping, a salt uptake-dependent cytosolic alkalization, and a return of the apoplast osmolality to pre-stress levels. Although, transcript numbers of abscisic acid- and Salt Overly Sensitive pathway elements remained unchanged, salt adaptation depended on the vacuolar H⁺ /Na⁺ -exchanger NHX1. Altogether, tobacco leaves can detoxify sodium ions (Na⁺ ) rapidly even under massive salt loads, based on pre-established posttranslational settings and NHX1 cation/H⁺ antiport activity. Unlike roots, signaling and processing of salt stress in tobacco leaves does not depend on Ca²⁺ signaling.

Membrane Proteomic Profiling of Soybean Leaf and Root Tissues Uncovers Salt-Stress-Responsive Membrane Proteins

Cultivated soybean (Glycine max (L.)), the world's most important legume crop, has high-to-moderate salt sensitivity. Being the frontier for sensing and controlling solute transport, membrane proteins could be involved in cell signaling, osmoregulation, and stress-sensing mechanisms, but their roles in abiotic stresses are still largely unknown. By analyzing salt-induced membrane proteomic changes in the roots and leaves of salt-sensitive soybean cultivar (C08) seedlings germinated under NaCl, we detected 972 membrane proteins, with those present in both leaves and roots annotated as receptor kinases, calcium-sensing proteins, abscisic acid receptors, cation and anion channel proteins, proton pumps, amide and peptide transporters, and vesicle transport-related proteins etc. Endocytosis, linoleic acid metabolism, and fatty acid biosynthesis pathway-related proteins were enriched in roots whereas phagosome, spliceosome and soluble NSF attachment protein receptor (SNARE) interaction-related proteins were enriched in leaves. Using label-free quantitation, 129 differentially expressed membrane proteins were found in both tissues upon NaCl treatment. Additionally, the 140 NaCl-induced proteins identified in roots and 57 in leaves are vesicle-, mitochondrial-, and chloroplast-associated membrane proteins and those with functions related to ion transport, protein transport, ATP hydrolysis, protein folding, and receptor kinases, etc. Our proteomic results were verified against corresponding gene expression patterns from published C08 RNA-seq data, demonstrating the importance of solute transport and sensing in salt stress responses.

Histidine-Containing Dipeptides Mitigate Salt Stress in Plants by Scavenging Reactive Carbonyl Species

Reactive oxygen species (ROS) are critical factors that cause damage in salt-stressed plants, but their mechanisms of action in living cells are largely unknown. We investigated the roles of reactive carbonyl species (RCS), i.e., the lipid peroxide-derived α,β-unsaturated aldehydes and ketones, in plant growth retardation under salt stress. When Arabidopsis thaliana Col-0 seeds were exposed to 100 mM NaCl, germination was delayed and the levels of ROS, RCS, and protein carbonylation in the seedlings were increased. Adding the histidine-containing dipeptides carnosine, N-acetylcarnosine, and anserine, which are reported RCS scavengers, restored the germination speed and suppressed the increases in RCS and protein carbonylation but did not affect the ROS level. Increases in the levels of the RCS acrolein, crotonaldehyde, (E)-2-pentenal, and 4-hydroxy-(E)-2-nonenal were positively correlated with the delay of germination and growth inhibition. These RCS, generated downstream of ROS, are thus primarily responsible for the salt-stress symptoms of plants.

Heterologous Expression of Arabidopsis AtARA6 in Soybean Enhances Salt Tolerance

Salt damage is an important abiotic stress affecting the agronomic traits of soybean. Soybeans rapidly sense and transmit adverse signals when salt-damaged, inducing a set of response mechanisms to resist salt stress. AtARA6 encodes a small GTPase, which plays an important role in Arabidopsis vesicle transport and salt tolerance. In this study, we transformed the Arabidopsis gene AtARA6 into the cultivated soybean Shen Nong 9 (SN9). To investigate the salt tolerance pathways affected by AtARA6 in soybean, we performed transcriptome sequencing using transgenic soybean and wild-type (SN9) under salt treatment and water treatment. Our results suggest that AtARA6 is involved in the regulation of soybean SNARE complexes in the vesicle transport pathway, which may directly strengthen salt tolerance. In addition, we comprehensively analyzed the RNA-seq data of transgenic soybean and SN9 under different treatments and obtained 935 DEGs. GO analysis showed that these DEGs were significantly enriched in transcription factor activity, sequence-specific DNA binding, and the inositol catabolic process. Three salt-responsive negative regulator transcription factors, namely MYC2, WRKY6, and WRKY86, were found to be significantly downregulated after salt treatment in transgenic soybeans. Moreover, four genes encoding inositol oxygenase were significantly enriched in the inositol catabolic process pathway, which could improve the salt tolerance of transgenic soybeans by reducing their reactive oxygen species content. These are unique salt tolerance effects produced by transgenic soybeans. Our results provide basic insights into the function of AtARA6 in soybeans and its role in abiotic stress processes in plants.

Genome-Wide Identification, Primary Functional Characterization of the NHX Gene Family in Canavalia rosea, and Their Possible Roles for Adaptation to Tropical Coral Reefs

Canavalia rosea, distributed in the coastal areas of tropical and subtropical regions, is an extremophile halophyte with good adaptability to high salinity/alkaline and drought tolerance. Plant sodium/hydrogen (Na⁺/H⁺) exchanger (NHX) genes encode membrane transporters involved in sodium ion (Na⁺), potassium ion (K⁺), and lithium ion (Li⁺) transport and pH homeostasis, thereby playing key roles in salinity tolerance. However, the NHX family has not been reported in this leguminous halophyte. In the present study, a genome-wide comprehensive analysis was conducted and finally eight CrNHXs were identified in C. rosea genome. Based on the bioinformatics analysis about the chromosomal location, protein domain, motif organization, and phylogenetic relationships of CrNHXs and their coding proteins, as well as the comparison with plant NHXs from other species, the CrNHXs were grouped into three major subfamilies (Vac-, Endo-, and PM-NHX). Promoter analyses of cis-regulatory elements indicated that the expression of different CrNHXs was affected by a series of stress challenges. Six CrNHXs showed high expression levels in five tested tissues of C. rosea in different levels, while CrNHX1 and CrNHX3 were expressed at extremely low levels, indicating that CrNHXs might be involved in regulating the development of C. rosea plant. The expression analysis based on RNA-seq showed that the transcripts of most CrNHXs were obviously decreased in mature leaves of C. rosea plant growing on tropical coral reefs, which suggested their involvement in this species' adaptation to reefs and specialized islands habitats. Furthermore, in the single-factor stress treatments mimicking the extreme environments of tropical coral reefs, the RNA-seq data also implied CrNHXs holding possible gene-specific regulatory roles in the environmental adaptation. The qRT-PCR based expression profiling exhibited that CrNHXs responded to different stresses to varying degrees, which further confirmed the specificity of CrNHXs' in responding to abiotic stresses. Moreover, the yeast functional complementation test proved that some CrNHXs could partially restore the salt tolerance of the salt-sensitive yeast mutant AXT3. This study provides comprehensive bio-information and primary functional identification of NHXs in C. rosea, which could help improve the salt/alkaline tolerance of genetically modified plants for further studies. This research also contributes to our understanding of the possible molecular mechanism whereby NHXs maintain the ion balance in the natural ecological adaptability of C. rosea to tropical coral islands and reefs.

Genome-wide identification of soybean Shaker K+ channel gene family and functional characterization of GmAKT1 in transgenic Arabidopsis thaliana under salt and drought stress

Potassium is a major cationic nutrient involved in numerous physiological processes in plants. The uptake of K+ is mediated by K+ channels and transporters, and the Shaker K+ channel gene family plays an essential role in K+ uptake and stress resistance in plants. However, little is known regarding this family in soybean. In this study, 14 members of the Shaker K+ channel gene family were identified in soybean and were classified into five groups. Protein domain analysis revealed that Shaker K+ channel gene members have an ion transport domain (ion trans), a cyclic nucleotide-binding domain, ankyrin repeat domains, and a dimerization domain in the potassium ion channel. Quantitative real-time polymerase chain reaction analysis indicated that the expression of eight genes (notably GmAKT1) in soybean leaves and roots was significantly increased in response to salt and drought stress. Furthermore, the overexpression of GmAKT1 in Arabidopsis enhanced root length, K+ concentration, and fresh/dry weight ratio compared with wild-type plants subjected to salt and drought stress; this suggests that GmAKT1 improves the tolerance of soybean to abiotic stress. Our results provide important insight into the characterization of Shaker K+ channel gene family members in soybean and highlight the function of GmAKT1 in soybean plants under salt and drought stress.

Resveratrol Alleviates the KCl Salinity Stress of Malus hupehensis Rhed

Applying large amounts of potash fertilizer in apple orchards for high apple quality and yield aggravates KCl stress. As a phytoalexin, resveratrol (Res) participates in plant resistance to biotic stress. However, its role in relation to KCl stress has never been reported. Herein we investigated the role of Res in KCl stress response of Malus hupehensis Rehd., a widely used apple rootstock in China which is sensitive to KCl stress. KCl-stressed apple seedlings showed significant wilting phenotype and decline in photosynthetic rate, and the application of 100 μmol Res alleviated KCl stress and maintained photosynthetic capacity. Exogenous Res can strengthen the activities of peroxidase and catalase, thus eliminating reactive oxygen species production induced by KCl stress. Moreover, exogenous Res can decrease the electrolyte leakage by accumulating proline for osmotic balance under KCl stress. Furthermore, exogenous Res application can affect K+/Na+ homeostasis in cytoplasm by enhancing K+ efflux outside the cells, inhibiting Na+ efflux and K+ absorption, and compartmentalizing K+ into vacuoles through regulating the expression of K+ and Na+ transporter genes. These findings provide a theoretical basis for the application of exogenous Res to relieve the KCl stress of apples.

A Golgi-Localized Sodium/Hydrogen Exchanger Positively Regulates Salt Tolerance by Maintaining Higher K+/Na+ Ratio in Soybean

Salt stress caused by soil salinization, is one of the main factors that reduce soybean yield and quality. A large number of genes have been found to be involved in the regulation of salt tolerance. In this study, we characterized a soybean sodium/hydrogen exchanger gene GmNHX5 and revealed its functional mechanism involved in the salt tolerance process in soybean. GmNHX5 responded to salt stress at the transcription level in the salt stress-tolerant soybean plants, but not significantly changed in the salt-sensitive ones. GmNHX5 was located in the Golgi apparatus, and distributed in new leaves and vascular, and was induced by salt treatment. Overexpression of GmNHX5 improved the salt tolerance of hairy roots induced by soybean cotyledons, while the opposite was observed when GmNHX5 was knockout by CRISPR/Cas9. Soybean seedlings overexpressing GmNHX5 also showed an increased expression of GmSOS1, GmSKOR, and GmHKT1, higher K+/Na+ ratio, and higher viability when exposed to salt stress. Our findings provide an effective candidate gene for the cultivation of salt-tolerant germplasm resources and new clues for further understanding of the salt-tolerance mechanism in plants.

Genome-wide identification, characterization and transcriptional profiling of NHX-type (Na+/H+) antiporters under salinity stress in soybean

This study was aimed at the genome-wide identification, a comprehensive in silico characterization of NHX genes from soybean (Glycine max L.) and their tissue-specific expression under varied levels (0-200 mM NaCl) of salinity stress. A total of nine putative NHX genes were identified from soybean. The phylogenetic analysis confirmed a total of five sub-groups and GmNHXs were distributed in three of them. Bioinformatics analyses confirmed all GmNHXs as ion transporters in nature, and all were localized on the vacuolar membrane. Several cis-acting regulatory elements involved in hormonal signal-responsiveness and abiotic stress including salinity responses were identified in the promoter regions of GmNHXs. Amiloride, which is a known Na⁺/H⁺ exchanger activity inhibitor, binding motifs were observed in all the GmNHXs. Furthermore, the identified GmNHXs were predicted-targets of 75 different miRNA candidates. To gain an insight into the functional divergence of GmNHX transporters, qRT-PCR based gene expression analysis was done in control and salt-treated root, stem and leaf tissues of two contrasting Indian soybean varieties MAUS-47 (tolerant) and Gujosoya-2 (sensitive). The gene up-regulation was tissue-specific and varied amongst the soybean varieties, with higher induction in tolerant variety. Maximum induction was observed in GmNHX2 in root tissues of MAUS-47 at 200 mM NaCl stress. Overall, identified GmNHXs may be explored further as potential gene candidates for soybean improvement.

Genome-Wide Identification and Functional Characterization of the Cation Proton Antiporter (CPA) Family Related to Salt Stress Response in Radish (Raphanus sativus L.)

The CPA (cation proton antiporter) family plays an essential role during plant stress tolerance by regulating ionic and pH homeostasis of the cell. Radish fleshy roots are susceptible to abiotic stress during growth and development, especially salt stress. To date, CPA family genes have not yet been identified in radish and the biological functions remain unclear. In this study, 60 CPA candidate genes in radish were identified on the whole genome level, which were divided into three subfamilies including the Na+/H+ exchanger (NHX), K+ efflux antiporter (KEA), and cation/H+ exchanger (CHX) families. In total, 58 of the 60 RsCPA genes were localized to the nine chromosomes. RNA-seq. data showed that 60 RsCPA genes had various expression levels in the leaves, roots, cortex, cambium, and xylem at different development stages, as well as under different abiotic stresses. RT-qPCR analysis indicated that all nine RsNHXs genes showed up regulated trends after 250 mM NaCl exposure at 3, 6, 12, and 24h. The RsCPA31 (RsNHX1) gene, which might be the most important members of the RsNHX subfamily, exhibited obvious increased expression levels during 24h salt stress treatment. Heterologous over-and inhibited-expression of RsNHX1 in Arabidopsis showed that RsNHX1 had a positive function in salt tolerance. Furthermore, a turnip yellow mosaic virus (TYMV)-induced gene silence (VIGS) system was firstly used to functionally characterize the candidate gene in radish, which showed that plant with the silence of endogenous RsNHX1 was more susceptible to the salt stress. According to our results we provide insights into the complexity of the RsCPA gene family and a valuable resource to explore the potential functions of RsCPA genes in radish.

Phylogenetic Diversity and Physiological Roles of Plant Monovalent Cation/H+ Antiporters

The processes of plant nutrition, stress tolerance, plant growth, and development are strongly dependent on transport of mineral nutrients across cellular membranes. Plant membrane transporters are key components of these processes. Among various membrane transport proteins, the monovalent cation proton antiporter (CPA) superfamily mediates a broad range of physiological and developmental processes such as ion and pH homeostasis, development of reproductive organs, chloroplast operation, and plant adaptation to drought and salt stresses. CPA family includes plasma membrane-bound Na⁺/H⁺ exchanger (NhaP) and intracellular Na⁺/H⁺ exchanger NHE (NHX), K⁺ efflux antiporter (KEA), and cation/H⁺ exchanger (CHX) family proteins. In this review, we have completed the phylogenetic inventory of CPA transporters and undertaken a comprehensive evolutionary analysis of their development. Compared with previous studies, we have significantly extended the range of plant species, including green and red algae and Acrogymnospermae into phylogenetic analysis. Our data suggest that the multiplication and complexation of CPA isoforms during evolution is related to land colonisation by higher plants and associated with an increase of different tissue types and development of reproductive organs. The new data extended the number of clades for all groups of CPAs, including those for NhaP/SOS, NHE/NHX, KEA, and CHX. We also critically evaluate the latest findings on the biological role, physiological functions and regulation of CPA transporters in relation to their structure and phylogenetic position. In addition, the role of CPA members in plant tolerance to various abiotic stresses is summarized, and the future priority directions for CPA studies in plants are discussed.

Genome-Wide Identification and Expression Analysis of the NHX (Sodium/Hydrogen Antiporter) Gene Family in Cotton

The sodium/hydrogen antiporter (NHX) gene family with the Na⁺/H⁺ exchange protein domain is a transporter of sodium and hydrogen ions and plays an important role in the response of plants to salt stress. Studying the response of cotton to salt stress through comprehensive identification and analysis of NHX genes in several species and their roles in salt tolerance mechanisms is of great significance. In this study, 23, 24, 12, and 12 NHX genes were identified from Gossypium hirsutum (Gh), G. barbadense, G. arboreum and G. raimondii, respectively. Phylogenetic analysis showed that these genes were mainly divided into three clades with significant subcellular localization, namely, endosome (Endo-class), plasma membrane (PM-class) and vacuole (Vac-class). By analyzing the structure of NHX genes and proteins, each branch of the NHX gene family was found to be structurally conserved, and collinearity analysis showed that NHX genes were mainly expressed through whole genome and segmental duplication. The non-synonymous (Ka)/synonymous (Ks) values showed that the NHX gene family experienced strong purifying selection during long-term evolution. Cis-acting element analysis showed that the NHX gene family may be related to the regulation of abscisic acid (ABA) and methyl jasmonate (MeJA) hormones. Additionally, transcriptomic data analysis and qRT-PCR showed that GhNHXs exhibited different expression patterns in each tissue and under different salinities. These results provide an important reference for us to further understand and analyze the molecular regulation mechanism of cotton NHX genes.

Functional Analysis of the Soybean GmCDPK3 Gene Responding to Drought and Salt Stresses

Plants have a series of response mechanisms to adapt when they are subjected to external stress. Calcium-dependent protein kinases (CDPKs) in plants function against a variety of abiotic stresses. We screened 17 CDPKs from drought- and salt-induced soybean transcriptome sequences. The phylogenetic tree divided CDPKs of rice, Arabidopsis and soybean into five groups (I-V). Cis-acting element analysis showed that the 17 CDPKs contained some elements associated with drought and salt stresses. Quantitative real-time PCR (qRT-PCR) analysis indicated that the 17 CDPKs were responsive after different degrees of induction under drought and salt stresses. GmCDPK3 was selected as a further research target due to its high relative expression. The subcellular localization experiment showed that GmCDPK3 was located on the membrane of Arabidopsis mesophyll protoplasts. Overexpression of GmCDPK3 improved drought and salt resistance in Arabidopsis. In the soybean hairy roots experiment, the leaves of GmCDPK3 hairy roots with RNA interference (GmCDPK3-RNAi) soybean lines were more wilted than those of GmCDPK3 overexpression (GmCDPK3-OE) soybean lines after drought and salt stresses. The trypan blue staining experiment further confirmed that cell membrane damage of GmCDPK3-RNAi soybean leaves was more severe than in GmCDPK3-OE soybean lines. In addition, proline (Pro) and chlorophyll contents were increased and malondialdehyde (MDA) content was decreased in GmCDPK3-OE soybean lines. On the contrary, GmCDPK3-RNAi soybean lines had decreased Pro and chlorophyll content and increased MDA. The results indicate that GmCDPK3 is essential in resisting drought and salt stresses.