Transcriptome analysis reveals molecular mechanisms for salt tolerance in wheat (Triticum aestivum L.).

Salt stress reduces wheat yield. Therefore, improvement for enhanced salt stress tolerance is necessary for stable production. To understand the molecular mechanism of salt tolerance in common wheat and synthetic hexaploid (SH) wheat, RNA sequencing was performed on the roots of three wheat lines salt-tolerant SH wheat, salt-tolerant common wheat, and salt-sensitive common wheat. Differentially expressed genes (DEGs) in response to salt stress were characterized using gene ontology enrichment analysis. Salt tolerance in common wheat has been suggested to be mainly regulated by the activation of transporters. In contrast, salt tolerance in SH wheat is enhanced through up-regulation of the reactive oxygen species signaling pathway, other unknown pathways, and different ERF transcription factors. These results indicate that salt tolerance is differentially controlled between common wheat and SH wheat. Furthermore, QTL analysis was performed using the F2 population derived from SH and salt-sensitive wheat. No statistically significant QTL was detected, suggesting that numerous QTLs with negligible contributions are involved in salt tolerance in SH wheat. We also identified DEGs specific to each line near one probable QTL. These findings show that SH wheat possesses salt tolerance mechanisms lacking in common wheat and may be potential breeding material for salt tolerance.

Soil salinity is major constraint for wheat production globally and breeding wheat cultivars for salt tolerance by conventional means is difficult. Therefore, understanding molecular components associated with salt tolerance is needed to facilitate breeding for salt tolerance in wheat. In this investigation, quantitative trait loci (QTL/s) associated with salt tolerance were identified using recombinant inbred lines (RILs) developed from a cross between Kharchia 65 (KH 65) and HD 2009 cultivars. Parents and RILs were evaluated under controlled and sodic stress conditions for 11 morpho-physiological and yield determining traits for two consecutive crop cycles. Simple sequence repeat (SSR) markers were employed for mapping studies. Using composite interval mapping approach, 11 QTLs on 6 chromosomal regions (1B, 2D, 5D, 6A, 6B and 7D) for 7 different traits were identified explaining proportion of the phenotypic variance (PVEs) (2.5–12.8%) under control condition. Three of the QTLs (QCph.iiwbr-2D.1, QCle.iiwbr-6A and QCle.iiwbr-6B) were most consistent in all the environments and explained PVEs (5.1–12.8%) under control condition. Twenty-five QTLs were detected on 7 chromosomal regions (1A, 1B, 2D, 4D, 5D, 6A and 7D) for 10 different traits explaining PVEs (2.6–15.1%) under salt stress. Six of the QTLs namely QSNa+.iiwbr-1B, QSK+.iiwbr-2D, QStn.iiwbr-4D, QSph.iiwbr-2D.1, QSph.iiwbr-6A and QSdth.iiwbr-2D were consistently reproducible in all the environments and explained PVEs ranging from 2.6 to 15.1%. SSR markers namely gwm 261, wmc 112, and cfd 84 were tightly linked with QTLs for K+ content; DTH and DTA; and TN and NE, respectively. Several QTLs contributing towards salt tolerance were present on 2D chromosome. Most of the QTLs linked with salt tolerant traits were inherited from KH 65 signifying the presence of several genes associated with salt tolerance in this cultivar. The information is very useful in marker assisted breeding to enhance salt tolerance in wheat.

Salt stress dramatically reduces crop yield and quality, but the molecular mechanisms underlying salt tolerance remain largely unknown. To explore the wheat transcriptional response to salt stress, we performed high-throughput transcriptome sequencing of 10-day old wheat roots under normal condition and 6, 12, 24 and 48 h after salt stress (HASS) in both a salt-tolerant cultivar and salt-sensitive cultivar. The results demonstrated global gene expression reprogramming with 36,804 genes that were up- or down-regulated in wheat roots under at least one stress condition compared with the controls and revealed the specificity and complexity of the functional pathways between the two cultivars. Further analysis showed that substantial expression partitioning of homeologous wheat genes occurs when the plants are subjected to salt stress, accounting for approximately 63.9% (2,537) and 66.1% (2,624) of the homeologous genes in ‘Chinese Spring’ (CS) and ‘Qing Mai 6’ (QM). Interestingly, 143 salt-responsive genes have been duplicated and tandemly arrayed on chromosomes during wheat evolution and polyploidization events, and the expression patterns of 122 (122/143, 85.3%) tandem duplications diverged dynamically over the time-course of salinity exposure. In addition, constitutive expression or silencing of target genes in Arabidopsis and wheat further confirmed our high-confidence salt stress-responsive candidates.

BackgroundSoil salinization is one of the vital factors threatening the world’s food security. To reveal the biological mechanism of response to salt stress in wheat, this study was conducted to resolve the transcription level difference to salt stress between CM6005 (salt-tolerant) and KN9204 (salt-sensitive) at the germination and seedling stage.ResultsTo investigate the molecular mechanism underlying salt tolerance in wheat, we conducted comprehensive transcriptome analyses at the seedling and germination stages. Two wheat cultivars, CM6005 (salt-tolerant) and KN9204 (salt-sensitive) were subjected to salt treatment, resulting in a total of 24 transcriptomes. Through expression-network analysis, we identified 17 modules, 16 and 13 of which highly correlate with salt tolerance-related phenotypes in the germination and seedling stages, respectively. Moreover, we identified candidate Hub genes associated with specific modules and explored their regulatory relationships using co-expression data. Enrichment analysis revealed specific enrichment of gibberellin-related terms and pathways in CM6005, highlighting the potential importance of gibberellin regulation in enhancing salt tolerance. In contrast, KN9204 exhibited specific enrichment in glutathione-related terms and activities, suggesting the involvement of glutathione-mediated antioxidant mechanisms in conferring resistance to salt stress. Additionally, glucose transport was found to be a fundamental mechanism for salt tolerance during wheat seedling and germination stages, indicating its potential universality in wheat. Wheat plants improve their resilience and productivity by utilizing adaptive mechanisms like adjusting osmotic balance, bolstering antioxidant defenses, accumulating compatible solutes, altering root morphology, and regulating hormones, enabling them to better withstand extended periods of salt stress.ConclusionThrough utilizing transcriptome-level analysis employing WGCNA, we have revealed a potential regulatory mechanism that governs the response to salt stress and recovery in wheat cultivars. Furthermore, we have identified key candidate central genes that play a crucial role in this mechanism. These central genes are likely to be vital components within the gene expression network associated with salt tolerance. The findings of this study strongly support the molecular breeding of salt-tolerant wheat, particularly by utilizing the genetic advancements based on CM6005 and KN9204.

Wheat (Triticum aestivum L.) is a mega‐staple for millions of the world's populations and its yield potential is impacted by soil salinization. This study investigated genotypic variation in salt tolerance among six wheat genotypes, Gladius, Drysdale, GD0014, GD0120, GD0180, and GD0185. The study also characterized shoot traits, photosynthetic traits, leaf Na and K concentrations, and phloem sucrose. The plants were grown under controlled growth room conditions at 0 mM NaCl (Control) and 100 mM NaCl. The results showed that the salt tolerance index (STISFW, SFW: shoot fresh weight) varied from 0.52 for GD0120 to 0.69 for GD0180. Based on the STISFW, salt tolerance for the wheat genotypes was in the order, GD0180 > Gladius > GD0185 > Drysdale > GD0014 > GD0120. Projected shoot area (PSA) at all growth stages, 14, 20, 27, 34, and 40 DAS were strongly correlated with SFW at 45 DAS. Salt treatment significantly increased phloem sucrose level in the salt intolerant, Drysdale, while having no effect on this parameter in Gladius. Gladius showed greater maintenance of stomatal conductance than Drysdale. The relative ratio of K/Na between treatment and control was strongly correlated with the relative ratio of SFW (r = .85). The correlation between PSA at 14 DAS and SFW at 45 DAS and the correlation between the relative ratio of K/Na between treatment and control with STISFW identify these parameters to be potential traits for screening salt tolerance in wheat. Higher salt tolerance in Gladius would be associated with higher maintenance of stomatal conductance and enhanced phloem sucrose transport.

To improve biotic and abiotic stress tolerance in common wheat ( Triticum aestivum L.), novel genotypes with genomic fragments introgressed from other cereal species are extensively developed. One of the most important abiotic environmental factors that impede the expansion of wheat cultivation areas is soil salinity. Salt-sensitive wheat varieties have poor yield and impaired grain quality when exposed to salinity. The aim of this study was to evaluate the degree of influence of alien genetic material on salinity tolerance in common wheat seedlings. Seedlings of introgression lines carrying single fragments of Aegilops speltoides and T. timopheevii genomes in common wheat chromosomes 2А, 5В, and 6В, were tested for salt tolerance. The parental common spring wheat genotypes Saratovskaya 29, Novosibirskaya 29 and Rodina-1, possessing mode- rate salt tolerance, were used as reference. The expe- riment showed that the presence of the translocation T5BS • 5BL-5SL either in Novosibirskaya 29 or in Rodina-1 increased salt tolerance. On the contrary, another translocation between T. aestivum and Ae. speltoides (T6BS • 6BL-6SL) made wheat more sensitive to salinity. Different fragments of T. timo- pheevii genome had different effects: introgression into the chromosome 2A increased salt tolerance, whereas introgression into chromosome 5B reduced it significantly. The observed differences between the parental wheat genotypes and the introgression lines derived from them are discussed with regard to the locations of alien introgression fragments in the lines tested and the map positions of known wheat QTLs and major genes related to salt tolerance. It is assumed that a locus yet undescribed that affects wheat salt tolerance is located distal to the Xgwm0604 marker on the long arm of chromosome 5B.

Seed priming by sodium nitroprusside improves salt tolerance in wheat (Triticum aestivum L.) by enhancing physiological and biochemical parameters

Soil salinity affects the plant growth and productivity detrimentally, but Solanum chilense, a wild relative of cultivated tomato (Solanum lycopersicum L.), is known to have exceptional salt tolerance. It has precise adaptations against direct exposure to salt stress conditions. Hence, a better understanding of the mechanism to salinity stress tolerance by S. chilense can be accomplished by comprehensive gene expression studies. In this study 1-month-old seedlings of S. chilense and S. lycopersicum were subjected to salinity stress through application of sodium chloride (NaCl) solution. Through RNA-sequencing here we have studied the differences in the gene expression patterns. A total of 386 million clean reads were obtained through RNAseq analysis using the Illumina HiSeq 2000 platform. Clean reads were further assembled de novo into a transcriptome dataset comprising of 514,747 unigenes with N50 length of 578 bp and were further aligned to the public databases. Genebank non-redundant (Nr), Viridiplantae, Gene Ontology (GO), KOG, and KEGG databases classification suggested enrichment of these unigenes in 30 GO categories, 26 KOG, and 127 pathways, respectively. Out of 265,158 genes that were differentially expressed in response to salt treatment, 134,566 and 130,592 genes were significantly up and down-regulated, respectively. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in cytokinin, ethylene, auxin, abscisic acid, gibberellin, and Ca2+ mediated signaling pathways were up-regulated. Furthermore, GO enrichment analysis was performed using REVIGO and up-regulation of multiple genes involved in various biological processes in chilense under salinity were identified. Through pathway analysis of DEGs, “Wnt signaling pathway” was identified as a novel pathway for the response to the salinity stress. Moreover, key genes for salinity tolerance, such as genes encoding proline and arginine metabolism, ROS scavenging system, transporters, osmotic regulation, defense and stress response, homeostasis and transcription factors were not only salt-induced but also showed higher expression in S. chilense as compared to S. lycopersicum. Thus indicating that these genes may have an important role in salinity tolerance in S. chilense. Overall, the results of this study improve our understanding on possible molecular mechanisms underlying salt tolerance in plants in general and tomato in particular.

The wheat protein disulfide isomerase TaPDI-15 ameliorates salt tolerance in wheat (Triticum aestivum L.).

Soil salinity is a serious threat to wheat yield affecting sustainable agriculture. Although salt tolerance is important for plant establishment at seedling stage, its genetic architecture remains unclear. In the present study, we have evaluated eight salt tolerance–related traits at seedling stage and identified the loci for salt tolerance by genome-wide association study (GWAS). This GWAS panel comprised 317 accessions and was genotyped with the wheat 90 K single-nucleotide polymorphism (SNP) chip. In total, 37 SNPs located at 16 unique loci were identified, and each explained 6.3 to 18.6% of the phenotypic variations. Among these, six loci were overlapped with previously reported genes or quantitative trait loci, whereas the other 10 were novel. Besides, nine loci were detected for two or more traits, indicating that the salt-tolerance genetic architecture is complex. Furthermore, five candidate genes were identified for salt tolerance–related traits, including kinase family protein, E3 ubiquitin-protein ligase-like protein, and transmembrane protein. SNPs identified in this study and the accessions with more favorable alleles could further enhance salt tolerance in wheat breeding. Our results are useful for uncovering the genetic mechanism of salt tolerance in wheat at seeding stage.

Sodicity is a critical stress that significantly affects the yield and productivity of wheat. This stress can result in a range of physiological, biochemical, and molecular responses in plants, which can hinder their overall health and yield potential. Understanding these responses is key to developing salt-tolerant wheat (Triticum aestivum L.) varieties. The present study was carried out during 2022–23 and 2023–24 at ICAR-Central Soil Salinity Research Institute, Karnal, Haryana in which a population of 195 recombinant inbred lines (RILs) of wheat (HD2851 × KH65) was evaluated under control and sodicity conditions. Genotype HD2851 showed a more significant yield reduction (65.51%) under sodicity conditions compared to KH65 (45.08%). Following exposure to salt stress, the leaf tissues of KH65 exhibited 1.9-fold increase in Na+ content, while HD2851 showed 3.1-fold increase. Significant positive correlations (P˂0.01) were found between grain yield and several traits: chlorophyll content, K+/Na+ ratio, plant height, spike length, flag leaf area, and 1000-grain weight. Conversely, Na+ content exhibited a significant negative correlation (P˂0.01) with grain yield. The first two principal components accounted for 38.39% of the overall trait variation (PC1, 21.14%; PC2, 17.25%). In this study, the expression of TaNHX1, TaSOS1 and TaHKT2 genes was evaluated in the leaf tissues of salt-tolerant (KH65, RIL8 and RIL130) and salt-sensitive (HD2851, RIL61 and RIL154) wheat genotypes under salt treatment. The expression levels of TaNHX1, TaSOS1 and TaHKT2 genes were significantly higher in KH65, RIL8 and RIL130 genotypes following salt stress, suggesting enhanced capabilities for Na+ exclusion at the plasma membrane and Na+ sequestration in vacuoles. The information generated in the present study will be beneficial for improving salt tolerance in elite wheat genotypes.

Efficient antioxidant enzymatic system contributes to salt tolerance of plants via avoiding ROS over-accumulation. Peroxiredoxins are crucial components of the reactive oxygen species (ROS) scavenging machinery in plant cells, but whether they offer salt tolerance with potential for germplasm improvement has not been well addressed in wheat. In this work, we confirmed the role of a wheat 2-Cys peroxiredoxin gene TaBAS1 that was identified through the proteomic analysis. TaBAS1 overexpression enhanced the salt tolerance of wheat at both germination and seedling stages. TaBAS1 overexpression enhanced the tolerance to oxidative stress, promoted the activities of ROS scavenging enzymes, and reduced ROS accumulation under salt stress. TaBAS1 overexpression promoted the activity of ROS production associated NADPH oxidase, and the inhibition of NADPH oxidase activity abolished the role of TaBAS1 in salt and oxidative tolerance. Moreover, the inhibition of NADPH-thioredoxin reductase C activity erased the performance of TaBAS1 in the tolerance to salt and oxidative stress. The ectopic expression of TaBAS1 in Arabidopsis exhibited the same performance, showing the conserved role of 2-Cys peroxiredoxins in salt tolerance in plants. TaBAS1 overexpression enhanced the grain yield of wheat under salt stress but not the control condition, not imposing the trade-offs between yield and tolerance. Thus, TaBAS1 could be used for molecular breeding of wheat with superior salt tolerance.

Salinized soil can significantly hinder soybean growth, leading to a reduction in overall yield. To address this issue, identifying key genes related to salt tolerance in soybeans is essential for improving their resistance to salinity and ensuring sustainable development of soybean production. While current research predominantly focuses on salt tolerance during the seedling stage, there is still a lack of comprehensive studies on the genes involved in salt tolerance during the germination stage. This study established the optimal screening criteria by phenotyping the salt-tolerant variety R063 and the salt-sensitive variety W82 during the germination stage under salt stress. RNA-seq analysis was performed on 24 samples from both varieties at 36 and 48 hours under two different salt concentrations (0 and 150 mM/L NaCl). Differential expression analysis revealed that the salt-tolerant variety R063 exhibited the fewest differentially expressed genes (DEGs) compared to its control after 48 hours of salt stress. A total of 305 DEGs were commonly identified between the salt-tolerant variety R063 and the salt-sensitive variety W82 under salt stress at both time points. Additionally, 187 DEGs were commonly identified between R063 under salt stress and its corresponding control group across the two time points. Gene ontology (GO) enrichment analysis revealed that the differentially expressed genes were significantly enriched in ADP binding, monooxygenase activity, oxidoreductase activity, defense response, and protein phosphorylation signaling pathways. The weighted gene co-expression network analysis (WGCNA) method was employed to identify modules strongly correlated with salt tolerance during soybean germination. Candidate genes associated with soybean sprouting salt tolerance were identified by evaluating the connectivity and expression profiles of genes within these modules. These findings provide a theoretical foundation for further elucidating the molecular mechanisms underlying salt tolerance during soybean germination and present new genetic resources for studying this trait.

There is considerable variability in salt tolerance amongst members of the Triticeae, with the tribe even containing a number of halophytes. This is a review of what is known of the differences in salt tolerance of selected species in this tribe of grasses, and the potential to use wild species to improve salt tolerance in wheat. Most investigators have concentrated on differences in ion accumulation in leaves, describing a desirable phenotype with low leaf Na+ concentration and a high K+/Na+ ratio. Little information is available on other traits (such as "tissue tolerance" of accumulated Na+ and Cl-) that might also contribute to salt tolerance. The sources of Na+ "exclusion" amongst the various genomes that make up tetraploid (AABB) durum wheat (Triticum turgidum L. ssp. durum), hexaploid (AABBDD) bread wheat (Triticum aestivum L. ssp. aestivum), and wild relatives (e.g. Aegilops spp., Thinopyrum spp., Elytrigia elongata syn. Lophopyrum elongatum, Hordeum spp.) are described. The halophytes display a capacity for Na+ "exclusion", and in some cases Cl- "exclusion", even at relatively high salinity. Significantly, it is possible to hybridize several wild species in the Triticeae with durum and bread wheat. Progenitors have been used to make synthetic hexaploids. Halophytic relatives, such as tall wheatgrass spp., have been used to produce amphiploids, disomic chromosome addition and substitution lines, and recombinant lines in wheat. Examples of improved Na+ "exclusion" and enhanced salt tolerance in various derivatives from these various hybridization programmes are given. As several sources of improved Na+ "exclusion" are now known to reside on different chromosomes in various genomes of species in the Triticeae, further work to identify the underlying mechanisms and then to pyramid the controlling genes for the various traits, that could act additively or even synergistically, might enable substantial gains in salt tolerance to be achieved.

In order to increase the bread wheat (Triticum aestivum L.) tolerance to different biotic and abiotic stress factors, the development of new genotypes using the introgressions of the genomic fragments from other cereals is widely used. One of the most significant abiotic environmental factors that impede the expansion of the wheat cultivation territory is soil salinity. Salt-sensitive wheat varieties have poor yield and impaired grain quality when exposed to salinity. The aim of the present study was the establishment of a degree of influence of the alien genetic material on the salinity tolerance of bread wheat T. aestivum seedlings. The method of laboratory screening of the seedling salinity tolerance was used for the analysis of introgression lines carrying single fragments from Aegilops speltoides and T. timopheevii in bread wheat chromosomes 2A, 5B, and 6B.The initial parental forms of the spring bread wheat (Saratovskaya 29, Novosibirskaya 29, and Rodina-1) with moderate salt tolerance were used as the control. As a result of the estimation, it was established that the presence of the T5BS ⋅ 5BL-5SL translocation in the genome of Novosibirskaya 29 and Rodina-1 increased salt tolerance. On the contrary, another translocation from Ae. speltoides (T6BS • 6BL-6SL) is associated with a reduction in the tolerance. Different T. timopheevii genome fragments also differently affected the salt tolerance; introgression in chromosome 2A increased, while in 5B considerably decreased the wheat tolerance to the salinization. The observed differences between the initial wheat genotypes and introgression lines derived from them are discussed taking into account the localization of alien introgressions in the studied lines and the localization of the known genes (controlling the salt tolerance) in wheat chromosomes. It is assumed that a previously undescribed gene, which influences wheat seedlings salt tolerance, is located distal to the Xgwm0604 marker on the long arm of chromosome 5B.