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

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

Comprehensive Evaluation of Salt Tolerance in Rice (Oryza sativa L.) Germplasm at the Germination Stage

Salt stress reduces the yield and quality of rice. It is of great significance to screen out salt-tolerant varieties for the development and utilization of saline land. The study was carried out on 114 rice varieties; first, seven varieties were selected and treated with different salt concentrations (0, 50, 85, 120, 155, 190, 225 mM), and seven traits, including germination energy, germination capacity, shoot length, root length, root number, plant fresh weight, and seedling vigor index, were measured. The salt concentration at which the sodium chloride injury index was 50% of the control was considered the optimal salt concentration. Second, 114 rice germplasms were carried out under an optimal salt concentration (120 mM). Then, principal component analysis, fuzzy function analysis, stepwise regression analysis, correlation analysis, and systematic cluster analysis were carried out on each parameter. There was a significant correlation between each parameter and the D-value, and the correlation coefficient between the seedling vigor index and D-value was the highest. D-value = − 0.272 + 1.335 × STI − SVI + 0.549 × STI − RN − 0.617 × STI-RL + 0.073 × STI − GE, R2 = 0.986. Using this equation, the sodium chloride tolerance of rice in the germination experiment could be quickly identified. This study showed that the seedling vigor index was a reliable parameter to identify the salinity tolerance of rice varieties. Five groups were obtained by classification at a Euclidean distance of 5. There were 8 highly salt-tolerant cultivars, 23 salt-tolerant cultivars, 42 cultivars with moderate salt tolerance, 33 salt-sensitive cultivars, and 8 highly salt-sensitive cultivars. In this study, we found that Riguang was the most salt-tolerant rice variety, and Xiangxuejing15 was the most salt-sensitive variety.

Evaluation of Capsicum annum L. genotypes against salinity induced by NaCl

Soil salinity harmfully effect bell pepper production being salt sensitive crop. The aim of this study was to compare capsicum (bell-pepper) cultivars for their ability to tolerate salt stress. Electrical conductivity of different levels i.e., control (no sodium chloride), 1.5, 3.0, 4.5, and 6.0 dS m-1, was developed by using NaCl, after 30 days of seedling emergence of six cultivars (Yolo Wonder, California Wonder, Cop-amber Hybrid, F1 Pangs No. 206, Sweet Pepper F1, Kaka F1). These cultivars were evaluated based on morphological (shoot and root length, plant fresh and dry biomass), physiological (chlorophyll content) and biochemical attributes (nitrogen concentration, and protein contents). Minimum chlorophyll contents (SPAD units) in Kaka F1 (16.77 SPAD units) at 1.5 dSm-1. However, maximum value of chlorophyll contents was observed in Sweet Pepper F1 (49.23 SPAD units) at control followed by “Yolo Wonder” (41.53 SPAD units) at control. Maximum dry biomass was found in California Wonder (0.468 g) at 1.5 dSm-1, while minimum value of dry biomass (g) was observed in Kaka F1 (0.095 g) at 4.5 dSm-1. Six cultivars of capsicum were categorized into three groups. Salt tolerant cultivars included “California Wonder” followed by “Yolo Wonder”. “Kaka F1” was proved most salt sensitive and all others were moderately salt tolerant.

Advances in Sensing, Response and Regulation Mechanism of Salt Tolerance in Rice

Soil salinity is a serious menace in rice production threatening global food security. Rice responses to salt stress involve a series of biological processes, including antioxidation, osmoregulation or osmoprotection, and ion homeostasis, which are regulated by different genes. Understanding these adaptive mechanisms and the key genes involved are crucial in developing highly salt-tolerant cultivars. In this review, we discuss the molecular mechanisms of salt tolerance in rice—from sensing to transcriptional regulation of key genes—based on the current knowledge. Furthermore, we highlight the functionally validated salt-responsive genes in rice.

Identification and development of novel salt-responsive candidate gene based SSRs (cg-SSRs) and MIR gene based SSRs (mir-SSRs) in bread wheat (Triticum aestivum)

Salt stress adversely affects the global wheat production and productivity. To improve salinity tolerance of crops, identification of robust molecular markers is highly imperative for development of salt-tolerant cultivars to mimic yield losses under saline conditions. In this study, we mined 171 salt-responsive genes (including 10 miRNAs) from bread wheat genome using the sequence information of functionally validated salt-responsive rice genes. Salt-stress, tissue and developmental stage-specific expression analysis of RNA-seq datasets revealed the constitutive as well as the inductive response of salt-responsive genes in different tissues of wheat. Fifty-four genotypes were phenotyped for salt stress tolerance. The stress tolerance index of the genotypes ranged from 0.30 to 3.18. In order to understand the genetic diversity, candidate gene based SSRs (cg-SSRs) and MIR gene based SSRs (miR-SSRs) were mined from 171 members of salt-responsive genes of wheat and validated among the contrasting panels of 54 tolerant as well as susceptible wheat genotypes. Among 53 SSR markers screened, 10 cg-SSRs and 8 miR-SSRs were found to be polymorphic. Polymorphic information content between the wheat genotypes ranged from 0.07 to 0.67, indicating the extant of wide genetic variation among the salt tolerant and susceptible genotypes at the DNA level. The genetic diversity analysis based on the allelic data grouped the wheat genotypes into three separate clusters of which single group encompassing most of the salt susceptible genotypes and two of them containing salt tolerance and moderately salt tolerance wheat genotypes were in congruence with penotypic data. Our study showed that both salt-responsive genes and miRNAs based SSRs were more diverse and can be effectively used for diversity analysis. This study reports the first extensive survey on genome-wide analysis, identification, development and validation of salt-responsive cg-SSRs and miR-SSRs in wheat. The information generated in the present study on genetic divergence among genotypes having a differential response to salt will help in the selection of suitable lines as parents for developing salt tolerant cultivars in wheat.

RNAseq Analysis Reveals Altered Expression of Key Ion Transporters Causing Differential Uptake of Selective Ions in Canola (Brassica napus L.) Grown under NaCl Stress

Salinity is one of the major abiotic stresses prevailing throughout the world that severely limits crop establishment and production. Every crop has an intra-specific genetic variation that enables it to cope with variable environmental conditions. Hence, this genetic variability is a good tool to exploit germplasms in salt-affected areas. Further, the selected cultivars can be effectively used by plant breeders and molecular biologists for the improvement of salinity tolerance. In the present study, it was planned to identify differential expression of genes associated with selective uptake of different ions under salt stress in selected salt-tolerant canola (Brassica napus L.) cultivar. For the purpose, an experiment was carried out to evaluate the growth response of different salt-sensitive and salt-tolerant canola cultivars. Plants were subjected to 200 mM NaCl stress. Canola cultivars—Faisal Canola, DGL, Dunkled, and CON-II—had higher growth than in cvs Cyclone, Ac-EXcel, Legend, and Oscar. Salt-tolerant cultivars were better able to maintain plant water status probably through osmotic adjustment as compared to salt-sensitive cultivars. Although salt stress increased shoot Na+ and shoot Cl− contents in all canola cultivars, salt-tolerant cultivars had a lower accumulation of these toxic nutrients. Similarly, salt stress reduced shoot K+ and Ca2+ contents in all canola cultivars, while salt-tolerant cultivars had a higher accumulation of K+ and Ca2+ in leaves, thereby having greater shoot K+/Na+ and Ca2+/Na+ ratios. Nutrient utilization efficiency decreased significantly in all canola cultivars due to the imposition of salt stress; however, it was greater in salt-tolerant cultivars—Faisal Canola, DGL, and Dunkled. Among four salt-tolerant canola cultivars, cv Dunkled was maximal in physiological attributes, and thus differentially expressed genes (DEGs) were assessed in it by RNA-seq analysis using next-generation sequencing (NGS) techniques. The differentially expressed genes (DEG) in cv Dunkled under salt stress were found to be involved in the regulation of ionic concentration, photosynthesis, antioxidants, and hormonal metabolism. However, the most prominent upregulated DEGs included Na/K transporter, HKT1, potassium transporter, potassium channel, chloride channel, cation exchanger, Ca channel. The RNA-seq data were validated through qRT-PCR. It was thus concluded that genes related to the regulation of ionic concentrate are significantly upregulated and expressed under salt stress, in the cultivar Dunkled.

Adaptation patterns of sixteen alfalfa (Medicago sativa L.) cultivars across contrasting environments of Algeria and implications for the crop improvement

The additive main effects and multiplicative interaction analysis was applied to assess the genotype × environment interaction (GEI) effects and stability for 4-year dry matter yield (DMY) of 16 alfalfa (Medicago sativa L.) cultivars of diversified geographic origin grown in four Algerian environments given by the combination of two water managements (rainfed and irrigated) and two evaluation sites, viz. the sub-humid location of Alger and the semi-arid, salinity-affected site of Hmadna. The analysis of variance (ANOVA) revealed significant variation among cultivars and environments (P<0.001). The GEI was significant (P<0.001) and the environment main effect had greater influence than the genotype effect on long-term yield according to ANOVA. Rainfed conditions had 41.6% and 48.5% lower yield than the irrigated ones in Alger and Hmadna, respectively. Alfalfa cropping in the semiarid location caused lower DMY than in the sub-humid one (– 38.0% under irrigated and –45.2% under rainfed conditions) and a slightly lower persistence over the 4-year period. Outstanding environment-specific cultivar responses were observed, fully justifying the large GEI effects, although the Italian cultivar Sicilian ecotype had remarkable yield stability and good mean yield. The American variety Ameristand 801S and the Moroccan landrace Erfoud 1 were the most salt-tolerant cultivars. The evaluated germplasm, and particularly some exotic cultivars, could be used as parents to breed new varieties more adapted to drought and salinity in the Mediterranean basin.

Stomatal and Photosynthetic Traits Are Associated with Investigating Sodium Chloride Tolerance of Brassica napus L. Cultivars

The negative effects of salt stress vary among different rapeseed cultivars. In this study, we investigated the sodium chloride tolerance among 10 rapeseed cultivars based on membership function values (MFV) and Euclidean cluster analyses by exposing seedlings to 0, 100, or 200 mM NaCl. The NaCl toxicity significantly reduced growth, biomass, endogenous K+ levels, relative water content and increased electrolyte leakage, soluble sugar levels, proline levels, and antioxidant enzyme activities. SPAD values were highly variable among rapeseed cultivars. We identified three divergent (tolerant, moderately tolerant, and sensitive) groups. We found that Hua6919 and Yunyoushuang2 were the most salt-tolerant cultivars and that Zhongshuang11 and Yangyou9 were the most salt-sensitive cultivars. The rapeseed cultivars were further subjected to photosynthetic gas exchange and anatomical trait analyses. Among the photosynthetic gas exchange and anatomical traits, the stomatal aperture was the most highly correlated with salinity tolerance in rapeseed cultivars and thus, is important for future studies that aim to improve salinity tolerance in rapeseed. Thus, we identified and characterized two salt-tolerant cultivars that will be useful for breeding programs that aim to develop salt-tolerant rapeseed.

Yield of different rice cultivars at two levels of soil salinity under seawater intrusion in West Java, Indonesia

Subekti NA, Sembiring H, Erythrina, Nugraha D, Priatmojo B, Nafisah. 2020. Yield of different rice cultivars at two levels of soil salinity under seawater intrusion in West Java, Indonesia. Biodiversitas 21: 14-20. A tendency to use saline water in rice production is rising in recent years, but the adaptation of variety under saline conditions is still questionable. The aim of the study was to evaluate the response of several rice cultivars on the growth and yield of rice under seawater intrusion in West Java. Two salt-tolerant cultivars (Inpari 34 and Inpari 35), two promising lines (PL-1 and PL-2) and two modern cultivars (Inpari 30 (Ciherang sub1) and Sidenuk) were evaluated in two soil salinity levels. In each farmer's field a Randomized Complete Block Design was applied with three replications per treatment. Results showed that Sidenuk and Inpari 30 produced same yield compared to tolerant varieties and promising lines during dry season under moderate soil salinity. There were not much different among the cultivars tested in terms of plant height and tiller number as well as the biomass and harvest index. However, under high soil salinity seed germination, plant height, number of tillers per plant, above-ground biomass, spikelet number, percent of sterile florets and productivity were significantly affected. Saline tolerant varieties Inpari 34 and Inpari 35 showed their superiority compared to non-tolerant varieties. Both varieties produced 40% higher yield than Inpari 30 (Ciherang sub 1) and Sidenuk.

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties.