Salt-sensitive Rice Varieties Research Articles

Comparative Physiological and Transcriptomic Profiling Reveals the Characteristics of Tissue Tolerance Mechanisms in the japonica Rice Landrace Under Salt Stress

AbstractThe aim of this study was to characterize the tissue tolerance mechanisms of rice under salt stress. Our preliminary experiment identified a japonica rice landrace Shuzenji-kokumai (SZK), which is considered to be tissue-tolerant because it can maintain better growth than salt-sensitive rice varieties while having a high-Na+ concentration in the shoots under salt stress. These mechanisms differ from those of most salt-tolerant rice varieties, which have low Na+ concentrations in the shoots. We compared the physiological and molecular characteristics of SZK with those of FL478, a salt-tolerant variety, and Kunishi, a salt-sensitive variety. Under salt stress conditions, SZK accumulated high levels of Na+ in the roots, leaf sheaths, and leaf blades, which were almost as high as those in the salt-sensitive Kunishi. Simultaneously, SZK maintained better growth and physiological status, as determined by its higher dry weight, lower electrolyte leakage ratio, and lower malondialdehyde concentration. Expressions of OsNHX1 and OsNHX2 were upregulated in the leaf sheaths of SZK, suggesting that Na+ might be compartmentalized in the vacuoles to avoid cytosolic Na+ toxicity. In contrast, FL478 showed upregulation of OsHKT1;5 and OsSOS1 in the roots, which may exclude Na+ from the shoots. RNA-seq analysis showed that 4623 and 1998 differentially expressed genes were detected in the leaf sheaths and leaf blades of SZK, respectively. Among them, the HSP (heat shock protein) gene expression was highly up-regulated only in SZK, indicating that SZK protects against the protein damage caused by Na+ toxicity. Our findings suggest that SZK has atypical survival mechanisms under salt stress conditions. These mechanisms offer potential traits for improving salt tolerance in rice in terms of tissue tolerance.

Development of early maturing salt-tolerant rice variety KKL(R) 3 using a combination of conventional and molecular breeding approaches.

Introduction: Soil salinity poses a severe threat to rice production, resulting in stunted growth, leaf damage, and substantial yield losses. This study focuses on developing an early maturing seedling stage salinity tolerant rice variety by integrating conventional breeding methods with marker assisted breeding (MAB) approaches. Methods: Seedling-stage salinity tolerance Quantitative Trait Locus (QTL) "Saltol" from the salt-tolerant parent FL478 was introduced into the high-yielding but salt-sensitive rice variety ADT 45. This was achieved through a combination of conventional breeding and MAB. The breeding process involved rigorous selection, screening, and physiological parameter assessments. Results: KKL(R) 3 (KR 15066) identified as the top performing Recombinant Inbred Line (RIL), consistently demonstrating maximum mean grain yields under both salinity (3435.6kg/ha) and normal (6421.8kg/ha) conditions. In comparison to the early maturing, salt-tolerant national check variety CSR 10, KKL(R) 3 exhibited a substantial yield increase over 50%. Discussion: The notable improvement observed in KKL(R) 3 positions it as a promising variety for release, offering a reliable solution to maximize yields, ensure food security, and promote agricultural sustainability in both saline and non-saline environments. The study highlights the effectiveness of MAB in developing salt-tolerant rice varieties and emphasizes the significance of the Saltol QTL in enhancing seedling stage salinity tolerance. The potential release of KKL(R) 3 has the capacity to revolutionize rice production in salt affected regions, providing farmers with a reliable solution to maximize yields and contribute to food security while ensuring agricultural sustainability.

Analysis of Morphological, Physiological, and Biochemical Traits of Salt Stress Tolerance in Asian Rice Cultivars at Seedling and Early Vegetative Stages

Rice (Oryza sativa L.) is a primary energy food for the Asian population. One of the greatest constraints in rice production is soil salinity because rice is very susceptible to salt. Meanwhile, many agricultural lands in Asia are in saline areas. It is important to identify and develop salt-tolerant rice varieties that highly adapt to Asian climates. By combining morphological, physiological, and biochemical assessments for screening the salt tolerance of 116 Asian rice cultivars, we were able to classify them into tolerant, moderate, and sensitive rice cultivars under salinity stress conditions and also understand salt tolerance mechanisms. The rice cultivars that are salt-tolerant include Pokkali from India, TCCP 266 and IR 45427 from the Philippines, and Namyang 7 from Republic of Korea. However, salt-sensitive rice varieties like IR29 and IR58 are from the Philippines, and Daegudo and Guweoldo are from Korea. The salt-tolerant varieties showed signs of tolerance, including a lower percent reduction in germination percentage, root length, root fresh weight, shoot length, plant biomass, and chlorophyll content. In order to maintain the cellular osmotic balance under saline conditions, the salt-tolerant varieties exhibited less membrane damage, a lower Na/K ratio, high proline and sugar accumulation, and lower levels of malondialdehyde (MDA) and hydrogen peroxide (H2O2). Pokkali from India, TCCP 266 and IR 45427 from the Philippines, and Namyang 7 from Republic of Korea are recommended as valuable germplasm resources for Asian rice breeding programs in saline agricultural areas.

Integrated Analysis of Transcriptome and Metabolome Reveals Molecular Mechanisms of Rice with Different Salinity Tolerances.

Rice is a crucial global food crop, but it lacks a natural tolerance to high salt levels, resulting in significant yield reductions. To gain a comprehensive understanding of the molecular mechanisms underlying rice's salt tolerance, further research is required. In this study, the transcriptomic and metabolomic differences between the salt-tolerant rice variety Lianjian5 (TLJIAN) and the salt-sensitive rice variety Huajing5 (HJING) were examined. Transcriptome analysis revealed 1518 differentially expressed genes (DEGs), including 46 previously reported salt-tolerance-related genes. Notably, most of the differentially expressed transcription factors, such as NAC, WRKY, MYB, and EREBP, were upregulated in the salt-tolerant rice. Metabolome analysis identified 42 differentially accumulated metabolites (DAMs) that were upregulated in TLJIAN, including flavonoids, pyrocatechol, lignans, lipids, and trehalose-6-phosphate, whereas the majority of organic acids were downregulated in TLJIAN. The interaction network of 29 differentially expressed transporter genes and 19 upregulated metabolites showed a positive correlation between the upregulated calcium/cation exchange protein genes (OsCCX2 and CCX5_Ath) and ABC transporter gene AB2E_Ath with multiple upregulated DAMs in the salt-tolerant rice variety. Similarly, in the interaction network of differentially expressed transcription factors and 19 upregulated metabolites in TLJIAN, 6 NACs, 13 AP2/ERFs, and the upregulated WRKY transcription factors were positively correlated with 3 flavonoids, 3 lignans, and the lipid oleamide. These results suggested that the combined effects of differentially expressed transcription factors, transporter genes, and DAMs contribute to the enhancement of salt tolerance in TLJIAN. Moreover, this study provides a valuable gene-metabolite network reference for understanding the salt tolerance mechanism in rice.

Variety-Specific Transcriptional and Alternative Splicing Regulations Modulate Salt Tolerance in Rice from Early Stage of Stress

Salt stress poses physiological drought, ionic toxicity and oxidative stress to plants, which causes premature senescence and death of the leaves if the stress sustained. Salt tolerance varied between different rice varieties, but how different rice varieties respond at the early stage of salt stress has been seldom studied comprehensively. By employing third generation sequencing technology, we compared gene expressional changes in leaves of three rice varieties that varied in their level of tolerance after salt stress treatment for 6 h. Commonly up-regulated genes in all rice varieties were related to water shortage response and carbon and amino acids metabolism at the early stage of salt stress, while reactive oxygen species cleavage genes were induced more in salt-tolerant rice. Unexpectedly, genes involved in chloroplast development and photosynthesis were more significantly down-regulated in the two salt tolerant rice varieties ‘C34’ and ‘Nona Bokra’. At the same time, genes coding ribosomal protein were suppressed to a more severe extent in the salt-sensitive rice variety ‘IR29’. Interestingly, not only variety-specific gene transcriptional regulation, but also variety-specific mRNA alternative splicing, on both coding and long-noncoding genes, were found at the early stage of salt stress. In summary, differential regulation in gene expression at both transcriptional and post-transcriptional levels, determine and fine-tune the observed response in level of damage in leaves of specific rice genotypes at early stage of salt stress.

Boron Facilitates Rice Growth, Development, and Related Attributes Under Saline Soil Conditions

Abstract Salinity is a severe environmental threat causing low productivity in field crops. Rice is a staple crop of the world whose yield and quality is highly affected by the salt content in the root zone. Nutrient management, however, is a key factor that can be used to boost rice production in saline soils. Boron (B), a micronutrient with diverse functions, plays a significant role in rice yield. However, little is known about the effects of B under saline conditions on the yield of rice components. ‘Swarna,’ is a local and salt-sensitive rice variety from Bangladesh. A field experiment was conducted in salt-treated soils to assess the possible functions of B for the improvement of ‘Swarna’ yield. The current study showed that B applications substantially improved the length and weight of panicles, number of tillers and grains, seed weight as well as the yield of grain and straw, indicating its role in rice production in saline environments.

Mapping the Salt Stress-Induced Changes in the Root miRNome in Pokkali Rice.

A plant’s response to stress conditions is governed by intricately coordinated gene expression. The microRNAs (miRs) have emerged as relatively new players in the genetic network, regulating gene expression at the transcriptional and post-transcriptional level. In this study, we performed comprehensive profiling of miRs in roots of the naturally salt-tolerant Pokkali rice variety to understand their role in regulating plant physiology in the presence of salt. For comparisons, root miR profiles of the salt-sensitive rice variety Pusa Basmati were generated. It was seen that the expression levels of 65 miRs were similar for roots of Pokkali grown in the absence of salt (PKNR) and Pusa Basmati grown in the presence of salt (PBSR). The salt-induced dis-regulations in expression profiles of miRs showed controlled changes in the roots of Pokkali (PKSR) as compared to larger variations seen in the roots of Pusa Basmati. Target analysis of salt-deregulated miRs identified key transcription factors, ion-transporters, and signaling molecules that act to maintain cellular Ca2+ homeostasis and limit ROS production. These miR:mRNA nodes were mapped to the Quantitative trait loci (QTLs) to identify the correlated root traits for understanding their significance in plant physiology. The results obtained indicate that the adaptability of Pokkali to excess salt may be due to the genetic regulation of different cellular components by a variety of miRs.

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

Endophytes, both of bacterial and fungal origin, are ubiquitously present in all plants. While their origin and evolution are enigmatic, there is burgeoning literature on their role in promoting growth and stress responses in their hosts. We demonstrate that a salt-tolerant endophyte isolated from salt-adapted Pokkali rice, a Fusarium sp., colonizes the salt-sensitive rice variety IR-64, promotes its growth under salt stress and confers salinity stress tolerance to its host. Physiological parameters, such as assimilation rate and chlorophyll stability index were higher in the colonized plants. Comparative transcriptome analysis revealed 1348 up-regulated and 1078 down-regulated genes in plants colonized by the endophyte. Analysis of the regulated genes by MapMan and interaction network programs showed that they are involved in both abiotic and biotic stress tolerance, and code for proteins involved in signal perception (leucine-rich repeat proteins, receptor-like kinases) and transduction (Ca2+ and calmodulin-binding proteins), transcription factors, secondary metabolism and oxidative stress scavenging. For nine genes, the data were validated by qPCR analysis in both roots and shoots. Taken together, these results show that salt-adapted Pokkali rice varieties are powerful sources for the identification of novel endophytes, which can be used to confer salinity tolerance to agriculturally important, but salt-sensitive rice varieties.

Biochar alleviated the salt stress of induced saline paddy soil and improved the biochemical characteristics of rice seedlings differing in salt tolerance

Biochar is used mainly to alleviate salt stress in arid and semiarid soils, or to regulate acidification stress in paddy soils. However, the effects of biochar on paddy soil environments under salt stress and the biochemical characteristics of rice seedlings differing in salt tolerance are unclear. This study explored whether and how biochar is involved in alleviating salt stress in paddy soil and regulating the biochemical characteristics of rice seedlings. The trial was conducted under pot culture conditions, and NaCl was used as the salt stress agent in paddy soil. Two rice varieties were used in this trial: Jinyuan 85 (a salt-tolerant rice variety) and Nipponbare (a salt-sensitive rice variety). The salt stress included three treatments: 0 g NaCl kg−1 dry soil (control, S0), 1 g NaCl kg−1 dry soil (S1), and 3 g NaCl kg−1 dry soil (S3). Biochar produced by rice straw involved three treatments: no biochar (control, C0), biochar produced at 300℃ applied into soil (C300), and biochar produced at 600℃ applied into soil (C600). The results suggested that the adsorption ability of the biochar produced at 600℃ was significantly higher than that of the biochar produced at 300℃. Bulk density, electrical conductivity, exchangeable Na+ and exchangeable Cl- in the soil under salt stress were greatly decreased by the application of biochar, and the soil environment of C600 was more favorable for rice seedlings. The salt accumulations in the rice seedling, and the microstructure of the root and leaf of the rice seedlings under salt stress were significantly and positively affected by the biochar, and the biochemical characteristics of the rice seedlings also greatly improved in response to biochar application. The responses of Nipponbare to salt stress were more severe than those of Jinyuan 85, while the regulatory effects of biochar were more favorable for Jinyuan 85 than for Nipponbare. In conclusion, biochar, especially that produced at 600℃ in this trial played a positive role in alleviating the inhibitory effects of salt stress on rice seedlings, and might be useful as an amendment in saline soils to improve rice plant growth.

Salt Tolerant and Sensitive Rice Varieties Display Differential Methylome Flexibility under Salt Stress.

DNA methylation has been referred as an important player in plant genomic responses to environmental stresses but correlations between the methylome plasticity and specific traits of interest are still far from being understood. In this study, we inspected global DNA methylation levels in salt tolerant and sensitive rice varieties upon salt stress imposition. Global DNA methylation was quantified using the 5-methylcytosine (5mC) antibody and an ELISA-based technique, which is an affordable and quite pioneer assay in plants, and in situ imaging of methylation sites in interphase nuclei of tissue sections. Variations of global DNA methylation levels in response to salt stress were tissue- and genotype-dependent. We show a connection between a higher ability of DNA methylation adjustment levels and salt stress tolerance. The salt-tolerant rice variety Pokkali was remarkable in its ability to quickly relax DNA methylation in response to salt stress. In spite of the same tendency for reduction of global methylation under salinity, in the salt-sensitive rice variety IR29 such reduction was not statistically supported. In ‘Pokkali’, the salt stress-induced demethylation may be linked to active demethylation due to increased expression of DNA demethylases under salt stress. In ‘IR29’, the induction of both DNA demethylases and methyltransferases may explain the lower plasticity of DNA methylation. We further show that mutations for epigenetic regulators affected specific phenotypic parameters related to salinity tolerance, such as the root length and biomass. This work emphasizes the role of differential methylome flexibility between salt tolerant and salt sensitive rice varieties as an important player in salt stress tolerance, reinforcing the need to better understand the connection between epigenetic networks and plant responses to environmental stresses.

Transcriptional Downregulation of Rice rpL32 Gene under Abiotic Stress Is Associated with Removal of Transcription Factors within the Promoter Region

BackgroundThe regulation of ribosomal proteins in plants under stress conditions has not been well studied. Although a few reports have shown stress-specific post-transcriptional and translational mechanisms involved in downregulation of ribosomal proteins yet stress-responsive transcriptional regulation of ribosomal proteins is largely unknown in plants.Methodology/Principal FindingsIn the present work, transcriptional regulation of genes encoding rice 60S ribosomal protein L32 (rpL32) in response to salt stress has been studied. Northern and RT-PCR analyses showed a significant downregulation of rpL32 transcripts under abiotic stress conditions in rice. Of the four rpL32 genes in rice genome, the gene on chromosome 8 (rpL32_8.1) showed a higher degree of stress-responsive downregulation in salt sensitive rice variety than in tolerant one and its expression reverted to its original level upon withdrawal of stress. The nuclear run-on and promoter:reporter assays revealed that the downregulation of this gene is transcriptional and originates within the promoter region. Using in vivo footprinting and electrophoretic mobility shift assay (EMSA), cis-elements in the promoter of rpL32_8.1 showing reduced binding to proteins in shoots of salt stressed rice seedlings were identified.ConclusionsThe present work is one of the few reports on study of stress downregulated genes. The data revealed that rpL32 gene is transcriptionally downregulated under abiotic stress in rice and that this transcriptional downregulation is associated with the removal of transcription factors from specific promoter elements.

Amelioration of salinity stress by exogenously applied spermidine or spermine in three varieties of indica rice differing in their level of salt tolerance

We present here the comparative protective potentiality of exogenously applied polyamines (PAs), namely spermidine (Spd) and spermine (Spm), in mitigating NaCl toxicity and inducing short-term salinity tolerance in three indica rice varieties, namely M-1-48 (salt-sensitive), Nonabokra (salt-tolerant) and Gobindobhog (highly sensitive). The retardation in root length or shoot length and toxic Na + accumulation or K + loss, the considerable increment in malondialdehyde/H 2O 2 accumulation or lipoxygenase activity, all of which were particularly noteworthy in M-1-48 and Gobindobhog during salinity stress, was appreciably reduced by co-treatment with Spd or Spm. Both the PAs also inhibited the extent of salt-induced protein carbonylation in all the varieties and enhanced protease activity, especially in Gobindobhog. The prevention of chlorophyll degradation was better with Spd in Nonabokra and Gobindobhog. While the salt-induced increase in anthocyanin or reducing sugar level was further prompted by Spd or Spm in all the varieties, the proline content was elevated by Spd particularly in Gobindobhog. During salinity stress, both the PAs were effective in lowering the putrescine accumulation in M-1-48 and Gobindobhog, and strikingly increasing the Spm level in all the varieties, the highest being in Gobindobhog. In addition, they enhanced the activity of peroxidases and compensated for the decreased catalase activity in all the varieties. Thus the two PAs could recuperate all the three varieties from salt-induced damages to different degrees. The salt injuries, encountered in M-1-48 and Gobindobhog, both of which showed greater susceptibility to salinity stress, were more pronouncedly alleviated and counteracted by the PAs, than the salt-tolerant Nonabokra. The reversal of inhibitory effect of salinity stress was conferred by preventing growth inhibition or various forms of cellular damages, maintaining proper K +/Na + balance or triggering the level of osmolytes and activity of antioxidant enzymes. Our communication offers a referenced evidence for an understanding of the mechanism by which higher PAs relieve the damages particularly in salt-sensitive rice varieties.

Comparative Effects of Salt Stress and Extreme pH Stress Combined on Glycinebetaine Accumulation, Photosynthetic Abilities and Growth Characters of Two Rice Genotypes

Glycinebetaine (Glybet) accumulation, photosynthetic efficiency and growth performance in indica rice cultivated under salt stress and extreme pH stress were investigated. Betaine aldehyde dehydrogenase (BADH) activity and Glybet accumulation in the seedlings of salt-tolerant and salt-sensitive rice varieties grown under saline and acidic conditions peaked after treatment for 72 h and 96 h, respectively, and were higher than those grown under neutral pH and alkaline salt stress. A positive correlation was found between BADH activity and Glybet content in both salt-tolerant ( r 2 = 0.71) and salt-sensitive ( r 2 = 0.86) genotypes. The chlorophyll a, chlorophyll b, total chlorophyll and total carotenoids contents in the stressed seedlings significantly decreased under both acidic and alkaline stresses, especially in the salt-sensitive genotype. Similarly, the maximum quantum yield of PSII ( F v/ F m), photon yield of PSII (Φ PSII), non-photochemical quenching (NPQ) and net photosynthetic rate ( P n) in the stressed seedlings were inhibited, leading to overall growth reduction. The positive correlations between chlorophyll a content and F v/ F m, total chlorophyll content and Φ PSII, Φ PSII and P n as well as P n and leaf area in both salt-tolerant and salt-sensitive genotypes were found. Saline acidic and saline alkaline soils may play a key role affecting vegetative growth prior to the reproductive stage in rice plants.

A group 3 LEA cDNA of rice, responsive to abscisic acid, but not to jasmonic acid, shows variety-specific differences in salt stress response

A cDNA clone oslea3, encoding a group 3 late-embryogenesis abundant (LEA) protein was isolated from roots of rice seedlings ( Oryza sativa L.). The encoded OSLEA3 protein has previously been found to accumulate to higher levels in roots of two salt-tolerant compared to a salt-sensitive rice variety in response to abscisic acid (ABA) [Moons et al., 1995. Plant Physiol. 107, 177–186]. The OSLEA3 protein ( M r 20.5, p I 6.5) characteristically contains ten imperfect 11-mer amino acid repeats. Exogenous application of ABA and exposure to salt shock (150 mM NaCl) rapidly induces a de novo, abundant oslea3 transcript accumulation in seedling roots, whereas application of jasmonic acid (9 μM) does not induce oslea3 expression. The stress-induced oslea3 transcript gradually declined upon prolonged salt shock, as wilting-induced damage became irreversible. oslea3 expression was compared for the salt-tolerant variety Pokkali and the salt-sensitive cultivar Taichung N1. Higher maximal mRNA levels were found in roots of the tolerant variety, also declining less rapidly upon sustained salt shock, concomitant with a delayed drop in shoot water content. DNA blot analysis indicated the existence of a small oslea3 gene family in rice with an equal gene number in both ecotypes. The results suggest that a differential regulation of oslea3 expression is an aspect of the varietal differences in salt stress tolerance.

Salinity, oxidative stress and antioxidant responses in shoot cultures of rice

When shoot cultures derived from salt-sensitive Oryza sativa var. Taipei 309 were grown at 25°C in medium containing 0.35 M NaCl, responses to possible oxidative stress in the early stages of exposure were observed. Overall levels of Mn-superoxide dismutase activity, Cu, Zn-superoxide dismutase activity and H2O2 were significantly elevated. After 1 d there was a notable decline in tissue concentrations of GSH and a corresponding increase in GSSG. However, after a further day, concentrations of GSH and GSSG returned to concentrations normally encountered in control cultures. Activities of ascorbate peroxidase and catalase were similar whether the shoots were grown in the presence or absence of NaCl. In contrast, there was an early increase in glutathione reductase activity in NaCl-exposed cultures, and no indication of extensive increases in lipid peroxidation. Thus although some indications of oxidative stress accompany exposure of this salt-sensitive rice variety to salinity, mechanisms appear to exist within its shoot tissue to permit the tolerance of such oxidative stress.

Sodium Chloride Stimulates Adenylate Kinase Level in Seedlings of Salt-Sensitive Rice Varieties

Summary Comparison of adenylate kinase activities in rice seedlings ( Oryza sativa L. cv. Yamahoushi) that had been grown in the absence or presence of NaCl indicated that NaCI apparently stimulated enzyme activities in roots of this salt-sensitive japonica rice cultivar. Such stimulation of enzyme activities is not limited to a specific portion of root tissues. Furthermore, NaCl-induced adenylate kinase activation was confirmed in the indica rice cultivar IR 28 susceptible to salinity-stress, but not in the NaCl-tolerant indica cultivar Nona Bokra. Thus in salt sensitive rice plants, adenylate kinase may play some role in the adenylate homeostatis at the early stages of rice seedling growth subjected to salt-stress.