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Keywords = salt-sensitive rice

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18 pages, 6628 KB  
Article
An Analysis of the Different Salt-Tolerance Mechanisms in Rice Cultivars Induced by Cerium Oxide Nanoparticles
by Chunmei Yang, Qing Bu, Tao Su, Tian Wang, Zaid Khan, Mingwei Li, Juntian Wu, Xiaodan Di, Yong Chen and Jing An
Antioxidants 2025, 14(8), 994; https://doi.org/10.3390/antiox14080994 - 13 Aug 2025
Viewed by 610
Abstract
Cerium oxide nanoparticles (CeO2NPs) can boost crops’ salt tolerance, yet their regulatory mechanisms in rice cultivars with contrasting salt tolerance remain unclear. This study investigated the regulatory differences in poly (acrylic acid)-coated nanoceria (PNC)-primed in salt-sensitive (Huanghuazhan, H) and salt-tolerant (Xiangliangyou900, [...] Read more.
Cerium oxide nanoparticles (CeO2NPs) can boost crops’ salt tolerance, yet their regulatory mechanisms in rice cultivars with contrasting salt tolerance remain unclear. This study investigated the regulatory differences in poly (acrylic acid)-coated nanoceria (PNC)-primed in salt-sensitive (Huanghuazhan, H) and salt-tolerant (Xiangliangyou900, X) rice. The results showed that PNC priming improved salt tolerance in two cultivars, but the underlying mechanisms differed. In the H cultivar, the enhanced tolerance was primarily attributed to enhanced photosynthesis (net photosynthesis and transpiration rates were 53.27% and 20.52% higher than the X cultivar); increased abscisic acid (ABA) content (up by 18.80% compared to the X cultivar), and activated stress-responsive signaling. Metabolomics further revealed that the differential metabolites were enriched in galactose metabolism, ascorbate, and aldarate metabolism, synergistically maintaining intracellular redox balance. In the X cultivar, PNC boosted reactive oxygen species’ (ROS) scavenging capacity (catalase (CAT) increased 36.07%, H2O2 and malondialdehyde (MDA) decreased 27.31% and 48.61% compared to H); elevated endogenous indole-3-acetic acid (IAA) and gibberellic acid3 (GA3) levels by 9.55% and 9.08%; and specifically activated cellular defense response and glutathione metabolism. Transcriptome analysis further revealed that the expression of IAA/GA3 signal-responsive genes (OsARGOS/OsGASR2) and antioxidant genes (OsCatA, OsAPX1) were significantly higher in the X cultivar than the H cultivar (p < 0.05), whereas the H cultivar showed higher expression of GST and ABA-related genes. This study provides a new perspective for the mechanism of PNC-enhanced salt tolerance in rice. Full article
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17 pages, 16726 KB  
Article
Genome-Wide Identification, Characterization, and Comparison of C3HC4 Family Genes in Salt Tolerance Between Barley and Rice
by Kerun Chen, Shuai Wang, Xiaohan Xu, Xintong Zheng, Hongkai Wu, Linzhou Huang, Liping Dai, Chenfang Zhan, Dali Zeng and Liangbo Fu
Plants 2025, 14(15), 2404; https://doi.org/10.3390/plants14152404 - 3 Aug 2025
Viewed by 611
Abstract
Soil salinization constitutes a major constraint on global agricultural production, with marked divergence in salt adaptation strategies between salt-tolerant barley (Hordeum vulgare) and salt-sensitive rice (Oryza sativa). This study systematically investigated the evolution and functional specialization of the C3HC4-type [...] Read more.
Soil salinization constitutes a major constraint on global agricultural production, with marked divergence in salt adaptation strategies between salt-tolerant barley (Hordeum vulgare) and salt-sensitive rice (Oryza sativa). This study systematically investigated the evolution and functional specialization of the C3HC4-type RING zinc finger gene family, known to mediate abiotic stress responses through E3 ubiquitin ligase activity, in these contrasting cereal species. Through comparative genomics, we identified 123 HvC3HC4 genes and 90 OsC3HC4 genes, phylogenetically classified into four conserved subgroups. Differences in C3HC4 genes in phylogenetic relationships, chromosomal distribution, gene structure, motif composition, gene duplication events, and cis-elements in the promoter region were observed between barley and rice. Moreover, HvC3HC4s in barley tissues preferentially adopted an energy-conserving strategy, which may be a key mechanism for barley’s higher salt tolerance. Additionally, we found that C3HC4 genes were evolutionarily conserved in salt-tolerant species. The current results reveal striking differences in salt tolerance between barley and rice mediated by the C3HC4 gene family and offer valuable insight for potential genetic engineering applications in improving crop resilience to salinity stress. Full article
(This article belongs to the Special Issue Cell Physiology and Stress Adaptation of Crops)
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15 pages, 1490 KB  
Article
Comparative Transcriptome and Hormonal Analysis Reveals the Mechanisms of Salt Tolerance in Rice
by Dingsha Jin, Yanchao Xu, Asif Iqbal, Yuqing Liu, Yage Zhang, Youzhen Lin, Liqiong Tang, Xinhua Wang, Junjie Wang, Mengshu Huang, Peng Xu and Xiaoning Wang
Int. J. Mol. Sci. 2025, 26(14), 6660; https://doi.org/10.3390/ijms26146660 - 11 Jul 2025
Viewed by 543
Abstract
Salt stress is a major constraint to seed germination and early seedling growth in rice, affecting crop establishment and productivity. To understand the mechanisms underlying salt tolerance, we investigated two rice varieties with contrasting responses as follows: salt-tolerant sea rice 86 (SR86) and [...] Read more.
Salt stress is a major constraint to seed germination and early seedling growth in rice, affecting crop establishment and productivity. To understand the mechanisms underlying salt tolerance, we investigated two rice varieties with contrasting responses as follows: salt-tolerant sea rice 86 (SR86) and salt-sensitive P559. Germination assays under increasing NaCl concentrations (50–300 mM) revealed that 100 mM NaCl induced clear phenotypic divergence. SR86 maintained bud growth and showed enhanced root elongation under moderate salinity, while P559 exhibited significant growth inhibition. Transcriptomic profiling of buds and roots under 100 mM NaCl identified over 3724 differentially expressed genes (DEGs), with SR86 showing greater transcriptional plasticity, particularly in roots. Gene ontology enrichment revealed tissue- and genotype-specific responses. Buds showed enrichment in photosynthesis-related and redox-regulating pathways, while roots emphasized ion transport, hormonal signaling, and oxidative stress regulation. SR86 specifically activated genes related to photosystem function, DNA repair, and transmembrane ion transport, while P559 showed activation of oxidative stress-related and abscisic acid (ABA)-regulated pathways. Hormonal profiling supported transcriptomic findings as follows: both varieties showed increased gibberellin 3 (GA3) and gibberellin 4 (GA4) levels under salt stress. SR86 showed elevated auxin (IAA) and reduced jasmonic acid (JA), whereas P559 maintained stable IAA and JA levels. Ethylene precursor and salicylic acid levels declined in both varieties. ABA levels rose slightly but not significantly. These findings suggest that SR86’s superior salt tolerance results from rapid growth, robust transcriptional reprogramming, and coordinated hormonal responses. This study offers key insights into early-stage salt stress adaptation and identifies molecular targets for improving stress resilience in rice. Full article
(This article belongs to the Section Molecular Plant Sciences)
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16 pages, 2462 KB  
Article
Potential of LP as a Biocontrol Agent for Vibriosis in Abalone Farming
by Ling Ke, Chenyu Huang, Song Peng, Mengshi Zhao, Fengqiang Lin and Zhaolong Li
Microorganisms 2025, 13(7), 1554; https://doi.org/10.3390/microorganisms13071554 - 2 Jul 2025
Viewed by 479
Abstract
Vibrio species are among the primary pathogenic bacteria affecting abalone aquaculture, posing significant threats to farming practices. Current clinical control predominantly relies on antibiotics, which can result in antibiotic residues in both abalone and the surrounding marine environments. Lactobacillus plantarum (LP) [...] Read more.
Vibrio species are among the primary pathogenic bacteria affecting abalone aquaculture, posing significant threats to farming practices. Current clinical control predominantly relies on antibiotics, which can result in antibiotic residues in both abalone and the surrounding marine environments. Lactobacillus plantarum (LP) has been shown to release bioactive antagonistic substances and exhibits potent inhibitory effects against marine pathogenic bacteria. This study aimed to screen and characterize the probiotic properties of LP strains isolated from rice wine lees to develop a novel biocontrol strategy against Vibriosis in abalone. The methods employed included selective media cultivation, streak plate isolation, and single-colony purification for strain screening, followed by Gram staining, 16S rDNA sequencing, and phylogenetic tree construction using MEGA11 for identification. The resilience, antimicrobial activity, and in vivo antagonistic efficacy of the strains were evaluated through stress tolerance assays, agar diffusion tests, and animal experiments. The results demonstrated the successful isolation and purification of four LP strains (NDMJ-1 to NDMJ-4). Phylogenetic analysis revealed closer genetic relationships between NDMJ-3 and NDMJ-4, while NDMJ-1 and NDMJ-2 were found to be more distantly related. All strains exhibited γ-hemolytic activity, bile salt tolerance (0.3–3.0%), and resistance to both acid (pH 2.5) and alkali (pH 8.5), although they were temperature sensitive (inactivated above 45 °C). The strains showed susceptibility to most of the 20 tested antibiotics, with marked variations in hydrophobicity (1.91–93.15%) and auto-aggregation (13.29–60.63%). In vitro antibacterial assays revealed that cell-free supernatants of the strains significantly inhibited Vibrio parahaemolyticus, V. alginolyticus, and V. natriegens, with NDMJ-4 displaying the strongest inhibitory activity. In vivo experiments confirmed that NDMJ-4 significantly reduced mortality in abalone infected with V. parahaemolyticus. In conclusion, the LP strains isolated from rice wine lees (NDMJ-1 to NDMJ-4) possess robust stress resistance, adhesion capabilities, and broad antibiotic susceptibility. Their metabolites exhibit significant inhibition against abalone-pathogenic Vibrios, particularly NDMJ-4, which demonstrates exceptional potential as a candidate strain for developing eco-friendly biocontrol agents against Vibriosis in abalone aquaculture. Full article
(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)
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21 pages, 3424 KB  
Article
Molecular Regulation of Antioxidant Defense and Metabolic Reprogramming in Xiaozhan Rice Genotypes: Differential Roles of Salicylic Acid and Melatonin Under Salt Stress
by Yang Wu, Yongbo Duan, Xifan Luo, Mingjun Li, Hengjie Gao, Wei Zhu, Fei Zhao, Jian Liu and Wenzhong Zhang
Curr. Issues Mol. Biol. 2025, 47(6), 432; https://doi.org/10.3390/cimb47060432 - 7 Jun 2025
Viewed by 729
Abstract
Against the background of increasing global soil salinity, exogenous salicylic acid (SA) and melatonin (MT) have attracted much attention for their potential in regulating plant stress tolerance and have become an important research direction for the development of green and sustainable agriculture. In [...] Read more.
Against the background of increasing global soil salinity, exogenous salicylic acid (SA) and melatonin (MT) have attracted much attention for their potential in regulating plant stress tolerance and have become an important research direction for the development of green and sustainable agriculture. In this study, the alleviating effects of different concentrations of SA (100–900 μM) and MT (100–900 μM) on salt stress (50 mM NaCl) and their physiological mechanisms were systematically investigated using the Tianjin specialty rice, Xiaozhan rice, as the research object. The results showed that salt stress significantly inhibited the germination and seedling growth of the two varieties, in which the salt-sensitive variety Jinchuan No. 1 showed significantly higher decreases in root length, plant height, and biomass (54.7–69.1%) than the salt-tolerant variety Jindao 919 (4.0–28.9%). Exogenous SA and MT were effective in mitigating salt stress injury, but there were genotypic differences in their pathways of action. For the first time in japonica rice, the genotype specificity of the SA/MT response was clearly revealed: SA dominated the response of salt-tolerant varieties by enhancing antioxidant defences, whereas MT optimized the overall performance of the salt-sensitive varieties through scavenging of reactive oxygen species, and in addition, it was further determined that SA and MT exhibited optimal mitigating effects on both varieties in the 300–700 μM concentration range, showing the best mitigation effect for both varieties. This finding provides an important theoretical basis and technological paradigm for precision stress tolerance cultivation of saline rice, and the application of appropriate concentrations of SA/MT according to genotype specificity to reduce the dependence on agrochemicals is of practical value in promoting green and sustainable production in saline agriculture. Full article
(This article belongs to the Special Issue Molecular Mechanisms in Plant Stress Tolerance)
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20 pages, 5731 KB  
Article
Enhancement of Antioxidant Enzymatic Defenses in Salt-Adapted Rice Seedlings
by Giuseppe Forlani
Agriculture 2025, 15(12), 1234; https://doi.org/10.3390/agriculture15121234 - 6 Jun 2025
Viewed by 569
Abstract
While a rapid activation of antioxidant defense mechanisms following the exposure to salt stress has been widely reported in plants, less is known about their role under prolonged ionic stress conditions. This study aimed at investigating whether increased levels of enzymatic antioxidants are [...] Read more.
While a rapid activation of antioxidant defense mechanisms following the exposure to salt stress has been widely reported in plants, less is known about their role under prolonged ionic stress conditions. This study aimed at investigating whether increased levels of enzymatic antioxidants are required in salt-acclimated plants. Rice, a staple crop for more than half of the world’s population, is very sensitive to excess salt, mainly at the seedling stage. The levels of selected antioxidant enzymes and the non-enzymatic antioxidant glutathione were measured in seedlings of a group of five Italian rice cultivars showing a natural variability in the susceptibility to a moderate saline environment. Up to 15.62 dS/m, the presence of salts caused a progressive growth inhibition, yet thiobarbituric acid reactive substance levels did not significantly increase. Accordingly, chlorophyll content appeared unaffected, suggesting successful acclimation. Immunological analysis showed increases of catalase protein levels in shoots, and of Cu/Zn- and Mn-dependent superoxide dismutases in both roots and shoots, whereas no variations were found for other enzymes. Only slight differences in glutathione content were evident between salt-grown seedlings and untreated controls. The data suggest that an enhancement of antioxidant defenses in different tissues takes place in rice plants to cope with sublethal salt stress conditions. Full article
(This article belongs to the Special Issue Physiological and Molecular Mechanisms of Stress Tolerance in Rice)
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22 pages, 7954 KB  
Article
Genome-Wide Identification and Expression Analysis of Thionin Family in Rice (Oryza sativa) and Functional Characterization of OsTHION15 in Drought Stress and ABA Stress
by Maokai Yan, Mengnan Chai, Chang An, Xiaohu Jiang, Fan Yang, Xunlian Fang, Tingyu Liu, Yunfei Ju, Boping Tang, Hanyang Cai and Yuan Qin
Int. J. Mol. Sci. 2025, 26(7), 3447; https://doi.org/10.3390/ijms26073447 - 7 Apr 2025
Viewed by 996
Abstract
The OsTHION family represents a class of cysteine-rich signal peptides widely recognized for their significant roles in plant disease resistance and immunity. While members of this family are known to be induced under various biotic and abiotic stresses, their responses to environmental stressors [...] Read more.
The OsTHION family represents a class of cysteine-rich signal peptides widely recognized for their significant roles in plant disease resistance and immunity. While members of this family are known to be induced under various biotic and abiotic stresses, their responses to environmental stressors beyond disease resistance remain underexplored. This study investigates the evolution, expression patterns, and functional roles of the OsTHION gene family in rice (Oryza sativa) under diverse stress conditions. Using sequence data from the Phytozome database, we identified 44 OsTHION family members and classified them into four groups based on phylogenetic analysis. Cis-acting element analysis revealed that the promoter regions of OsTHION genes are enriched with regulatory elements associated with light response, hormone signaling, plant growth, and stress responses. The OsTHION genes exhibit complex organ-specific expression patterns, with OsTHION30 and OsTHION36 showing ubiquitous expression, while other members are highly expressed in specific tissues or developmental stages. Under drought, salt, and low-temperature stress, OsTHION genes undergo significant expression changes, underscoring their critical role in plant adaptation to environmental challenges. Notably, OsTHION15 was markedly upregulated under drought stress, and the Osthion15 mutant displayed heightened sensitivity to drought and ABA stress, confirming its pivotal role in stress resistance. RNA sequencing analysis identified many differentially expressed genes (DEGs), primarily enriched in pathways related to ribosomal function and plant hormone signaling, suggesting that OsTHION15 may regulate stress responses through multiple mechanisms. In summary, this study advances our understanding of the OsTHION gene family and highlights its intricate involvement in regulating rice growth, development, and environmental stress responses. These findings offer valuable insights and technical support for crop improvement, with potential applications in enhancing environmental adaptability and yield stability in crops. Full article
(This article belongs to the Special Issue Plant Response to Drought, Heat, and Light Stress)
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19 pages, 2441 KB  
Article
Unveiling the Impact of Organic Fertilizer on Rice (Oryza sativa L.) Salinity Tolerance: Insights from the Integration of NDVI and Metabolomics
by Jiaolong Li, Yunluo Li, Qiyun Xu, Xiaolei Niu, Guangping Cao and Hongyan Liu
Plants 2025, 14(6), 902; https://doi.org/10.3390/plants14060902 - 13 Mar 2025
Cited by 1 | Viewed by 1208
Abstract
Soil salinization threatens global agriculture, reducing crop productivity and food security. Developing strategies to improve salt tolerance is crucial for sustainable agriculture. This study examines the role of organic fertilizer in mitigating salt stress in rice (Oryza sativa L.) by integrating NDVI [...] Read more.
Soil salinization threatens global agriculture, reducing crop productivity and food security. Developing strategies to improve salt tolerance is crucial for sustainable agriculture. This study examines the role of organic fertilizer in mitigating salt stress in rice (Oryza sativa L.) by integrating NDVI and metabolomics. Using salt-sensitive (19X) and salt-tolerant (HHZ) cultivars, we aimed to (1) evaluate changes in NDVI and metabolite content under salt stress, (2) assess the regulatory effects of organic fertilizer, and (3) identify key metabolites involved in stress response and fertilizer-induced regulation. Under salt stress, survival rate of the 19X plants dropped to 6%, while HHZ maintained 38%, with organic fertilizer increasing survival rate to 25% in 19X and 66% in HHZ. NDVI values declined sharply in 19X (from 0.56 to <0.25) but remained stable in HHZ (~0.56), showing a strong correlation with survival rate (R2 = 0.87, p < 0.01). NDVI provided a dynamic, non-destructive assessment of rice health, offering a faster and more precise evaluation of salt tolerance than survival rate analysis. Metabolomic analysis identified 12 key salt-tolerant metabolites, including citric acid, which is well recognized for regulating salt tolerance. HTPA, pipecolic acid, maleamic acid, and myristoleic acid have previously been reported but require further study. Additionally, seven novel salt-tolerant metabolites—tridecylic acid, propentofylline, octadeca penten-3-one, 14,16-dihydroxy-benzoxacyclotetradecine-dione, cyclopentadecanolide, HpODE, and (±)8,9-DiHETE—were discovered, warranting further investigation. Organic fertilizer alleviated salt stress through distinct metabolic mechanisms in each cultivar. In 19X, it enhanced antioxidant defenses and energy metabolism, mitigating oxidative damage and improving fatty acid metabolism. In contrast, HHZ primarily benefitted from improved membrane stability and ion homeostasis, reducing lipid peroxidation and oxidative stress. These findings primarily support the identification and screening of salt-tolerant rice cultivars while also highlighting the need for cultivar-specific fertilization strategies to optimize stress resilience and crop performance. Based on the correlation analysis, 26 out of 53 differential metabolites were significantly correlated with NDVI, confirming a strong association between NDVI shifts and key metabolic changes in response to salt stress and organic fertilizer application. By integrating NDVI and metabolomics, this study provides a refined method for evaluating salt stress responses, capturing early NDVI changes and key salinity stress biomarkers. This approach may prove valuable for application in salt-tolerant variety screening, precision agriculture, and sustainable farming, contributing to scientific strategies for future crop improvement and agricultural resilience. Full article
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16 pages, 13657 KB  
Article
Genetic Variation and Assessment of Seven Salt-Tolerance Genes in an Indica/Xian Rice Population
by Yuanhang Cheng, Tao Wang, Yeying Wen, Xingfei Zheng, Haifeng Liu, Xiangsong Chen, Ying Diao, Zhongli Hu, Wenjie Feng and Zhaohui Chu
Agronomy 2025, 15(3), 570; https://doi.org/10.3390/agronomy15030570 - 25 Feb 2025
Cited by 1 | Viewed by 990
Abstract
Natural variations conferring salt tolerance (ST) are of great value for breeding salt-tolerant rice varieties. The major ST genes, including SKC1, RST1, OsWRKY53 and STG5, have been identified to contain or be associated with a specific single nucleotide polymorphism (SNP). [...] Read more.
Natural variations conferring salt tolerance (ST) are of great value for breeding salt-tolerant rice varieties. The major ST genes, including SKC1, RST1, OsWRKY53 and STG5, have been identified to contain or be associated with a specific single nucleotide polymorphism (SNP). However, the distribution and genetic effects of those ST genes in rice cultivars remain poorly understood. Here, we investigated the distribution of seven cloned ST genes, including SKC1 (P140A, R184H), RST1 (A530G, E611G), OsWRKY53 (A173G), STG5 (I12S), OsHKT1;1 (L94K), OsHKT2;3 (I77T) and OsSTL1 (P289S), which contain one or two ST-related SNPs in a sequenced Indica/Xian rice population comprising 550 accessions. On the basis of the SNPs, the population was categorized into 21 haplotypes (Haps), each of which contained at least four out of seven ST genes. To precisely evaluate each SNP, grouped rice varieties that only differed at one SNP were chosen from two Haps for salt treatment with 150 mM NaCl for 7 d. The results revealed that RST1611G showed up to 88.6% improvement in salt tolerance considering the relative shoot fresh weight (rSFW). Alternatively, OsWRKY53173G, OsHKT2;377T, SKC1140A and SKC1184H showed an improvement in rSFW of 38.6%, 37%, 27.5% and 19.0%, respectively, indicating that they contribute different genetic effects for ST. OsHKT1;194K showed no function with salt treatment for 7 d, but showed a 37.9% rSFW improvement with salt treatment for 14 d. Furthermore, we found that the expression of OsWRKY53173G was positively correlated with SKC1 and conditionally participated in ST dependent on SKC1140A. Interestingly, RST1530A was previously reported to be associated with salt sensitivity, but it was found to be associated with salt tolerance in this study. Overall, our results provide further insight into the mechanism and marker-assisted selection improvement of ST in Indica/Xian rice. Full article
(This article belongs to the Special Issue New Insights into Pest and Disease Control in Rice)
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18 pages, 2405 KB  
Article
Screening and Assessment of Genetic Diversity of Rice (Oryza sativa L.) Germplasm in Response to Soil Salinity Stress at Germination Stage
by Alia Anwar, Javaria Tabassum, Shakeel Ahmad, Muhammad Ashfaq, Adil Hussain, Muhammad Asad Ullah, Nur Shuhadah Binti Mohd Saad, Abdelhalim I. Ghazy and Muhammad Arshad Javed
Agronomy 2025, 15(2), 376; https://doi.org/10.3390/agronomy15020376 - 31 Jan 2025
Cited by 4 | Viewed by 1720
Abstract
Salinity stress significantly affects rice yield, especially when it occurs during the germination stage. Direct seeding is an emerging method to conserve water in rice cultivation. However, to date, there have been limited efforts to screen rice germplasm for salt tolerance under this [...] Read more.
Salinity stress significantly affects rice yield, especially when it occurs during the germination stage. Direct seeding is an emerging method to conserve water in rice cultivation. However, to date, there have been limited efforts to screen rice germplasm for salt tolerance under this approach. In this study, 40 rice genotypes were evaluated for salt tolerance using a combination of germination and growth parameters. A total of 59 microsatellite markers were used to assess genetic diversity, revealing significant variation in both germination and growth traits. Based on germination parameters, IR36, Sri Malaysia 2, and MR185 performed well under saline conditions, while Hashemi Tarom and BAS2000 exhibited weak tolerance. MR219, MR211, and MR263 were identified as superior salt-tolerant genotypes against all growth parameters. BAS2000 and MCHKAB were identified as salt-sensitive, showing reduced growth in key traits, including root and shoot development. Marker-based genotyping identified a total of 287 alleles. The number of alleles per locus ranged from two to nine with an average of 4.86. The polymorphic information content (PIC) ranged from four to eight. The markers RM21, RM481 RM566, RM488, RM9, RM217, RM333, RM242, RM209, RM38, RM539, RM475, RM267, RM279, and RM430 were found highly polymorphic with PIC value > 0.7 and contain the highest number of alleles (≥6). Model- and distance-based population structures both inferred the presence of three clusters in the studied rice germplasm. Based on cluster analysis, Shiroodi, Hashemi Tarom, and BAS2000 were found as weak salt-tolerant varieties, whereas MR211 and MR219 are two Malaysian varieties found to be highly tolerant and have a high potential for direct seeding methods. An AMOVA test suggested that 95% genetic diversity was within the population, which implies that significant genetic variation was present in rice germplasm to be used to select parents for future breeding programs. Full article
(This article belongs to the Special Issue Genetics and Breeding of Field Crops in the 21st Century)
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26 pages, 8623 KB  
Article
Prohexadione Calcium Improves Rice Yield Under Salt Stress by Regulating Source–Sink Relationships During the Filling Period
by Rui Deng, Dianfeng Zheng, Naijie Feng, Aaqil Khan, Jianqin Zhang, Zhiyuan Sun, Jiahuan Li, Jian Xiong, Linchong Ding, Xiaohui Yang, Zihui Huang and Yuecen Liao
Plants 2025, 14(2), 211; https://doi.org/10.3390/plants14020211 - 13 Jan 2025
Cited by 4 | Viewed by 1769
Abstract
Salt stress is an important factor affecting the growth and development of rice, and prohexadione calcium (Pro-Ca) plays an important role in alleviating rice salt stress and improving rice yield. However, there are few studies on how Pro-Ca improves rice yield under salt [...] Read more.
Salt stress is an important factor affecting the growth and development of rice, and prohexadione calcium (Pro-Ca) plays an important role in alleviating rice salt stress and improving rice yield. However, there are few studies on how Pro-Ca improves rice yield under salt stress by regulating the source–sink metabolism. In this study, we used Guanghong 3 (salt-tolerant variety) and Huanghuazhan (salt-sensitive variety) as experimental materials to investigate the dynamic changes in the synthesis and partitioning of nonstructural carbohydrates among source–sink, the dynamic changes in related enzyme activities, the effects of the source–sink metabolism on yield in rice under salt stress and the effect of Pro-Ca during the filling period. The results of this study showed that Pro-Ca improved photosynthetic efficiency by increasing leaf photosynthetic gas exchange parameters and other stomatal factors on the one hand and, on the other hand, promoted sugar catabolism and reduced sugar synthesis by increasing leaf sucrose synthase activity and decreasing sucrose phosphate synthase activity, alleviating the inhibitory effect of high concentrations of sugars in the leaves on photosynthesis. Meanwhile, Pro-Ca promotes the transport of sugars from source (leaves) to sink (seeds), increases the sugar content in the seeds, and promotes starch synthesis in the seeds by increasing starch phosphorylase, which promotes seed filling, thus increasing the number of solid grains on the primary and secondary branches of the panicle in rice, increasing the 1000-grain weight, and ultimately increasing the seed setting rate and yield. These results indicated that Pro-Ca alleviated the inhibitory effect of salt stress on rice leaf photosynthesis through stomatal and non-stomatal factors. Meanwhile, Pro-Ca promotes the transport of rice sugars from source to sink under salt stress, regulates the source–sink relationship during the filling period of rice, promotes starch synthesis, and ultimately improves rice yield. Full article
(This article belongs to the Section Plant Physiology and Metabolism)
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27 pages, 4250 KB  
Article
The RAD6-like Ubiquitin Conjugase Gene OsUBC7 Has a Positive Role in the Early Cold Stress Tolerance Response of Rice
by Huy Phan and Michael Schläppi
Genes 2025, 16(1), 66; https://doi.org/10.3390/genes16010066 - 8 Jan 2025
Cited by 1 | Viewed by 1323
Abstract
Background/Objectives: Cold stress poses a significant threat to Asian rice cultivation, disrupting important physiological processes crucial for seedling establishment and overall plant growth. It is, thus, crucial to elucidate genetic pathways involved in cold stress tolerance response mechanisms. Methods: We mapped OsUBC7, [...] Read more.
Background/Objectives: Cold stress poses a significant threat to Asian rice cultivation, disrupting important physiological processes crucial for seedling establishment and overall plant growth. It is, thus, crucial to elucidate genetic pathways involved in cold stress tolerance response mechanisms. Methods: We mapped OsUBC7, a Radiation-sensitive 6 (RAD6)-type homolog of rice, to a low-temperature seedling survivability (LTSS) QTL and used genomics, molecular genetics, and physiological assays to assess its role in plant resilience against low-temperature stress. Results: OsUBC7 is cold responsive and has higher expression levels in cold-tolerant japonica than cold-sensitive indica. Overexpression of OsUBC7 enhances LTSS of indica and freezing tolerance of Arabidopsis, increases levels of soluble sugars and chlorophyll A, boosts leaf development after cold exposure, and increases leaf cell numbers and plants size, but it does not affect membrane stability after cold stress exposure. Additionally, OsUBC7 has a positive role for germinability in the presence of salt and for flowering and yield-related traits. The OsUBC7 protein physically interacts with the developmental stage-specific and histone-modifying E3 ligases OsRFPH2-12 and OsHUB1/2, respectively, and potential target genes such as cell cycle dependent kinases were identified. Conclusions: OsUBC7 might contribute to cold resilience by regulating sugar metabolism to provide energy for promoting cellular homeostasis restoration after cold stress exposure via new cell growth, particularly in leaf cells crucial for photosynthesis and metabolic activity, possibly by interacting with cell cycle regulating proteins. Overall, the present study suggests that OsUBC7 may be involved in plant development, reproduction, and stress adaptation, and contributes to a deeper understanding of rice plant cold stress tolerance response mechanisms. OsUBC7 may be a promising candidate for improving crop productivity and resilience to stressful environments. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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22 pages, 5774 KB  
Article
Comprehensive In Silico Analysis of the NHX (Na+/H+ Antiporter) Gene in Rice (Oryza sativa L.)
by Hoa Hai Thi Bui, Duong Huy Nguyen, Le Thu Thi Dinh, Hang Thu Thi Trinh, Thoa Kim Vu and Van Ngoc Bui
Int. J. Plant Biol. 2025, 16(1), 6; https://doi.org/10.3390/ijpb16010006 - 6 Jan 2025
Cited by 2 | Viewed by 1920
Abstract
The Na+/H+ antiporter (NHX) gene family plays a pivotal role in plant salt tolerance in regulating intracellular Na+ and H+ homeostasis. In this study, seven candidate OsNHX genes (OsNHX1 to OsNHX7) were identified in [...] Read more.
The Na+/H+ antiporter (NHX) gene family plays a pivotal role in plant salt tolerance in regulating intracellular Na+ and H+ homeostasis. In this study, seven candidate OsNHX genes (OsNHX1 to OsNHX7) were identified in the rice genome and classified into three phylogenetic clusters (Vac, Endo, and PM) based on their predicted subcellular localization. Five OsNHX gene pairs (OsNHX1/OsNHX2, OsNHX1/OsNHX3, OsNHX1/OsNHX4, OsNHX2/OsNHX6, and OsNHX5/OsNHX6) were found to have arisen from dispersed duplication events and exhibited purifying selection, indicating functional conservation. Analysis of cis-regulatory elements (CREs) revealed a diverse range of elements associated with tissue-specific expression, hormone signaling, and stress responses, particularly to dehydration and salinity. Notably, CREs associated with tissue/organelle-specific expression and stress responses were the most abundant, suggesting a potential role for OsNHX genes in regulating growth, development, and stress tolerance in rice. Importantly, expression profiling revealed that OsNHX1, OsNHX2, OsNHX3, and OsNHX5 were upregulated under salt stress, with significantly higher expression levels in the salt-tolerant rice cultivar Pokkali compared to the salt-sensitive cultivar IR64. Our findings provide a comprehensive analysis of the evolutionary, structural, and functional features of the OsNHX gene family and highlights their critical role in rice salt tolerance, offering insights into potential applications for crop improvement. Full article
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21 pages, 5403 KB  
Article
Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant Rice
by Wenna Meng, Zhenling Zhou, Mingpu Tan, Anqi Liu, Shuai Liu, Jiaxue Wang, Zhiguang Sun, Yiluo Tan, Yan Liu, Baoxiang Wang and Yanming Deng
Plants 2025, 14(1), 36; https://doi.org/10.3390/plants14010036 - 26 Dec 2024
Cited by 4 | Viewed by 1340
Abstract
Salt stress poses a significant constraint on rice production, so further exploration is imperative to elucidate the intricate molecular mechanisms governing salt tolerance in rice. By manipulating the rhizosphere microbial communities or targeting specific microbial functions, it is possible to enhance salt tolerance [...] Read more.
Salt stress poses a significant constraint on rice production, so further exploration is imperative to elucidate the intricate molecular mechanisms governing salt tolerance in rice. By manipulating the rhizosphere microbial communities or targeting specific microbial functions, it is possible to enhance salt tolerance in crops, improving crop yields and food security in saline environments. In this study, we conducted rice rhizospheric microbial amplicon sequencing and metatranscriptome analysis, revealing substantial microbiomic differences between the salt-tolerant rice cultivar TLJIAN and the salt-sensitive HUAJING. Fungal taxa including Hormiactis, Emericellopsis, Ceriosporopsis, Dirkmeia, and Moesziomyces predominated in the rhizosphere of salt-tolerant rice, while bacterial genera such as Desulfoprunum and Hydrogenophaga exhibited notable differences. Metatranscriptomic analysis identified 7192 differentially expressed genes (DEGs) in the two rice varieties, with 3934 genes being upregulated and 3258 genes being downregulated. Enrichment analyses in KEGG and GO pathways highlighted the majority of DEGs were associated with the “two-component system”, “sulfur metabolism”, and “microbial metabolism in diverse environments”. The interaction network of DEGs and microbial taxa revealed upregulation of transporters, transcriptional factors, and chaperones, such as ABC transporters and chaperonin GroEL, in the rhizosphere microbiomes of salt-tolerant varieties. Our multi-omics network analysis unveiled that fungi like Ceriosporopsis and Dirkmeria, along with bacteria such as Desulfoprunum, Rippkaea, and Bellilinea, showed a positive correlation with flavonoid synthesis in salt-tolerant rice. This study provides an in-depth exploration of the distinctive microbial communities associated with the rhizosphere of salt-tolerant rice varieties, shedding light on the complex interactions between these microbial consortia and their host plants under stress conditions. Full article
(This article belongs to the Special Issue Physiological and Molecular Responses for Stress Tolerance in Rice)
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22 pages, 4969 KB  
Article
Effects of Exogenous Spermidine on Seed Germination and Physiological Metabolism of Rice Under NaCl Stress
by Xiaohui Yang, Jian Xiong, Xiaole Du, Minmin Sun, Linchong Ding, Wanqi Mei, Zhiyuan Sun, Naijie Feng, Dianfeng Zheng and Xuefeng Shen
Plants 2024, 13(24), 3599; https://doi.org/10.3390/plants13243599 - 23 Dec 2024
Cited by 2 | Viewed by 1599
Abstract
Salt stress is one of the principal abiotic stresses limiting agricultural production and seriously inhibiting seed germination rates. This study selected the salt-tolerant rice variety HD961 and the salt-sensitive rice variety 9311 as experimental materials to investigate the physiological and metabolic effects of [...] Read more.
Salt stress is one of the principal abiotic stresses limiting agricultural production and seriously inhibiting seed germination rates. This study selected the salt-tolerant rice variety HD961 and the salt-sensitive rice variety 9311 as experimental materials to investigate the physiological and metabolic effects of exogenous Spd seed priming on rice seeds and seedlings under NaCl stress. The experiment involved treating rice seeds with 0.1 mmol·L−1 Spd and then subjecting them to 100 mmol·L−1 NaCl stress for 24 h, with sampling for analysis at the 24 h and the four-leaf-one-heart stage. The results indicated that under NaCl stress, the rice’s germination and vigor indices significantly decreased. However, exogenous Spd seed priming reduced the accumulation of malondialdehyde, enhanced the capacity for osmotic adjustment, and increased the amylase and antioxidant activity by 50.07% and 26.26%, respectively. Under NaCl stress, the morphological development of rice seedlings was markedly inhibited, whereas exogenous Spd seed priming improved the aboveground and belowground biomass of the rice under stress conditions, as well as the content of photosynthetic pigments. It also reduced the damage to seedlings from electrical conductivity, helped maintain ionic balance, and promoted the excretion of Na+ and Cl and the absorption of K+ and Ca2+. In the salt-sensitive rice variety 9311, the soluble protein content increased by 15.12% compared to the salt-tolerant rice variety HD961, especially under 100 mmol·L−1 NaCl stress, when the effect of exogenous Spd seed priming was more pronounced. In summary, these findings might provide new research perspectives and strategies for improving the salt tolerance of rice under NaCl stress. Full article
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