Salt tolerance in rice: seedling and reproductive stage QTL mapping come of age

Germination and stress tolerance of oats treated with pulsed electric field at different phases of seedling growth

This study explores the impact of pulsed electric field (PEF) application on oat seedling growth and stress tolerance. PEF treatment (99 monopolar, rectangular pulses lasting 10 µs each, with a frequency of 13 Hz and a nominal electric field strength of 2250 V/cm) was applied at two growth stages: (i) when the seedlings had 0.2 cm roots emerging from the kernel, and (ii) when they had a 0.4 cm shoot emerging from the kernel. Post-treatment, the seedlings were hydroponically grown for 8 days. To induce stress, the hydroponic medium was augmented with PEG (15 %) to induce drought stress and NaCl (150 mM) to induce salinity stress. Results demonstrate that applying PEF improved the growth of the root and shoot of oat seedlings. This effect was more pronounced when applied to more developed seedlings. When PEF was applied during the later stage of germination, seedlings exposed to salinity stress showed enhanced shoot growth compared to the control. Under the studied conditions, the application of PEF had no impact on the growth of seedlings under drought stress.

Screening of Rice (Oryza sativa L.) Genotypes for Salinity Tolerance and Dissecting Determinants of Tolerance Mechanism

Soil salinity imposes osmotic, ionic, and oxidative stresses on plants, resulting in growth inhibition, developmental changes, metabolic adaptations, and ion sequestration or exclusion. Identifying salinity-tolerant resources and understanding physiological and molecular mechanisms of salinity tolerance could lay a foundation for the improvement of salinity tolerance in rice. In this study, a series of salinity-tolerance-related morphological and physiological traits were investigated in 46 rice genotypes, including Sea Rice 86, to reveal the main strategies of rice in responding to salinity stress at the seedling stage. No genotypes showed the same tolerance level as the two landraces Pokkali and Nona Bokra, which remain the donors for improving the salinity tolerance of rice. However, due to undesirable agronomic traits of these donors, alternative cultivars such as JC118S and R1 are recommended as novel source of salinity tolerance. Correlation and principal component analyses revealed that the salinity tolerance of rice seedlings is not only controlled by growth vigor but also regulated by ion transport pathways such as long-distance Na+ transport, root Na+ sequestration, and root K+ retention. Therefore, such key traits should be targeted in future breeding programs as the strategy of obtaining better Na+ exclusion is still the bottleneck for improving salinity tolerance in rice.

CRISPR/Cas9 targeted mutations of OsDSG1 gene enhanced salt tolerance in rice

Salinization is one of the leading causes of arable land shrinkage and rice yield decline, recently. Therefore, developing and utilizing salt-tolerant rice varieties have been seen as a crucial and urgent strategy to reduce the effects of saline intrusion and protect food security worldwide. In the current study, the CRISPR/Cas9 system was utilized to induce targeted mutations in the coding sequence of the OsDSG1, a gene involved in the ubiquitination pathway and the regulation of biochemical reactions in rice. The CRISPR/Cas9-induced mutations of the OsDSG1 were generated in a local rice cultivar and the mutant inheritance was validated at different generations. The OsDSG1 mutant lines showed an enhancement in salt tolerance compared to wild type plants at both germination and seedling stages indicated by increases in plant height, root length, and total fresh weight as well as the total chlorophyll and relative water contents under the salt stress condition. In addition, lower proline and MDA contents were observed in mutant rice as compared to wild type plants in the presence of salt stress. Importantly, no effect on seed germination and plant growth parameters was recorded in the CRISRP/Cas9-induced mutant rice under the normal condition. This study again indicates the involvement of the OsDSG1 gene in the salt resistant mechanism in rice and provides a potential strategy to enhance the tolerance of local rice varieties to the salt stress.

Soil salinization in agriculture: Mitigation and adaptation strategies combining nature-based solutions and bioengineering

Soil salinization is among the most critical threats to agriculture and food security. Excess of salts adversely affects soil structure and fertility, plant growth, crop yield, and microorganisms. It is caused by natural processes, such as dry climates and low precipitations, high evaporation rate, poor waterlogging, and human factors, such as inappropriate irrigation practices, poor drainage systems, and excessive use of fertilizers. The growing extremization of climate with prolonged drought conditions is worsening the phenomenon. Nature-based solutions (NBS), combined with precision or conservation agriculture, represent a sustainable response, and offer benefits through revitalizing ecosystem services. This perspective explores NBS that can be adopted, along with their challenges and implementation limitations. We also argue that NBS could not be enough to combat hunger in the world's most vulnerable regions and fully achieve the Sustainable Development Goal - Zero Hunger (SDG2). We therefore discuss their possible combination with salt-tolerant crops based on bioengineering.

Enhancing stress resilience in rice (Oryza sativa L.) through profiling early-stage morpho-physiological and molecular responses to multiple abiotic stress tolerance

Under changing climatic conditions, crop plants are more adversely affected by a combination of various abiotic stresses than by a single abiotic stress. Therefore, it is essential to identify potential donors to multiple abiotic stresses for developing climate-resilient crop varieties. Hence, the present study was undertaken with 41 germplasm accessions comprising native landraces of Tamil Nadu, Prerelease lines and cultivars were screened independently for drought, salinity, and submergence at the seedling stage during Kharif and Rabi 2022-2023. Stress was imposed separately for these three abiotic stresses on 21-day-old seedlings and was maintained for 10 days. The studied genotypes showed a significant reduction in plant biomass (PB), Relative Growth Index (RGI), relative water content (RWC), leaf photosynthesis, chlorophyll fluorescence, and Chlorophyll Concentration Index (CCI) under drought followed by salinity and submergence. Stress-tolerant indices for drought, salinity, and submergence revealed significant variation for plant biomass. Furthermore, a set of 30 SSR markers linked to drought, salinity, and submergence QTLs has been used to characterize 41 rice germplasm accessions. Our analysis suggests a significantly high polymorphism, with 28 polymorphic markers having a 93.40% in 76 loci. The mean values of polymorphic information content (PIC), heterozygosity index (HI), marker index (MI), and resolving power (RP) were 0.369, 0.433, 1.140, and 2.877, respectively. Jaccard clustering grouped all the genotypes into two major and six subclusters. According to STRUCTURE analysis, all genotypes were grouped into two major clusters, which are concurrent with a very broad genetic base (K = 2). Statistically significant marker-trait associations for biomass were observed for five polymorphic markers, viz., RM211, RM212 (drought), RM10694 (salinity), RM219, and RM21 (submergence). Similarly, significant markers for relative shoot length were observed for RM551 (drought), RM10694 (salinity), and ART5 (submergence). Notably, the genotypes Mattaikar, Varigarudan samba, Arupatham samba, and APD19002 were identified as potential donors for multiple abiotic stress tolerance. Thus, identifying the genetic potential of germplasm could be useful for enhancing stress resilience in rice.

Natural variation in a K+ -preferring HKT transporter contributes to wheat shoot K+ accumulation and salt tolerance

Soil salinity can adversely affect crop growth and yield, and an improved understanding of the genetic factors that confer salt tolerance could inform breeding strategies to engineer salt-tolerant crops and improve productivity. Here, a group of K+ -preferring HKT transporters, TaHKT8, TaHKT9 and TaHKT10, were identified and negatively regulate the wheat shoot K+ accumulation and salt tolerance. A genome-wide association study (GWAS) and candidate gene association analysis further revealed that TaHKT9-B substantially underlies the natural variation of wheat shoot K+ accumulation under saline soil conditions. Specifically, an auxin responsive element (ARE) within an 8-bp insertion in the promoter of TaHKT9-B is strongly associated with shoot K+ content among wheat accessions. This ARE can be directly bound by TaARF4 for transcriptional activation of TaHKT9-B, which subsequently attenuates shoot K+ accumulation and salt tolerance. Moreover, the tae-miR390/TaTAS3/TaARF4 pathway was identified to regulate the salt-induced root development and salt tolerance in wheat. Taken together, our study describes the genetic basis and accompanying mechanism driving phenotypic variation in wheat shoot K+ accumulation and salt tolerance. The identified tae-miR390/TaTAS3/TaARF4/TaHKT9-B module is an important regulator in wheat subjected to salt stress, which provides the potentially important genetic resources for breeders to improve wheat salt tolerance.

Activity-directed selection of natural variants of a receptor kinase facilitates salt-tolerant rice breeding

Reduced the kinase activity of SALT INTOLERANCE 1 in a natural variant is better-suited to maintain the balance between growth and salt tolerance in rice.

Progress and prospects in harnessing wild relatives for genetic enhancement of salt tolerance in rice

Salt stress is the second most devastating abiotic stress after drought and limits rice production globally. Genetic enhancement of salinity tolerance is a promising and cost-effective approach to achieve yield gains in salt-affected areas. Breeding for salinity tolerance is challenging because of the genetic complexity of the response of rice plants to salt stress, as it is governed by minor genes with low heritability and high G × E interactions. The involvement of numerous physiological and biochemical factors further complicates this complexity. The intensive selection and breeding efforts targeted towards the improvement of yield in the green-revolution era inadvertently resulted in the gradual disappearance of the loci governing salinity tolerance and a significant reduction in genetic variability among cultivars. The limited utilization of genetic resources and narrow genetic base of improved cultivars have resulted in a plateau in response to salinity tolerance in modern cultivars. Wild species are an excellent genetic resource for broadening the genetic base of domesticated rice. Exploiting novel genes of underutilized wild rice relatives to restore salinity tolerance loci eliminated during domestication can result in significant genetic gain in rice cultivars. Wild species of rice, Oryza rufipogon and Oryza nivara, have been harnessed in the development of a few improved rice varieties like Jarava and Chinsura Nona 2. Furthermore, increased access to sequence information and enhanced knowledge about the genomics of salinity tolerance in wild relatives has provided an opportunity for the deployment of wild rice accessions in breeding programs, while overcoming the cross-incompatibility and linkage drag barriers witnessed in wild hybridization. Pre-breeding is another avenue for building material that are ready for utilization in breeding programs. Efforts should be directed towards systematic collection, evaluation, characterization, and deciphering salt tolerance mechanisms in wild rice introgression lines and deploying untapped novel loci to improve salinity tolerance in rice cultivars. This review highlights the potential of wild relatives of Oryza to enhance tolerance to salinity, track the progress of work, and provide a perspective for future research.

Genetic gains in IRRI's rice salinity breeding and elite panel development as a future breeding resource

KEY MESSAGE

Estimating genetic gains and formulating a future salinity elite breeding panel for rice pave the way for developing better high-yielding salinity tolerant lines with enhanced genetic gains. Genetic gain is a crucial parameter to check the breeding program's success and help optimize future breeding strategies for enhanced genetic gains. To estimate the genetic gains in IRRI's salinity breeding program and identify the best genotypes based on high breeding values for grain yield (kg/ha), we analyzed the historical data from the trials conducted in the IRRI, Philippines and Bangladesh. A two-stage mixed-model approach accounting for experimental design factors and a relationship matrix was fitted to obtain the breeding values for grain yield and estimate genetic trends. A positive genetic trend of 0.1% per annum with a yield advantage of 1.52 kg/ha was observed in IRRI, Philippines. In Bangladesh, we observed a genetic gain of 0.31% per annum with a yield advantage of 14.02 kg/ha. In the released varieties, we observed a genetic gain of 0.12% per annum with a 2.2 kg/ha/year yield advantage in the IRRI, Philippines. For the Bangladesh dataset, a genetic gain of 0.14% per annum with a yield advantage of 5.9 kg/ha/year was observed in the released varieties. Based on breeding values for grain yield, a core set of the top 145 genotypes with higher breeding values of > 2400 kg/ha in the IRRI, Philippines, and > 3500 kg/ha in Bangladesh with a reliability of > 0.4 were selected to develop the elite breeding panel. Conclusively, a recurrent selection breeding strategy integrated with novel technologies like genomic selection and speed breeding is highly required to achieve higher genetic gains in IRRI's salinity breeding programs.

Effects of integrated nutrient management and urea deep placement on rice yield, nitrogen use efficiency, farm profits and greenhouse gas emissions in saline soils of Bangladesh

Soil salinity is one of the major yield-limiting factors in the coastal ecosystems of Bangladesh. An efficient fertilizer management practice and selection of appropriate crop cultivars could play a crucial role in improving yield and promoting low-carbon agriculture across saline soils. A two-year multi-location field experiment was conducted during the Boro (dry) season (December-April) to investigate the effects of fertilizer management and rice cultivar selection on rice yield, economic viability, and global warming potential (GWP) in coastal saline soils of Bangladesh. The study included seven fertilizer treatments with varying nitrogen rates and sources, as well as two rice cultivars (BRRI dhan67 and BRRI dhan88). The results showed that integrated nutrient management-2 (INM-2) significantly (p < 0.05) increased rice yield and nitrogen use efficiency compared to other treatments for both BRRI dhan67 and BRRI dhan88. Similarly, INM-2 gave a higher return on fertilizer investment and marginal benefit-cost ratio than other treatments in both locations and under both cultivars. BRRI dhan67 significantly (p < 0.05) increased rice yield relative to BRRI dhan88 by 21 % and 52 % at the BRRI farm and Kaliganj in Satkhira, respectively. The cost-dominant analysis excluded BRRI dhan88 and all fertilizer treatments, except urea deep placement (UDP) and INM-2, from consideration in both locations. Consequently, INM-2 and UDP proved to be economically viable in both locations, with INM showing a higher marginal rate of return than UDP in BRRI dhan67. In terms of environmental sustainability, UDP significantly (p < 0.05) reduced GWP and yield-scaled emissions of CH4 by 31 % and 38 % without causing yield loss compared to INM-2. Similarly, BRRI dhan67 significantly (p < 0.05) reduced GWP and yield-scaled emissions of CH4 by 5 and 22 % compared to BRRI dhan88. These findings suggest that selecting salt-tolerant rice cultivars and implementing appropriate fertilizer management practices can enhance economic profitability, ensure food security, and mitigate the adverse effects of climate change in coastal saline soils.

Uncovering Novel QTLs and Candidate Genes for Salt Tolerance at the Bud Burst Stage in Rice through Genome-Wide Association Study

Salt stress is one of the most important factors limiting rice growth and yield increase. Salt tolerance of rice at the bud burst (STB) stage determines whether germinated seeds can grow normally under salt stress, which is very important for direct seeding. However, reports on quantitative trait loci (QTLs) and candidate genes for STB in rice are very limited. In this study, a natural population of 130 indica and 81 japonica rice accessions was used to identify STB-related QTLs and candidate genes using a genome-wide association study (GWAS). Nine QTLs, including five for relative shoot length (RSL), two for relative root length (RRL), and two for relative root number (RRN), were identified. Five of these STB-related QTLs are located at the same site as the characterized salt tolerance genes, such as OsMDH1, OsSRFP1, and OsCDPK7. However, an important QTL related to RSL, qRSL1-2, has not been previously identified and was detected on chromosome 1. The candidate region for qRSL1-2 was identified by linkage disequilibrium analysis, 18 genes were found to have altered expression levels under salt stress through the RNA-seq database, and 10 of them were found to be highly expressed in the shoot. It was also found that, eight candidate genes (LOC_Os01g62980, LOC_Os01g63190, LOC_Os01g63230, LOC_Os01g63280, LOC_Os01g63400, LOC_Os01g63460, and LOC_Os01g63580) for qRSL1-2 carry different haplotypes between indica and japonica rice, which exactly corresponds to the significant difference in RSL values between indica and japonica rice in this study. Most of the accessions with elite haplotypes were indica rice, which had higher RSL values. These genes with indica-japonica specific haplotypes were identified as candidate genes. Rice accessions with elite haplotypes could be used as important resources for direct seeding. This study also provides new insights into the genetic mechanism of STB.

Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Genes for Salinity Tolerance in Oryza sativa L. ssp. Japonica Seedlings

Salinity stress is one of the major abiotic stresses affecting crop growth and production. Rice is an important food crop in the world, but also a salt-sensitive crop, and the rice seedling stage is the most sensitive to salt stress, which directly affects the final yield formation. In this study, two RIL populations derived from the crosses of CD (salt-sensitive)/WD (salt-tolerant) and KY131 (salt-sensitive)/XBJZ (salt-tolerant) were used as experimental materials, and the score of salinity toxicity (SST), the relative shoot length (RSL), the relative shoot fresh weight (RSFW), and the relative shoot dry weight (RSDW) were used for evaluating the degree of tolerance under salt stress in different lines. The genetic linkage map containing 978 and 527 bin markers were constructed in two RIL populations. A total of 14 QTLs were detected on chromosomes 1, 2, 3, 4, 7, 9, 10, 11, and 12. Among them, qSST12-1, qSST12-2, and qRSL12 were co-localized in a 140-kb overlap interval on chromosome 12, which containing 16 candidate genes. Furthermore, transcriptome sequencing and qRT-PCR were analyzed in CD and WD under normal and 120 mM NaCl stress. LOC_Os12g29330, LOC_Os12g29350, LOC_Os12g29390, and LOC_Os12g29400 were significantly induced by salt stress in both CD and WD. Sequence analysis showed that LOC_Os12g29400 in the salt-sensitive parents CD and KY131 was consistent with the reference sequence (Nipponbare), whereas the salt-tolerant parents WD and XBJZ differed significantly from the reference sequence both in the promoter and exon regions. The salt-tolerant phenotype was identified by using two T3 homozygous mutant plants of LOC_Os12g29400; the results showed that the score of salinity toxicity (SST) of the mutant plants (CR-3 and CR-5) was significantly lower than that of the wild type, and the seedling survival rate (SSR) was significantly higher than that of the wild type, which indicated that LOC_Os12g29400 could negatively regulate the salinity tolerance of rice at the seedling stage. The results lay a foundation for the analysis of the molecular mechanism of rice salinity tolerance and the cultivation of new rice varieties.

Smart reprograming of plants against salinity stress using modern biotechnological tools

Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO.

Transcriptome-Wide Analysis of Core Transcription Factors Associated with Defense Responses in Autotetraploid versus Diploid Rice under Saline Stress and Recovery

Saline stress is a major abiotic stress that inhibits plant growth and yields worldwide. The plant transcription factor (TF) family plays an important role in converting abiotic stress signals into gene expression changes. In this study, a transcriptome-based comparative analysis was performed to investigate the global gene expression of all the TFs in diploid and autotetraploid rice during the early stage of NaCl stress and recovery period. The phenotypic data indicated that the tetraploid rice exhibited a superior salt-tolerant ability compared to the diploid rice. A total of 55 TF families were co-expressed in the tetraploid and diploid rice, and the cumulative number of TF-expressed genes was relatively higher in the diploid rice than in the tetraploid rice at all time points. Unlike the diploid rice, the overall gene expression levels of the tetraploid rice were comparable to the control during recovery. The number of differentially expressed TFs (DE-TFs) in the tetraploid rice decreased after recovery, whereas it increased to a large extent in the diploid rice. GO and KEGG pathway enrichment analysis of the DE-TFs discovered the early switching of the ABA-activated signaling pathway and specific circadian rhythm in the tetraploid rice. Combining the PPI network and heatmap analysis, some core DE-TFs were found that may have potential roles to play in tetraploid salt tolerance. This study will pave the way for elucidating the complex network regulatory mechanisms of salt tolerance in tetraploid rice.

Morpho-physiological profiling of rice (Oryza sativa) genotypes at germination stage with contrasting tolerance to salinity stress

Salinity is among the harshest environmental stress conditions that negatively affects productivity of salt-sensitive rice. Since, germination is the most crucial phase in the life-cycle of plants, the present study was carried out to study the morpho-physiological traits associated with salinity stress. Evaluation of tolerance in four contrasting rice genotypes was assessed on the basis of specific morpho-physiological parameters including radicle emergence, seedling vigour index, germination index, mean germination time, radicle and plumule growth and seedling water uptake. Largely, our findings revealed that mean germination time (MGT) and seedling vigour index (SVI) are fast-screening procedures to test seedling performance in salt stress conditions. Salt sensitive genotypes showed higher MGT and lower SVI, confirming that these indices are good indicators of poor germination response. Salt-tolerant genotypes were shown to be inhibited to a lesser extent in alpha-amylase activity in spite of high concentrations of imposed NaCl stress, that correlated with better regulation of water-uptake and increased accumulation of total soluble sugar content. Exogenous supplementation of soluble sugars improved the germination rate in a salt sensitive genotype, Jyothi, confirming the importance of soluble sugars in signaling under NaCl stress conditions. Increased total phenols and flavonoids were observed to be relative to higher Total Antioxidant Capacity in salt tolerant genotypes underlying the significance of seed phenolic compounds in early germination response in NaCl stress conditions. Kagga, a landrace grown in coastal Karnataka performed comparably with that of salt tolerant rice, Pokkali. In conclusion, the determination of early seedling response may be utilized as a useful strategy to uncover genetic variation in rice germplasm to salinity stress.

OsCIPK9 Interacts with OsSOS3 and Affects Salt-Related Transport to Improve Salt Tolerance

Salt is harmful to crop production. Therefore, it is important to understand the mechanism of salt tolerance in rice. CIPK genes have various functions, including regulating salt tolerance and other types of stress and nitrogen use efficiency. In rice, OsCIPK24 is known to regulate salt tolerance, but other OsCIPKs could also function in salt tolerance. In this study, we identified another OsCIPK-OsCIPK9-that can regulate salt tolerance. Knockout of OsCIPK9 in rice could improve salt tolerance. Through expression analyses, OsCIPK9 was found to be mainly expressed in the roots and less expressed in mature leaves. Meanwhile, OsCIPK9 had the highest expression 6 h after salt treatment. In addition, we proved the interaction between OsCIPK9 and OsSOS3. The RNA-seq data showed that OsCIPK9 strongly responded to salt treatment, and the transporters related to salt tolerance may be downstream genes of OsCIPK9. Finally, haplotype analyses revealed that Hap6 and Hap8 mainly exist in indica, potentially providing a higher salt tolerance. Overall, a negative regulator of salt tolerance, OsCIPK9, which interacted with OsSOS3 similarly to OsCIPK24 and influenced salt-related transporters, was identified, and editing OsCIPK9 potentially could be helpful for breeding salt-tolerant rice.

Genomic selection for salinity tolerance in japonica rice

Improving plant performance in salinity-prone conditions is a significant challenge in breeding programs. Genomic selection is currently integrated into many plant breeding programs as a tool for increasing selection intensity and precision for complex traits and for reducing breeding cycle length. A rice reference panel (RP) of 241 Oryza sativa L. japonica accessions genotyped with 20,255 SNPs grown in control and mild salinity stress conditions was evaluated at the vegetative stage for eight morphological traits and ion mass fractions (Na and K). Weak to strong genotype-by-condition interactions were found for the traits considered. Cross-validation showed that the predictive ability of genomic prediction methods ranged from 0.25 to 0.64 for multi-environment models with morphological traits and from 0.05 to 0.40 for indices of stress response and ion mass fractions. The performances of a breeding population (BP) comprising 393 japonica accessions were predicted with models trained on the RP. For validation of the predictive performances of the models, a subset of 41 accessions was selected from the BP and phenotyped under the same experimental conditions as the RP. The predictive abilities estimated on this subset ranged from 0.00 to 0.66 for the multi-environment models, depending on the traits, and were strongly correlated with the predictive abilities on cross-validation in the RP in salt condition (r = 0.69). We show here that genomic selection is efficient for predicting the salt stress tolerance of breeding lines. Genomic selection could improve the efficiency of rice breeding strategies for salinity-prone environments.

Impacts of salinity stress on crop plants: improving salt tolerance through genetic and molecular dissection

Improper use of water resources in irrigation that contain a significant amount of salts, faulty agronomic practices such as improper fertilization, climate change etc. are gradually increasing soil salinity of arable lands across the globe. It is one of the major abiotic factors that inhibits overall plant growth through ionic imbalance, osmotic stress, oxidative stress, and reduced nutrient uptake. Plants have evolved with several adaptation strategies at morphological and molecular levels to withstand salinity stress. Among various approaches, harnessing the crop genetic variability across different genepools and developing salinity tolerant crop plants offer the most sustainable way of salt stress mitigation. Some important major genetic determinants controlling salinity tolerance have been uncovered using classical genetic approaches. However, its complex inheritance pattern makes breeding for salinity tolerance challenging. Subsequently, advances in sequence based breeding approaches and functional genomics have greatly assisted in underpinning novel genetic variants controlling salinity tolerance in plants at the whole genome level. This current review aims to shed light on physiological, biochemical, and molecular responses under salt stress, defense mechanisms of plants, underlying genetics of salt tolerance through bi-parental QTL mapping and Genome Wide Association Studies, and implication of Genomic Selection to breed salt tolerant lines.

Natural variation in ZmNAC087 contributes to total root length regulation in maize seedlings under salt stress

Soil salinity poses a significant challenge to crop growth and productivity, particularly affecting the root system, which is vital for water and nutrient uptake. To identify genetic factors that influence root elongation in stressful environments, we conducted a genome-wide association study (GWAS) to investigate the natural variation associated with total root length (TRL) under salt stress and normal conditions in maize seedlings. Our study identified 69 genetic variants associated with 38 candidate genes, among which a specific single nucleotide polymorphism (SNP) in ZmNAC087 was significantly associated with TRL under salt stress. Transient expression and transactivation assays revealed that ZmNAC087 encodes a nuclear-localized protein with transactivation activity. Further candidate gene association analysis showed that non-coding variations in ZmNAC087 promoter contribute to differential ZmNAC087 expression among maize inbred lines, potentially influencing the variation in salt-regulated TRL. In addition, through nucleotide diversity analysis, neutrality tests, and coalescent simulation, we demonstrated that ZmNAC087 underwent selection during maize domestication and improvement. These findings highlight the significance of natural variation in ZmNAC087, particularly the favorable allele, in maize salt tolerance, providing theoretical basis and valuable genetic resources for the development of salt-tolerant maize germplasm.

Drought and salinity stresses induced physio-biochemical changes in sugarcane: an overview of tolerance mechanism and mitigating approaches

Sugarcane productivity is being hampered globally under changing environmental scenarios like drought and salinity. The highly complex nature of the plant responses against these stresses is determined by a variety of factors such as genotype, developmental phase of the plant, progression rate and stress, intensity, and duration. These factors influence plant responses and can determine whether mitigation approaches associated with acclimation are implemented. In this review, we attempt to summarize the effects of drought and salinity on sugarcane growth, specifically on the plant's responses at various levels, viz., physiological, biochemical, and metabolic responses, to these stresses. Furthermore, mitigation strategies for dealing with these stresses have been discussed. Despite sugarcane's complex genomes, conventional breeding approaches can be utilized in conjunction with molecular breeding and omics technologies to develop drought- and salinity-tolerant cultivars. The significant role of plant growth-promoting bacteria in sustaining sugarcane productivity under drought and salinity cannot be overlooked.

The basic helix-loop-helix transcription factor gene, OsbHLH38, plays a key role in controlling rice salt tolerance

The plant hormone abscisic acid (ABA) is crucial for plant seed germination and abiotic stress tolerance. However, the association between ABA sensitivity and plant abiotic stress tolerance remains largely unknown. In this study, 436 rice accessions were assessed for their sensitivity to ABA during seed germination. The considerable diversity in ABA sensitivity among rice germplasm accessions was primarily reflected by the differentiation between the Xian (indica) and Geng (japonica) subspecies and between the upland-Geng and lowland-Geng ecotypes. The upland-Geng accessions were most sensitive to ABA. Genome-wide association analyses identified four major quantitative trait loci containing 21 candidate genes associated with ABA sensitivity of which a basic helix-loop-helix transcription factor gene, OsbHLH38, was the most important for ABA sensitivity. Comprehensive functional analyses using knockout and overexpression transgenic lines revealed that OsbHLH38 expression was responsive to multiple abiotic stresses. Overexpression of OsbHLH38 increased seedling salt tolerance, while knockout of OsbHLH38 increased sensitivity to salt stress. A salt-responsive transcription factor, OsDREB2A, interacted with OsbHLH38 and was directly regulated by OsbHLH38. Moreover, OsbHLH38 affected rice abiotic stress tolerance by mediating the expression of a large set of transporter genes of phytohormones, transcription factor genes, and many downstream genes with diverse functions, including photosynthesis, redox homeostasis, and abiotic stress responsiveness. These results demonstrated that OsbHLH38 is a key regulator in plant abiotic stress tolerance.

Economic Uses of Salt-Tolerant Plants

Climate change is likely to affect the ability of world agricultural systems to provide food, fibre, and fuel for the growing world population, especially since the area of salinised land will increase. However, as few species of plants (less than 1% of all plant species) can tolerate saline soils, we believe it is important to evaluate their potential as crops for salinised soils. We have analysed the economic and potential economic uses of plants that are listed in the database eHALOPH, including the most tolerant species, halophytes. For nine main categories of economic value, we found a total of 1365 uses amongst all species listed in eHALOPH as of July 2022; this number reduced to 918 amongst halophytes. We did not find any obvious differences in rankings between the more tolerant halophytes and the whole group of salt-tolerant plants, where the order of use was medical, followed by forage, traditional medicine, food and drink, fuel, fuelwood, and bioenergy. While many species are potentially important as crops, the effects of salt concentration on their uses are much less well documented. Increasing salt concentration can increase, decrease, or have no effect on the concentration of antioxidants found in different species, but there is little evidence on the effect of salinity on potential yield (the product of concentration and biomass). The effect of salinity on forage quality again varies with species, often being reduced, but the overall consequences for livestock production have rarely been evaluated. Salt-tolerant plants have potential uses in the bioremediation of degraded land (including revegetation, phytoremediation, and extraction of NaCl) as well as sources of biofuels, although any use of saline water for the sustainable irrigation of salt-tolerant crops must be viewed with extreme caution.

Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice

Achieving high-yield potential is always the ultimate objective of any breeding program. However, various abiotic stresses such as salinity, drought, cold, flood, and heat hampered rice productivity tremendously. Salinity is one of the most important abiotic stresses that adversely affect rice grain yield. The present investigation was undertaken to dissect new genetic loci, which are responsible for salt tolerance at the early seedling stage in rice. A bi-parental mapping population (F_2:3) was developed from the cross between BRRI dhan28/Akundi, where BRRI dhan28 (BR28) is a salt-sensitive irrigated (boro) rice mega variety and Akundi is a highly salinity-tolerant Bangladeshi origin indica rice landrace that is utilized as a donor parent. We report reliable and stable QTLs for salt tolerance from a common donor (Akundi) irrespective of two different genetic backgrounds (BRRI dhan49/Akundi and BRRI dhan28/Akundi). A robust 1k-Rice Custom Amplicon (1k-RiCA) SNP marker genotyping platform was used for genome-wide analysis of this bi-parental population. After eliminating markers with high segregation distortion, 886 polymorphic SNPs built a genetic linkage map covering 1526.5 cM of whole rice genome with an average SNP density of 1.72 cM for the 12 genetic linkage groups. A total of 12 QTLs for nine different salt tolerance-related traits were identified using QGene and inclusive composite interval mapping of additive and dominant QTL (ICIM-ADD) under salt stress on seven different chromosomes. All of these 12 new QTLs were found to be unique, as no other map from the previous study has reported these QTLs in the similar chromosomal location and found them different from extensively studied Saltol, SKC1, OsSalT, and salT locus. Twenty-eight significant digenic/epistatic interactions were identified between chromosomal regions linked to or unlinked to QTLs. Akundi acts like a new alternate donor source of salt tolerance except for other usually known donors such as Nona Bokra, Pokkali, Capsule, and Hasawi used in salt tolerance genetic analysis and breeding programs worldwide, including Bangladesh. Integration of the seven novel, reliable, stable, and background independent salinity-resilient QTLs (qSES1, qSL1, qRL1, qSUR1, qSL8, qK8, qK1) reported in this investigation will expedite the cultivar development that is highly tolerant to salt stress.

Fulvic Acid Improves Salinity Tolerance of Rice Seedlings: Evidence from Phenotypic Performance, Relevant Phenolic Acids, and Momilactones

Salinity is a severe stress that causes serious losses in rice production worldwide. This study, for the first time, investigated the effects of fulvic acid (FA) with various concentrations of 0.125, 0.25, 0.5, and 1.0 mL/L on the ability of three rice varieties, Koshihikari, Nipponbare, and Akitakomachi, to cope with a 10 dS/m salinity level. The results show that the T3 treatment (0.25 mL/L FA) is the most effective in stimulating the salinity tolerance of all three varieties by enhancing their growth performance. T3 also promotes phenolic accumulation in all three varieties. In particular, salicylic acid, a well-known salt-stress-resistant substance, is found to increase during salinity stress in Nipponbare and Akitakomachi treated with T3 by 88% and 60%, respectively, compared to crops receiving salinity treatment alone. Noticeably, the levels of momilactones A (MA) and B (MB) fall in salt-affected rice. However, their levels markedly rise in rice treated with T3 (by 50.49% and 32.20%, respectively, in Nipponbare, and by 67.76% and 47.27%, respectively, in Akitakomachi), compared to crops receiving salinity treatment alone. This implies that momilactone levels are proportional to rice tolerance against salinity. Our findings suggest that FA (0.25 mL/L) can effectively improve the salinity tolerance of rice seedlings even in the presence of a strong salt stress of 10 dS/m. Further studies on FA application in salt-affected rice fields should be conducted to confirm its practical implications.

Fine mapping of a novel QTL DM9.1 conferring downy mildew resistance in melon

Downy mildew (DM) is a major foliar disease globally causing great economic loss in melon production. Utilizing disease-resistant cultivars is the most efficient approach for disease control, while discovery of disease-resistant genes is crucial for the success of DM-resistant breeding. To address this problem, two F₂ populations were constructed using the DM-resistant accession PI 442177 in this study, and QTLs conferring DM resistance were mapped using linkage map and QTL-seq analysis, respectively. A high-density genetic map with the length of 1096.7 cM and density of 0.7 cM was generated by using the genotyping-by-sequencing data of a F₂ population. A major QTL DM9.1 with the phenotypic variance explained proportion of 24.3-37.7% was consistently detected at the early, middle, and late growth stages using the genetic map. QTL-seq analyses on the two F₂ populations also validated the presence of DM9.1. Kompetitive Allele-Specific PCR (KASP) assay was further carried out to fine map DM9.1 into 1.0 Mb interval. A KASP marker co-segregating with DM9.1 was successfully developed. These results not only provided valuable information for DM-resistant gene cloning, but also offered useful markers for melon DM-resistant breeding programs.

Genetic Dissection of Salt Tolerance and Yield Traits of Geng (japonica) Rice by Selective Subspecific Introgression

Salinity is a major factor limiting rice productivity, and developing salt-tolerant (ST) varieties is the most efficient approach. Seventy-eight ST introgression lines (ILs), including nine promising lines with improved ST and yield potential (YP), were developed from four BC₂F₄ populations from inter-subspecific crosses between an elite Geng (japonica) recipient and four Xian (indica) donors at the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences. Genome-wide characterization of donor introgression identified 35 ST QTLs, 25 of which harbor 38 cloned ST genes as the most likely QTL candidates. Thirty-four are Xian-Geng differentiated ones with the donor (Xian) alleles associated with ST, suggesting differentiated responses to salt stress were one of the major phenotypic differences between the two subspecies. At least eight ST QTLs and many others affecting yield traits were identified under salt/non-stress conditions. Our results indicated that the Xian gene pool contains rich 'hidden' genetic variation for developing superior Geng varieties with improved ST and YP, which could be efficiently exploited by selective introgression. The developed ST ILs and their genetic information on the donor alleles for ST and yield traits would provide a useful platform for developing superior ST and high-yield Geng varieties through breeding by design in the future.

Photosynthesis Performance at Different Growth Stages, Growth, and Yield of Rice in Saline Fields

Photosynthetic performance and biomass at different growth stages of the salt-sensitive KDML105 rice cultivar, three improved lines (RD73, CSSL8-94, and TSKC1-144), and the salt-tolerant standard genotype (Pokkali) were investigated under non-saline, semi-saline, and the heavy-saline field conditions in the northeast of Thailand. In the non-saline field, net photosynthesis rates (P_n) of all genotypes remained high from the early vegetative stage to the milky stage and then dramatically reduced at maturity. In contrast, in both saline fields, P_n was the highest at the early vegetative stage and continuously declining until maturity. Leaf chlorophyll content remained high from the early vegetative to milky stage then reduced at maturity for all three field conditions. During the reproductive phase, P_n of KDML105 and the improved lines were reduced by 4-17% in the heavy-saline field, while that of Pokkali was increased (11-19% increase over that of the non-saline). Pokkali also showed a prominent increase in water use efficiency (WUE) under salinity. Nevertheless, rice leaves under saline conditions maintained the PSII integrity, as indicated by the pre-dawn values of maximum quantum yield of PSII photochemistry (F_v/F_m) of higher than 0.8. Pokkali under the semi-saline and the heavy-saline conditions exhibited 51% and 27% increases in final biomass, and 64% and 42% increases in filled grain weight plant^-1, respectively. In the semi-saline condition, RD73, TSKC1-144, CSSL8-94, and KDML105 showed moderate salt tolerance by displaying 24%, 18.6%, 15%, and 11.3% increases in final biomass, and 24%, 4%, 13%, and 6% increases in filled grain weight plant^-1, respectively. In contrast, in the heavy-saline field, final biomass of RD73, KDML105, CSSL8-94, and TSKC1-144 showed 48%, 45%, 38%, and 36% reductions from that in the non-saline field, while the filled grain weight plant^-1 were reduced by 45%, 58%, 35%, and 32%, respectively. This indicated that the improved lines carrying drought- and/or salt-tolerance genes achieved an increased salt tolerance level than the parental elite cultivar, KDML105.

Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice

Salt stress is a major constraint in rice production worldwide. Salt stress is estimated to cause annual losses of 30-50% in rice production. Discovering and deploying salt-resistance genes are the most effective ways to control salt stress. We performed a genome-wide association study (GWAS) to detect QTLs related to salt tolerance at the seedling stage using the japonica-multiparent advanced generation intercross (MAGIC) population. Four QTLs (qDTS1-1, qDTS1-2, qDTS2, and qDTS9) associated with salt tolerance were identified on chromosomes 1, 2, and 9. Among these QTLs, a novel QTL, qDTS1-2, was located between flanking SNPs (1354576 and id1028360) on chromosome 1, with the largest -log10(P) value of 5.81 and a total phenotypic variance of 15.2%. RNA-seq analysis revealed that among the seven differentially expressed genes (DEGs) commonly identified in both P6 and JM298 showing salt tolerance, two upregulated genes, Os01g0963600 (ASR transcription factor) and Os01g0975300 (OsMYB48), related to salt and drought tolerance, were also involved in the target region of qDTS1-2. The results of this study can provide insights into further understanding of salt tolerance mechanisms and developing DNA markers for marker-assisted selection (MAS) breeding to improve the salt tolerance of cultivars in rice breeding programs.

Integrated Transcriptome and Metabolome Analysis of Rice Leaves Response to High Saline-Alkali Stress

Rice (Oryza sativa) is one of the most important crops grown worldwide, and saline-alkali stress seriously affects the yield and quality of rice. It is imperative to elucidate the molecular mechanisms underlying rice response to saline-alkali stress. In this study, we conducted an integrated analysis of the transcriptome and metabolome to elucidate the effects of long-term saline-alkali stress on rice. High saline-alkali stress (pH > 9.5) induced significant changes in gene expression and metabolites, including 9347 differentially expressed genes (DEGs) and 693 differentially accumulated metabolites (DAMs). Among the DAMs, lipids and amino acids accumulation were greatly enhanced. The pathways of the ABC transporter, amino acid biosynthesis and metabolism, glyoxylate and dicarboxylate metabolism, glutathione metabolism, TCA cycle, and linoleic acid metabolism, etc., were significantly enriched with DEGs and DAMs. These results suggest that the metabolites and pathways play important roles in rice's response to high saline-alkali stress. Our study deepens the understanding of mechanisms response to saline-alkali stress and provides references for molecular design breeding of saline-alkali resistant rice.

Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice

Soil salinization has a serious influence on rice yield and quality. How to enhance salt tolerance in rice is a topical issue. In this study, 120 recombinant inbred line populations were generated through nonstop multi-generation selfing using a male indica rice variety Huazhan (Oryza sativa L. subsp. indica cv. 'HZ') and a female variety of Nekken2 (Oryza sativa L. subsp. japonica cv. 'Nekken2') as the parents. Germination under 80 mM NaCl conditions was measured and analyzed, and quantitative trait locus (QTL) mapping was completed using a genetic map. A total of 16 salt-tolerance QTL ranges were detected at bud stage in rice, which were situated on chromosomes 3, 4, 6, 8, 9, 10, 11, and 12. The maximum limit of detection was 4.69. Moreover, the qST12.3 was narrowed to a 192 kb region on chromosome 12 using map-based cloning strategy. Statistical analysis of the expression levels of these candidate genes under different NaCl concentrations by qRT-PCR revealed that qST12.3 (LOC_Os12g25200) was significantly down-regulated with increasing NaCl concentration, and the expression level of the chlorine-transporter-encoding gene LOC_Os12g25200 in HZ was significantly higher than that of Nekken2 under 0 mM NaCl. Sequencing analysis of LOC_Os12g25200 promoter region indicated that the gene expression difference between parents may be due to eight base differences in the promoter region. Through QTL mining and analysis, a plurality of candidate genes related to salt tolerance in rice was obtained, and the results showed that LOC_Os12g25200 might negatively regulate salt tolerance in rice. The results provide the basis for further screening and cultivation of salt-tolerant rice varieties and have laid the foundation for elucidating further molecular regulation mechanisms of salt tolerance in rice.

Identification of a Saltol-Independent Salinity Tolerance Polymorphism in Rice Mekong Delta Landraces and Characterization of a Promising Line, Doc Phung

The Mekong Delta River in Vietnam is facing salinity intrusion caused by climate change and sea-level rise that is severely affecting rice cultivation. Here, we evaluated salinity responses of 97 rice accessions (79 landraces and 18 improved accessions) from the Mekong Delta population by adding 100 mM NaCl to the nutrient solution for up to 20 days. We observed a wide distribution in salinity tolerance/sensitivity, with two major peaks across the 97 accessions when using the standard evaluation system (SES) developed by the International Rice Research Institute. SES scores revealed strong negative correlations (ranging from - 0.68 to - 0.83) with other phenotypic indices, such as shoot elongation length, root elongation length, shoot dry weight, and root dry weight. Mineral concentrations of Na⁺ in roots, stems, and leaves and Ca²⁺ in roots and stems were positively correlated with SES scores, suggesting that tolerant accessions lower their cation exchange capacity in the root cell wall. The salinity tolerance of Mekong Delta accessions was independent from the previously described salinity tolerance-related locus Saltol, which encodes an HKT1-type transporter in the salinity-tolerant cultivars Nona Bokra and Pokkali. Indeed, genome-wide association studies using SES scores and shoot dry weight ratios of the 79 accessions as traits identified a single common peak located on chromosome 1. This SNP did not form a linkage group with other nearby SNPs and mapped to the 3' untranslated region of gene LOC_Os01g32830, over 6.5 Mb away from the Saltol locus. LOC_Os01g32830 encodes chloroplast glycolate/glycerate translocator 1 (OsPLGG1), which is responsible for photorespiration and growth. SES and shoot dry weight ratios differed significantly between the two possible haplotypes at the causal SNP. Through these analyses, we characterize Doc Phung, one of the most salinity-tolerant varieties in the Mekong Delta population and a promising new genetic resource.

QTL analysis for sodium removal ability in rice leaf sheaths under salinity using an IR-44595/318 F2 population

Over-accumulation of salt in rice plants is an effect of salt stress which decreases growth and grain yield. Salt removal ability in leaf sheaths is a tolerance mechanism to decrease salt entry and accumulation in leaf blades and maintain photosynthesis under salinity. In this study, a QTL analysis of removal ability of sodium ions (Na⁺) in leaf sheaths and Na⁺ accumulation-related traits, was conducted using F₂ population between two rice varieties, IR-44595 with superior Na⁺ removal ability, and 318 with contrasting Na⁺ removal ability in leaf sheaths under salinity. Suggestive QTLs for Na⁺ removal ability in leaf sheaths were found on chromosomes 4 and 11. The suggestive QTL on chromosome 11 overlapped with other significant QTLs for Na⁺ concentration in shoots, leaf blades and leaf sheaths, and Na⁺/K⁺ ratio in leaf blades. Correlation analysis indicated that Na⁺ removal ability in leaf sheaths is important in reducing Na⁺ accumulation in leaf blades. The varietal difference of Na⁺ removal ability in leaf sheaths at the whole plant level was greater at lower NaCl concentrations and became smaller as the treatment NaCl concentration increased. Although the Na⁺ removal ability in leaf sheath was comparable between IR-44595 and 318 under high salinity at the whole plant level, the younger leaves of IR-44595 still showed a higher Na⁺ sheath-blade ratio than 318, which implied the Na⁺ removal ability functions in the younger leaves in IR-44595 to reduce Na⁺ entry in young leaf blades even under high salinity.

Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops

The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.

The classical SOS pathway confers natural variation of salt tolerance in maize

Sodium (Na⁺ ) is the major cation damaging crops in the salinised farmland. Previous studies have shown that the Salt Overly Sensitive (SOS) pathway is important for salt tolerance in Arabidopsis. Nevertheless, the SOS pathway remains poorly investigated in most crops. This study addresses the function of the SOS pathway and its association with the natural variation of salt tolerance in maize. First, we showed that a naturally occurring 4-bp frame-shifting deletion in ZmSOS1 caused the salt hypersensitive phenotype of the maize inbred line LH65. Accordingly, mutants lacking ZmSOS1 also displayed a salt hypersensitive phenotype, due to an impaired root-to-rhizosphere Na⁺ efflux and an increased shoot Na⁺ concentration. We next showed that the maize SOS3/SOS2 complex (ZmCBL4/ZmCIPK24a and ZmCBL8/ZmCIPK24a) phosphorylates ZmSOS1 therefore activating its Na⁺ -transporting activity, with their loss-of-function mutants displaying salt hypersensitive phenotypes. Moreover, we observed that a LTR/Gypsy insertion decreased the expression of ZmCBL8, thereby increasing shoot Na⁺ concentration in natural maize population. Taken together, our study demonstrated that the maize SOS pathway confers a conservative salt-tolerant role, and the components of SOS pathway (ZmSOS1 and ZmCBL8) confer the natural variations of Na⁺ regulation and salt tolerance in maize, therefore providing important gene targets for breeding salt-tolerant maize.

Mapping QTLs for Reproductive Stage Salinity Tolerance in Rice Using a Cross between Hasawi and BRRI dhan28

Salinity stress is a major constraint to rice production in many coastal regions due to saline groundwater and river sources, especially during the dry season in coastal areas when seawater intrudes further inland due to reduced river flows. Since salinity tolerance is a complex trait, breeding efforts can be assisted by mapping quantitative trait loci (QTLs) for complementary salt tolerance mechanisms, which can then be combined to provide higher levels of tolerance. While an abundance of seedling stage salinity tolerance QTLs have been mapped, few studies have investigated reproductive stage tolerance in rice due to the difficulty of achieving reliable stage-specific phenotyping techniques. In the current study, a BC₁F₂ mapping population consisting of 435 individuals derived from a cross between a salt-tolerant Saudi Arabian variety, Hasawi, and a salt-sensitive Bangladeshi variety, BRRI dhan28, was evaluated for yield components after exposure to EC 10 dS/m salinity stress during the reproductive stage. After selecting tolerant and sensitive progeny, 190 individuals were genotyped by skim sequencing, resulting in 6209 high quality single nucleotide polymorphic (SNP) markers. Subsequently, a total of 40 QTLs were identified, of which 24 were for key traits, including productive tillers, number and percent filled spikelets, and grain yield under stress. Importantly, three yield-related QTLs, one each for productive tillers (qPT3.1), number of filled spikelets (qNFS3.1) and grain yield (qGY3.1) under salinity stress, were mapped at the same position (6.7 Mb or 26.1 cM) on chromosome 3, which had not previously been associated with grain yield under salinity stress. These QTLs can be investigated further to dissect the molecular mechanisms underlying reproductive stage salinity tolerance in rice.

Transcriptome Analyses in a Selected Gene Set Indicate Alternative Oxidase (AOX) and Early Enhanced Fermentation as Critical for Salinity Tolerance in Rice

Plants subjected to stress need to respond rapidly and efficiently to acclimatize and survive. In this paper, we investigated a selected gene set potentially involved in early cell reprogramming in two rice genotypes with contrasting salinity tolerance (Pokkali tolerant and IR29 susceptible) in order to advance knowledge of early molecular mechanisms of rice in dealing with salt stress. Selected genes were evaluated in available transcriptomic data over a short period of 24 h and involved enzymes that avoid ROS formation (AOX, UCP and PTOX), impact ATP production (PFK, ADH and COX) or relate to the antioxidant system. Higher transcript accumulation of AOX (ROS balancing), PFK and ADH (alcohol fermentation) was detected in the tolerant genotype, while the sensitive genotype revealed higher UCP and PTOX transcript levels, indicating a predominant role for early transcription of AOX and fermentation in conferring salt stress tolerance to rice. Antioxidant gene analyses supported higher oxidative stress in IR29, with transcript increases of cytosolic CAT and SOD from all cell compartments (cytoplasm, peroxisome, chloroplast and mitochondria). In contrast, Pokkali increased mRNA levels from the AsA-GSH cycle as cytosolic/mitochondrial DHAR was involved in ascorbate recovery. In addition, these responses occurred from 2 h in IR29 and 10 h in Pokkali, indicating early but ineffective antioxidant activity in the susceptible genotype. Overall, our data suggest that AOX and ADH can play a critical role during early cell reprogramming for improving salt stress tolerance by efficiently controlling ROS formation in mitochondria. We discuss our results in relation to gene engineering and editing approaches to develop salinity-tolerant crops.

Molecular tools, potential frontiers for enhancing salinity tolerance in rice: A critical review and future prospective

Improvement of salinity tolerance in rice can minimize the stress-induced yield losses. Rice (Oryza sativa) is one of Asia's most widely consumed crops, native to the subtropical regions, and is generally associated with sensitivity to salinity stress episodes. Salt-tolerant rice genotypes have been developed using conventional breeding methods; however, the success ratio is limited because of the complex nature of the trait and the high cost of development. The narrow genetic base of rice limited the success of conventional breeding methods. Hence, it is critical to launch the molecular tools for screening rice novel germplasm for salt-tolerant genes. In this regard, the latest molecular techniques like quantitative trait loci (QTL) mapping, genetic engineering (GE), transcription factors (TFs) analysis, and clustered regularly interspaced short palindromic repeats (CRISPR) are reliable for incorporating the salt tolerance in rice at the molecular level. Large-scale use of these potent genetic approaches leads to identifying and editing several genes/alleles, and QTL/genes are accountable for holding the genetic mechanism of salinity tolerance in rice. Continuous breeding practices resulted in a huge decline in rice genetic diversity, which is a great worry for global food security. However, molecular breeding tools are the only way to conserve genetic diversity by exploring wild germplasm for desired genes in salt tolerance breeding programs. In this review, we have compiled the logical evidences of successful applications of potent molecular tools for boosting salinity tolerance in rice, their limitations, and future prospects. This well-organized information would assist future researchers in understanding the genetic improvement of salinity tolerance in rice.

QTL mapping under salt stress in rice using a Kalarata-Azucena population

Salt stress is a major constraint across large rice production areas in Asia, because of the high sensitivity of modern rice varieties. To identify quantitative trait loci (QTL) associated with salt tolerance in rice, we developed an F₂ population from a cross between the salt-tolerant landrace, Kalarata, and the salt-sensitive parent, Azucena. F3 families from this population were screened and scored for salt tolerance using IRRI's Standard evaluation system (SES). Growth, biomass, Na⁺ and K⁺ concentrations in leaf tissues, and chlorophyll concentration were determined. A genetic linkage map was constructed with 151 SSRs and InDel markers, which cover 1463 cM with an average distance of 9.69 cM between loci. A total of 13 QTL were identified using Composite Interval Mapping for 16 traits. Several novel QTL were identified in this study, the largest is for root sodium concentration (LOD = 11.0, R² = 25.0) on chromosome 3, which also co-localize with a QTL for SES. Several QTL on the short arm of chromosome 1 coincide with the Saltol locus identified before. The novel QTL identified in this study constitute future targets for molecular breeding, to combine them with other QTL identified before, for higher tolerance and stable performance of rice varieties in salt affected soils.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10681-022-03026-8.

Development and Characterization of Chromosome Segment Substitution Lines Derived from Oryza rufipogon in the Background of the Oryza sativa indica Restorer Line R974

Dongxiang wild rice (DXWR) (O. rufipogon Griff.), which has the northernmost worldwide distribution of a wild rice species, is a valuable genetic resource with respect to improving stress tolerance in cultivated rice (Oryza sativa L.). In the three-line hybrid rice breeding system, restorer lines play important roles in enhancing the tolerance of hybrid rice. However, restorer lines have yet to be used as a genomic background for development of substitution lines carrying DXWR chromosome segments. We developed a set of 84 chromosome segment substitution lines (CSSLs) from a donor parent DXWR × recurrent parent restorer line R974 (Oryza sativa indica) cross. On average, each CSSL carried 6.27 introgressed homozygous segments, with 93.37% total genome coverage. Using these CSSLs, we identified a single QTL, qDYST-1, associated with salt stress tolerance on chromosome 3. Furthermore, five CSSLs showing strong salt stress tolerance were subjected to whole-genome single-nucleotide polymorphism chip analyses, during which we detected a common substitution segment containing qDYST-1 in all five CSSLs, thereby implying the validity and efficacy of qDYST-1. These novel CSSLs could make a significant contribution to detecting valuable DXWR QTLs, and provide important germplasm resources for breeding novel restorer lines for use in hybrid rice breeding systems.

Seedling-stage salinity tolerance in rice: Decoding the role of transcription factors

Rice is an important staple food crop that feeds over half of the human population, particularly in developing countries. Increasing salinity is a major challenge for continuing rice production. Though rice is affected by salinity at all the developmental stages, it is most sensitive at the early seedling stage. The yield thus depends on how many seedlings can withstand saline water at the stage of transplantation, especially in coastal farms. The rapid development of "omics" approaches has assisted researchers in identifying biological molecules that are responsive to salt stress. Several salinity-responsive quantitative trait loci (QTL) contributing to salinity tolerance have been identified and validated, making it essential to narrow down the search for the key genes within QTLs. Owing to the impressive progress of molecular tools, it is now clear that the response of plants toward salinity is highly complex, involving multiple genes, with a specific role assigned to the repertoire of transcription factors (TF). Targeting the TFs for improving salinity tolerance can have an inbuilt advantage of influencing multiple downstream genes, which in turn can contribute toward tolerance to multiple stresses. This is the first comparative study for TF-driven salinity tolerance in contrasting rice cultivars at the seedling stage that shows how tolerant genotypes behave differently than sensitive ones in terms of stress tolerance. Understanding the complexity of salt-responsive TF networks at the seedling stage will be helpful to alleviate crop resilience and prevent crop damage at an early growth stage in rice.

Physiological Responses to Drought, Salinity, and Heat Stress in Plants: A Review

On the world stage, the increase in temperatures due to global warming is already a reality that has become one of the main challenges faced by the scientific community. Since agriculture is highly dependent on climatic conditions, it may suffer a great impact in the short term if no measures are taken to adapt and mitigate the agricultural system. Plant responses to abiotic stresses have been the subject of research by numerous groups worldwide. Initially, these studies were concentrated on model plants, and, later, they expanded their studies in several economically important crops such as rice, corn, soybeans, coffee, and others. However, agronomic evaluations for the launching of cultivars and the classical genetic improvement process focus, above all, on productivity, historically leaving factors such as tolerance to abiotic stresses in the background. Considering the importance of the impact that abiotic stresses can have on agriculture in the short term, new strategies are currently being sought and adopted in breeding programs to understand the physiological, biochemical, and molecular responses to environmental disturbances in plants of agronomic interest, thus ensuring the world food security. Moreover, integration of these approaches is bringing new insights on breeding. We will discuss how water deficit, high temperatures, and salinity exert effects on plants.

Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review

Simple Summary

Globally, soil salinity, which refers to salt-affected soils, is increasing due to various environmental factors and human activities. Soil salinity poses one of the most serious challenges in the field of agriculture as it significantly reduces the growth and yield of crop plants, both quantitatively and qualitatively. Over the last few decades, several studies have been carried out to understand plant biology in response to soil salinity stress with a major emphasis on genetic and other hereditary components. Based on the outcome of these studies, several approaches are being followed to enhance plants’ ability to tolerate salt stress while still maintaining reasonable levels of crop yields. In this manuscript, we comprehensively list and discuss various biological approaches being followed and, based on the recent advances in the field of molecular biology, we propose some new approaches to improve salinity tolerance of crop plants. The global scientific community can make use of this information for the betterment of crop plants. This review also highlights the importance of maintaining global soil health to prevent several crop plant losses.

Abstract

Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.