Salinity Effects on Seedling Growth and Yield Components of Rice

The zinc finger protein DHHC09 S-acylates the kinase STRK1 to regulate H2O2 homeostasis and promote salt tolerance in rice

Soil salinity results in oxidative stress and heavy losses to crop production. The S-acylated protein SALT TOLERANCE RECEPTOR-LIKE CYTOPLASMIC KINASE 1 (STRK1) phosphorylates and activates CATALASE C (CatC) to improve rice (Oryza sativa L.) salt tolerance, but the molecular mechanism underlying its S-acylation involved in salt signal transduction awaits elucidation. Here, we show that the DHHC-type zinc finger protein DHHC09 S-acylates STRK1 at Cys5, Cys10, and Cys14 and promotes salt and oxidative stress tolerance by enhancing rice H2O2-scavenging capacity. This modification determines STRK1 targeting to the plasma membrane or lipid nanodomains and is required for its function. DHHC09 promotes salt signaling from STRK1 to CatC via transphosphorylation, and its deficiency impairs salt signal transduction. Our findings demonstrate that DHHC09 S-acylates and anchors STRK1 to the plasma membrane to promote salt signaling from STRK1 to CatC, thereby regulating H2O2 homeostasis and improving salt stress tolerance in rice. Moreover, overexpression of DHHC09 in rice mitigates grain yield loss under salt stress. Together, these results shed light on the mechanism underlying the role of S-acylation in RLK/RLCK-mediated salt signal transduction and provide a strategy for breeding highly salt-tolerant rice.

Physiological Responses to Salt Stress at the Seedling Stage in Wild (Oryza rufipogon Griff.) and Cultivated (Oryza sativa L.) Rice

Domesticated rice Oryza sativa L. is a major staple food worldwide, and the cereal most sensitive to salinity. It originated from the wild ancestor Oryza rufipogon Griff., which was reported to possess superior salinity tolerance. Here, we examined the morpho-physiological responses to salinity stress (80 mM NaCl for 7 days) in seedlings of an O. rufipogon accession and two Italian O. sativa genotypes, Baldo (mildly tolerant) and Vialone Nano (sensitive). Under salt treatment, O. rufipogon showed the highest percentage of plants with no to moderate stress symptoms, displaying an unchanged shoot/root biomass ratio, the highest Na+ accumulation in roots, the lowest root and leaf Na+/K+ ratio, and highest leaf relative water content, leading to a better preservation of the plant architecture, ion homeostasis, and water status. Moreover, O. rufipogon preserved the overall leaf carbon to nitrogen balance and photosynthetic apparatus integrity. Conversely, Vialone Nano showed the lowest percentage of plants surviving after treatment, and displayed a higher reduction in the growth of shoots rather than roots, with leaves compromised in water and ionic balance, negatively affecting the photosynthetic performance (lowest performance index by JIP-test) and apparatus integrity. Baldo showed intermediate salt tolerance. Being O. rufipogon interfertile with O. sativa, it resulted a good candidate for pre-breeding towards salt-tolerant lines.

Integration of genome-wide association studies reveal loci associated with salt tolerance score of rice at the seedling stage

Salt threatens rice cultivation in many countries. Hence, breeding new varieties with high salt tolerance is important.A panel of 2,391 rice accessions from the 3 K Rice Genome Project was selected to evaluate salt tolerance via the standard evaluation score (SES) in hydroponics under 60 mM NaCl at the seedling stage. Three sub-population panels including 1,332, 628, and 386 accessions from the original 2,391 ones were constructed based on low relatedness revealed by a phylogenetic tree generated by Archaeopteryx Tree. A genome-wide association study (GWAS) was conducted on the entire and sub-population panels using SES data and a selection of 5, 10, 20, and 40% of SNPs selected from the original 1,011,601 SNPs by filtering minor allele frequency > 5% and missing rate < 5%. To perform GWAS, three methods implemented in three different software packages were utilized.Using the integration of GWAS programs, a total of four QTLs associated with SES scores were identified in different panels. Some QTLs co-located with previously detected QTL-related traits. qSES1.1 was detected in three panels, qSES1.3 and qSES2.1 in two panels, and qSES3.1 in one panel through GWAS by all three methods used and selected SNPs. These four QTLs were selected to detect candidate genes. Combining gene-based association study plus haplotype analysis in the entire population and the three sub-populations let us shortlist three candidate genes, viz. LOC_Os01g23640 and LOC_Os01g23680 for qSES1.1, and LOC_Os01g71240 for qSES1.3 region affecting salt tolerance. The identified QTLs and candidate genes provided useful materials and genetic information for future functional characterization and genetic improvement of salt tolerance in 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.

Plant-Derived Smoke Mitigates the Inhibitory Effects of the Auxin Inhibitor 2,3,5-Triiodo Benzoic Acid (TIBA) by Enhancing Root Architecture and Biochemical Parameters in Maize

The present study was designed to investigate and compare the effects of plant-derived smoke (PDS) and auxin (IAA and IBA) on maize growth under the application of 2,3,5-triiodo benzoic acid (TIBA). For this purpose, indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA), each at a concentration of 10 ppm, along with PDS at a ratio of 1:500 (v/v) were used alone and in combination with 10 ppm of TIBA. The results indicate that the germination percentage (%) of maize seeds was enhanced under IAA, IBA and PDS treatment. However, IAA and IBA resulted in reduced germination when applied in combination with TIBA. Importantly, the germination percentage (%) was improved by PDS under TIBA treatment. The analysis of seedling height, length of leaves, and number of primary, seminal and secondary/lateral roots showed improvement under individual treatments of IAA and IBA, PDS and PDS + TIBA treatment, while these values were reduced under IAA + TIBA and IBA + TIBA application. Chlorophyll content, total soluble sugars and antioxidative enzymatic activity including POD and SOD increased in seedlings treated with PDS alone or both PDS and TIBA, while in seedlings treated with IAA and TIBA or IBA and TIBA, their levels were decreased. APX and CAT responded in the opposite way-under IAA, IBA and PDS treatment, their levels were found to be lower than the control (simple water treatment), while TIBA treatment with either IAA, IBA or PDS enhanced their levels as compared to the control. These results reveal that PDS has the potential to alleviate the inhibitory effects of TIBA. This study highlights the role of PDS in preventing TIBA from blocking the auxin entry sites.

Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs

Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.

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.

Rice yield penalty and quality deterioration is associated with failure of nitrogen uptake from regreening to panicle initiation stage under salinity

In recent years, the development and utilization of saline land for rice cultivation have effectively expanded grain productivity. Rice is a salt-sensitive crop, and the increasing salinity problem threatens rice yield and quality. Therefore, we conducted open field experiments to study the effect of salinity on different growth stages of rice. Irrigating saline treatment was conducted at three different growth stages: irrigating saline from the regreening stage to the panicle initiation stage (S1), irrigating saline from the panicle initiation stage to the flowering stage (S2), and irrigating saline from the flowering stage to the maturity stage (S3). Each treatment period lasted for about 30 days. At the same time, irrigating saline water from the regreening stage to the maturity stage (S4) treatment was added in 2022 to explore the performance of salt stress during the whole growth period of rice. Based on the treatment of these different saline irrigation growth periods, three saline concentrations were incorporated, including salinity 0‰ (T1), 3‰ (T2), and 6‰ (T3) concentrations. No irrigating saline during the whole growth period was also used as a control (CK). The results indicated that rice grain yield and quality were most sensitive to saline treatment during S1 among the three stress periods. At the S1 stage, salinity mainly reduced the nitrogen uptake, resulting in stunted plant growth, reducing tillering, yield, and yield components, and deteriorating the rice quality. Compared to the control, IE_N (grain yield over the total amount of N uptake in plants at maturity) was more sensitive at the S1 stage than S2 and S3 stages under salinity. Furthermore, the findings of our study suggest that under salinity, rice growth is not only directly affected by the higher sodium (Na⁺) content in plants, but the higher concentration of Na⁺ reduced the ability of plants to uptake nitrogen. Thus, more attention should be paid to the field management of the S1 stage, the most sensitive stage during rice cultivation in salinized areas. It is necessary to avoid salt damage to rice during this period and ensure irrigation with precious freshwater resources.

Prohexadione calcium enhances rice growth and tillering under NaCl stress

Salt stress affects crop quality and reduces crop yields, and growth regulators enhance salt tolerance of crop plants. In this report, we examined the effects of prohexadione-calcium (Pro-Ca) on improving rice (Oryza sativa L.) growth and tillering under salt stress. We found that NaCl stress inhibited the growth of two rice varieties and increased malondialdehyde (MDA) levels, electrolyte leakage, and the activities of the antioxidant enzymes. Foliar application of Pro-Ca reduced seedling height and increased stem base width and lodging resistance of rice. Further analyses showed that Pro-Ca application reduced MDA content, electrolyte leakage, and membrane damage in rice leaves under NaCl stress. Pro-Ca enhanced the net photosynthetic rate (Pn), stomatal conductance (Gs), and intercellular CO₂ concentration (Ci) of rice seedlings, while increasing the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbic acid peroxidase (APX) at the tillering stage under salt stress. Overall, Pro-Ca improves salt tolerance of rice seedlings at the tillering stage by enhancing lodging resistance, reducing membrane damages, and enhancing photosynthesis and antioxidant capacities of rice seedlings.

DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials

BACKGROUND

Improved Samba Mahsuri (ISM) is an elite, high-yielding, bacterial blight resistant, fine-grained rice variety with low glycaemic index. It is highly sensitive to salt stress, particularly at seedling stage, which significantly reduces its yield potential in coastal areas. A salinity tolerant QTL, Saltol, associated with seedling stage tolerance was previously mapped on chromosome 1 (10.6-11.5 Mb) from the Indian landrace, Pokkali and is effective in different genetic backgrounds. The objective of this study was to enhance salinity tolerance of ISM by incorporating the Saltol QTL through marker-assisted backcross breeding using the breeding line, FL478 (Pokkali/IR29).

RESULTS

Foreground selection was carried out at each generation using five Saltol-specific markers and three bacterial blight resistance genes, Xa21, xa13 and xa5. Background selection was conducted using 66 well distributed polymorphic SSR markers and at the BC₃F₂ generation, a single plant with maximum recurrent parent genome recovery (95.3%) was identified and advanced to the BC₃F₄ generation. Based on bacterial blight resistance, seedling stage salinity tolerance and resemblance to ISM, four advanced breeding lines were selected for testing in replicated experiments near Hyderabad, India. A promising near-isogenic line, DRR Dhan 58, was evaluated in multi-location trials-coastal salinity and it showed significant salinity tolerance, resistance to bacterial blight disease, high yield and excellent grain quality during the 2019 and 2020 trials. DRR Dhan 58 was 95.1% similar to ISM based on genotyping with the 90 K SNP chip. Whole genome resequencing analysis of Pokkali and FL478 which were salinity tolerant checks, ISM and DRR Dhan 58 showed a high degree of relatedness with respect to the candidate gene loci for Saltol and OsSKC1 (Shoot K⁺ Concentration 1).

CONCLUSION

DRR Dhan 58, possessing Saltol and three bacterial blight resistance genes (Xa21, xa13 and xa5) in the genetic background of the Indian mega-variety of rice, Samba Mahsuri, was developed for potential cultivation in areas prone to seedling stage salinity, as well as areas with endemic bacterial blight disease. This entry had a 24% yield advantage over the recurrent parent ISM under coastal saline conditions in multi-location trials and was recently released for commercial cultivation in India.

Salinity Stress Response of Rice (Oryza sativa L. cv. Luem Pua) Calli and Seedlings

Soil salinity limits plant growth and production. This research investigated a suitable medium for callus induction and plantlet regeneration in the Luem Pua rice cultivar. The effect of salt stress on seedling growth was determined using in vitro culture and soil conditions. An efficient protocol for callus induction has been developed by culture sterilized seeds on the Murashige and Skoog (MS, 1962) medium containing 0.5 mg/l benzyladenine (BA) with 1 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D) that resulted in a 100% callus induction. Plantlet regeneration percentage of 49% was recorded on the MS medium containing 4 mg/l BA with 0.5 mg/l 1-naphthaleneacetic acid (NAA) after 4 weeks. For salt stress investigation, the calli were treated on an induction medium containing various concentrations of NaCl (0, 50, 100, 150, and 200 mM), while two-week-old rice seedlings were planted in soil and treated with the same concentration of NaCl for 4 weeks. In vitro culture revealed that callus survival percentage decreased when NaCl concentration increased, similar to soil culture. Seedling growth under salinity treatment also decreased when NaCl concentration increased, while other physiological parameters such as total chlorophyll, chlorophyll a, chlorophyll b, green intensity, and chlorophyll fluorescence under light conditions increased under salinity stress. These changes define the growth and physiological salinity tolerance characteristics of Luem Pua rice calli and seedlings. They can be utilized as a baseline for demand-driven in vitro rice propagation, providing useful information that can be combined with other agronomic features in rice development or breeding programs to improve the flexibility of abiotic stress-tolerant cultivars.

Effect of Different Salts on Nutrients Uptake, Gene Expression, Antioxidant, and Growth Pattern of Selected Rice Genotypes

Climate change leads to soil salinization, and the dynamic scarcity of freshwater has negatively affected crop production worldwide, especially Oryza sativa. The association among ion uptake, gene expression, antioxidant, biomass, and root and shoot development under different salt stress are not fully understood. Many studies are related to the effect of NaCl only. This study used two salts (CaCl₂ and MgCl₂) along with NaCl and analyzed their effects on mineral uptake (macronutrients and micronutrients), gene expression, seed germination, antioxidants, plant growth, and biomass in different rice genotypes. CaCl₂ (up to 200 mM) slightly increased the germination percentage and seedling growth, whereas, 150 mM MgCl₂ in the soil increased the root, shoot length, and fresh and dry weight in cultivars IR 28 and Cheongcheong. All agronomic traits among rice genotypes were drastically reduced by NaCl stress compared to other salts. Different salt stress differentially regulated ion uptake in the roots and shoots among different rice genotypes. Under different salt stress, a consistent decrease in Ca²⁺, Mn²⁺, and Fe²⁺ ions was observed in the roots of Cheongcheong, Nagdong, and IR 28. Similarly, under different salts, the stress in the shoots of Cheongcheong (Ca²⁺, Na⁺, and Zn²⁺) and Nagdong (Ca²⁺, Mg²⁺, Na⁺, and Zn²⁺) and the shoots of IR 28 (Ca²⁺ and Mg²⁺) consistently increased. Under different salts, a salt stress-related gene was expressed differentially in the roots of rice genotypes. However, after 6 and 12 h, there was consistent OsHKT1, OsNHX1, and OsSOS1 gene upregulation in the shoots of Nagdong and roots and shoots of the salt-tolerant cultivar Pokkali. Under different salt stress, glutathione (GSH) content increased in the shoot of IR 28 and Nagdong by NaCl, and MgCl₂ salt, whereas, POD activity increased significantly by CaCl₂ and MgCl₂ in cultivar Cheongcheong and IR 28 shoot. Therefore, this study suggested that Pokkali responded well to NaCl stress only, whereas, the plant molecular breeding lab cultivar Nagdong showed more salt tolerance to different salts (NaCl, CaCl₂, and MgCl₂). This can potentially be used by agriculturists to develop the new salt-tolerant cultivar "Nagdong"-like Pokkali.

The outward shaker channel OsK5.2 improves plant salt tolerance by contributing to control of both leaf transpiration and K+ secretion into xylem sap

Soil salinity constitutes a major environmental constraint to crop production worldwide. Leaf K⁺ /Na⁺ homoeostasis, which involves regulation of transpiration, and thus of the xylem sap flow, and control of the ionic composition of the ascending sap, is a key determinant of plant salt tolerance. Here, we show, using a reverse genetics approach, that the outwardly rectifying K⁺ -selective channel OsK5.2, which is involved in both K⁺ release from guard cells for stomatal closure in leaves and K⁺ secretion into the xylem sap in roots, is a strong determinant of rice salt tolerance (plant biomass production and shoot phenotype under saline constraint). OsK5.2 expression was upregulated in shoots from the onset of the saline treatment, and OsK5.2 activity in guard cells led to a fast decrease in transpirational water flow and, therefore, reduced Na⁺ translocation to shoots. In roots, upon saline treatment, OsK5.2 activity in xylem sap K⁺ loading was maintained, and even transiently increased, outperforming the negative effect on K⁺ translocation to shoots resulting from the reduction in xylem sap flow. Thus, the overall activity of OsK5.2 in shoots and roots, which both reduces Na⁺ translocation to shoots and benefits shoot K⁺ nutrition, strongly contributes to leaf K⁺ /Na⁺ homoeostasis.

Genome wide association study of MAGIC population reveals a novel QTL for salinity and sodicity tolerance in rice

The present study was conducted to identify the novel QTLs controlling salinity and sodicity tolerance using indica MAGIC rice population. Phenotyping was carried out in salinity (EC ~ 10 dS/m) and sodicity (pH ~ 9.8) at the seedling stage. Among 391 lines, 43 and 98 lines were found tolerant and moderately tolerant to salinity. For sodicity condition, 2 and 45 lines were showed tolerance and moderately tolerance at seedling stage. MAGIC population was genotyped with the help of genotyping by sequencing (GBS) and filtered 27041SNPs were used for genome wide marker trait association studies. With respect to salinity tolerance, 25 SNPs were distributed on chromosomes 1, 5, 11 and 12, whereas 18 SNPs were mapped on chromosomes 6, 4 and 11 with LOD value of > 3.25 to sodicity tolerance in rice. The candidate gene analysis detected twelve causal genes including SKC1 gene at Saltol region for salinity and six associated genes for sodic stress tolerance. The significant haplotypes responsible for core histone protein coding gene (LOC_Os12g25120) and three uncharacterized protein coding genes (LOC_Os01g20710, LOC_Os01g20870 and LOC_Os12g22020) were identified under saline stress. Likewise, five significant haplotypes coding for ribose 5-phosphate isomerise (LOC_Os04g24140), aspartyl protease (LOC_Os06g15760), aluminum-activated malate transporter (LOC_Os06g15779), OsFBX421-Fbox domain containing protein (LOC_Os11g32940) and one uncharacterized protein (LOC_Os11g32930) were detected for sodic stress tolerance. The identified novel SNPs could be the potential candidates for functional characterization. These candidate genes aid to further understanding of genetic mechanism on salinity and sodicity stress tolerance in rice. The tolerant line could be used in future breeding programme to enhance the salinity and sodicity tolerance in rice.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01174-8.

Root Na+ Content Negatively Correlated to Salt Tolerance Determines the Salt Tolerance of Brassica napus L. Inbred Seedlings

Soil salinization is a major environmental stressor that reduces the growth and yield of crops. Maintaining the balance of ions under salinity is vital for plant salt tolerance; however, little is known about the correlation between the salt tolerance of crops and the ion contents of their roots and shoots. Here, we investigated the poorly understood salt-tolerance mechanisms, particularly regarding ion contents (particularly Na+), in Brassica napus subsp. napus L., an agriculturally important species. Twenty B. napus inbred lines were randomly chosen from five salt-tolerance categories and treated with increasing concentrations of NaCl (0–200 mmol) for this work. We found that the root Na+ content is the most correlated limiting factor for the salt tolerance of B. napus; the higher the salt tolerance, the lower the root Na+ content. Correspondingly, the Ca2+/Na+ and K+/Na+ ratios of the roots were highly correlated with B. napus salt tolerance, indicating that the selective absorption ability of these ions by the roots and their translocation to the shoots play a pivotal role in this trait. These data provide a foundation for the further study of the molecular mechanisms underlying salt tolerance and for breeding salt-tolerant B. napus cultivars.

Genome-Wide Association Analysis for Salt-Induced Phenotypic and Physiologic Responses in Rice at Seedling and Reproductive Stages

Salinity is one of the main adverse environmental factors severely inhibiting rice growth and decreasing grain productivity. Developing rice varieties with salt tolerance (ST) is one of the most economical approaches to cope with salinity stress. In this study, the salt tolerance of 220 rice accessions from rice diversity panel l (RDP1), representing five subpopulations, were evaluated based on 16 ST indices at both seedling and reproductive stages under salt stress. An apparent inconsistency was found for ST between the two stages. Through a gene-based/tightly linked genome-wide association study with 201,332 single nucleotide polymorphisms (SNPs) located within genes and their flanking regions were used, a total of 214 SNPs related to 251 genes, significantly associated with 16 ST-related indices, were detected at both stages. Eighty-two SNPs with low frequency favorable (LFF) alleles in the population were proposed to hold high breeding potential in improving rice ST. Fifty-four rice accessions collectively containing all these LFF alleles were identified as donors of these alleles. Through the integration of meta-quantitative trait locus (QTL) for ST and the response patterns of differential expression genes to salt stress, thirty-eight candidate genes were suggested to be involved in the regulation of rice ST. In total, the present study provides valuable information for further characterizing ST-related genes and for breeding ST varieties across whole developmental stages through marker-assisted selection (MAS).

Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines

Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress, which is currently worsened due to climate change. This study reports the development of salt tolerant introgression lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol quantitative trait loci (QTL), and the salt-sensitive japonica elite cultivar OLESA. Genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASPar) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL (IL22). A total of 1,595 genes were identified in indica regions of IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes were identified in the introgressed indica segments of IL22 whose expression was confirmed [e.g., genes involved in ion transport, callose synthesis, transcriptional regulation of gene expression, hormone signaling and reactive oxygen species (ROS) accumulation]. These genes might well contribute to salt stress tolerance in IL22 plants. Furthermore, comparative transcript profiling revealed that indica introgressions caused important alterations in the background gene expression of IL22 plants (japonica cultivar) compared with its salt-sensitive parent, both under non-stress and salt-stress conditions. In response to salt treatment, only 8.6% of the salt-responsive genes were found to be commonly up- or down-regulated in IL22 and OLESA plants, supporting massive transcriptional reprogramming of gene expression caused by indica introgressions into the recipient genome. Interactions among indica and japonica genes might provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines. Collectively, this study illustrates the usefulness of transcriptomics in the characterization of new rice lines obtained in breeding programs in rice.

Salt tolerance at vegetative stage is partially associated with changes in grain quality and starch physicochemical properties of rice exposed to salinity stress at reproductive stage

BACKGROUND

Rice yield and grain quality are highly sensitive to soil salinity. Distinct rice genotypes respond to salinity stress differently. To explore the variation in grain yield and grain trait adaptation to moderate, reproductive-stage salinity stress (4 dS/m electrical conductivity), four rice cultivars differing in degrees of vegetative salt tolerance, including Pokkali (salt-tolerant), RD15 (moderately salt-tolerant), KDML105 (moderately salt-susceptible) and IR29 (salt-susceptible), were examined.

RESULTS

Grain fertility and 100-grain weight of RD15, KDML105 and IR29, as well as grain morphology of KDML105 and IR29, were significantly disturbed. Interestingly, grain starch accumulation in RD15 and KDML105 was enhanced under stress. However, only RD15 showed changes in starch physicochemical properties, including increased granule diameter, decreased gelatinization peak temperature (T_p ) and decreased retrogradation onset temperature (T_o ). Notably, Pokkali maintained productivity, grain quality, and starch properties, while the grain quality of IR29 remained unchanged under salinity stress. Multivariate analysis displayed clear separation of productivity, grain morphology, and starch variables of RD15 in the salt-treated group relative to the control group, suggesting that it was the cultivar most impacted by salt stress despite its moderate salt-tolerance at vegetative stage.

CONCLUSION

Our results demonstrate specific salinity responses among the rice genotypes, and suggest discrepancies between degrees of salt tolerance at vegetative stage versus the ability to maintain both grain quality and starch properties in response to salinity stress imposed at reproductive stage. © 2021 Society of Chemical Industry.

Suffer or Survive: Decoding Salt-Sensitivity of Lemongrass and Its Implication on Essential Oil Productivity

The cultivation of lemongrass (Cymbopogon flexuosus) crop is dominated by its medicinal, food preservative, and cosmetic demands. The growing economy of the lemongrass market suggests the immense commercial potential of lemongrass and its essential oil. Nevertheless, the continuous increase of the saline regime threatens the growth and productivity of most of the plant life worldwide. In this regard, the present experiment explores the salt sensitiveness of the lemongrass crop against five different levels of salt stress. Metabolomic analyses suggest that lemongrass plants can effectively tolerate a salt concentration of up to 80 mM and retain most of their growth and productivity. However, extreme NaCl concentrations (≥160 mM) inflicted significant (α = 0.05) damage to the plant physiology and exhausted the lemongrass antioxidative defence system. Therefore, the highest NaCl concentration (240 mM) minimised plant height, chlorophyll fluorescence, and essential oil production by up to 50, 27, and 45%. The overall data along with the salt implications on photosynthetic machinery and ROS metabolism suggest that lemongrass can be considered a moderately sensitive crop to salt stress. The study, sensu lato, can be used in reclaiming moderately saline lands with lemongrass cultivation converting such lands from economic liability to economic asset.

A rice transcription factor, OsMADS57, positively regulates high salinity tolerance in transgenic Arabidopsis thaliana and Oryza sativa plants

MADS-box transcription factors (TFs) play indispensable roles in various aspects of plant growth, development as well as in response to environmental stresses. Several MADS-box genes have been reported to be involved in the salt tolerance in different plant species. However, the role of the transcription factor OsMADS57 under salinity stress is still unknown. Here, the results of this study showed that OsMADS57 was mainly expressed in roots and leaves of rice plants (Oryza sativa). Gene expression pattern analysis revealed that OsMADS57 was induced by NaCl. Overexpression of OsMADS57 in both Arabidopsis thaliana (A. thaliana) and rice could improve their salt tolerance, which was demonstrated by higher germination rates, longer root length and better growth status of overexpression plants than wild type (WT) under salinity conditions. In contrast, RNA interference (RNAi) lines of rice showed more sensitivity towards salinity. Moreover, less reactive oxygen species (ROS) accumulated in OsMADS57 overexpressing lines when exposed to salt stress, as measured by 3, 3'-diaminobenzidine (DAB) or nitroblue tetrazolium (NBT) staining. Further experiments exhibited that overexpression of OsMADS57 in rice significantly increased the tolerance ability of plants to oxidative damage under salt stress, mainly by increasing the activities of antioxidative enzymes such as superoxide dismutase (SOD) and peroxidase (POD), reducing malonaldehyde (MDA) content and improving the expression of stress-related genes. Taken together, these results demonstrated that OsMADS57 plays a positive role in enhancing salt tolerance by activating the antioxidant system.

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

Reproductive stage salinity tolerance is most critical for rice as it determines the yield under stress. Few studies have been undertaken for this trait as phenotyping was cumbersome, but new methodology outlined in this review seeks to redress this deficiency. Sixty-three meta-QTLs, the most important genomic regions to target for enhancing salinity tolerance, are reported. Although rice has been categorized as a salt-sensitive crop, it is not equally affected throughout its growth, being most sensitive at the seedling and reproductive stages. However, a very poor correlation exists between sensitivity at these two stages, which suggests that the effects of salt are determined by different mechanisms and sets of genes (QTLs) in seedlings and during flowering. Although tolerance at the reproductive stage is arguably the more important, as it translates directly into grain yield, more than 90% of publications on the effects of salinity on rice are limited to the seedling stage. Only a few studies have been conducted on tolerance at the reproductive stage, as phenotyping is cumbersome. In this review, we list the varieties of rice released for salinity tolerance traits, those being commercially cultivated in salt-affected soils and summarize phenotyping methodologies. Since further increases in tolerance are needed to maintain future productivity, we highlight work on phenotyping for salinity tolerance at the reproductive stage. We have constructed an exhaustive list of the 935 reported QTLs for salinity tolerance in rice at the seedling and reproductive stages. We illustrate the chromosome locations of 63 meta-QTLs (with 95% confidence interval) that indicate the most important genomic regions for salt tolerance in rice. Further study of these QTLs should enhance our understanding of salt tolerance in rice and, if targeted, will have the highest probability of success for marker-assisted selections.

Salinity Influences Plant-Pest-Predator Tritrophic Interactions

Climate change-induced salinity intrusion into agricultural soils is known to negatively impact crop production and food security. However, the effects of salinity increase on plant-herbivore-natural enemy systems and repercussions for pest suppression services are largely unknown. Here, we examine the effects of increased salinity on communities of rice (Oryza sativa), brown planthopper (BPH), Nilaparvata lugens, and green mirid bug (GMB), Cyrtorhinus lividipennis, under greenhouse conditions. We found that elevated salinity significantly suppressed the growth of two rice cultivars. Meanwhile, BPH population size also generally decreased due to poor host plant quality induced by elevated salinity. The highest BPH density occurred at 2.0 dS/m salinity and declined thereafter with increasing salinity, irrespective of rice cultivar. The highest population density of GMB also occurred under control conditions and decreased significantly with increasing salinity. Higher salinity directly affected the rice crop by reducing plant quality measured with reference to biomass production and plant height, whereas inducing population developmental asynchrony between BPH and GMB observed at 2 dS/m salinity and potentially uncoupling prey-predator dynamics. Our results suggest that increased salinity has harmful effects on plants, herbivores, natural enemies, as well as plant-pest-predator interactions. The effects measured here suggest that the bottom-up effects of predatory insects on rice pests will likely decline in rice produced in coastal areas where salinity intrusion is common. Our findings indicate that elevated salinity influences tritrophic interactions in rice production landscapes, and further research should address resilient rice insect pest management combining multipests and predators in a changing environment.

Expression dynamics of genes encoding nitrate and ammonium assimilation enzymes in rice genotypes exposed to reproductive stage salinity stress

Understanding the reproductive stage salinity stress tolerance is a key target for breeding stress tolerant rice genotypes. Nitrate and ammonium are equally important nitrogen forms utilized by rice. We evaluated nitrate and ammonium assimilation during reproductive stage in control and salinity (10dSm^-1 using NaCl) stressed rice plants. Osmotic stress tolerant rice genotype Shabhagidhan (SD) and high yielding yet osmotic and salinity stress sensitive genotype Pusa sugandh-5 (PS5) were evaluated. Salinity stress was given to plants during panicle emergence and flag leaves was collected after 1d, 3d 5d, 7d, 9d,12d and 15d after anthesis. Reproductive stage salinity stress resulted in decrease of membrane stability, relative water content and osmotic potential of rice plants. Reproductive stage salinity stress decreased the expression of nitrate reductase (OsNIA), nitrite reductase (OsNiR), Glutamine synthetase (OsGLN1.1, OsGLN1.2, OsGLN2) and glutamate synthase/GOGAT (OsFd-GOGAT, OsNADH-GOGAT) in flag leaves. In response to stress, SD showed better stress tolerance than PS5 in terms of higher yield stability. Variety SD showed higher leaf nitrate and ammonium content and maintained comparatively higher nitrate and ammonia metabolism enzyme activity than PS5. Salinity stress upregulated the activity of glutamate dehydrogenase enzyme and indirectly contributed to the higher proline content and maintenance of favourable osmotic potential in SD. Expression of GS2 which has role in photo respiratory ammonia assimilation was upregulated by salinity stress in PS5 in comparison to SD. Rice genotype showing better induction of nitrogen assimilatory genes will be more tolerant to reproductive stage salinity stress.

Genetic mapping of the early responses to salt stress in Arabidopsis thaliana

Salt stress decreases plant growth prior to significant ion accumulation in the shoot. However, the processes underlying this rapid reduction in growth are still unknown. To understand the changes in salt stress responses through time and at multiple physiological levels, examining different plant processes within a single set-up is required. Recent advances in phenotyping has allowed the image-based estimation of plant growth, morphology, colour and photosynthetic activity. In this study, we examined the salt stress-induced responses of 191 Arabidopsis accessions from 1 h to 7 days after treatment using high-throughput phenotyping. Multivariate analyses and machine learning algorithms identified that quantum yield measured in the light-adapted state (F_v' /F_m' ) greatly affected growth maintenance in the early phase of salt stress, whereas the maximum quantum yield (QY_max ) was crucial at a later stage. In addition, our genome-wide association study (GWAS) identified 770 loci that were specific to salt stress, in which two loci associated with QY_max and F_v' /F_m' were selected for validation using T-DNA insertion lines. We characterized an unknown protein kinase found in the QY_max locus that reduced photosynthetic efficiency and growth maintenance under salt stress. Understanding the molecular context of the candidate genes identified will provide valuable insights into the early plant responses to salt stress. Furthermore, our work incorporates high-throughput phenotyping, multivariate analyses and GWAS, uncovering details of temporal stress responses and identifying associations across different traits and time points, which are likely to constitute the genetic components of salinity tolerance.

Genome-Wide Association Study Reveals Marker-Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker-trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.

Prediction of Future Natural Suitable Areas for Rice under Representative Concentration Pathways (RCPs)

Extreme temperature events, which are part of global climate change, are a growing threat to crop production, especially to such temperature-sensitive crops as rice. As a result, the traditional rice-growing areas are also likely to shift. The MaxEnt model was used for predicting the areas potentially suitable for rice in the short term (2016–2035) and in the medium term (2046–2065) and under two scenarios developed by the Intergovernmental Panel on Climate Change, namely representative concentration pathway (RCP) 4.5 (the intermediate scenario) and RCP 8.5 (sometimes referred to as the worst-case scenario). The predictions, on verification, were seen to be highly accurate: the AUC—area under the curve—value of the MaxEnt model was > 0.85. The model made the following predictions. (1) Areas highly suitable for rice crops will continue to be concentrated mainly in the current major rice-production areas, and areas only marginally suitable will be concentrated mainly in the rainforest region. (2) Overall, although the current pattern of the distribution of such areas would remain more or less unchanged, their extent will mainly decrease in the subtropics but increase in the tropics and in high-latitude regions. (3) The extent of such areas will decrease in the short term but increase in the medium term.

A GWAS approach to find SNPs associated with salt removal in rice leaf sheath

BACKGROUND AND AIMS

The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice.

METHODS

In this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl- concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress.

KEY RESULTS

For the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress.

CONCLUSIONS

These GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress.

Effects of nitric oxide on nitrogen metabolism and the salt resistance of rice (Oryza sativa L.) seedlings with different salt tolerances

Salt stress inhibits rice productivity seriously. Nitric oxide (NO) is an endogenous signaling molecule in plants that can improve the resistance of rice to abiotic stresses. Previous studies also showed that nitrogen metabolism is essential for rice stress-tolerance. However, the physiological and molecular mechanisms by how NO affects the nitrogen metabolisms of rice seedlings remain unclear. A hydroponic experiment with two rice varieties, Jinyuan85 (salt tolerant) and Liaojing763 (salt sensitive), was carried out to explore whether NO could alleviate the negative effects of salt stress on nitrogen metabolism and increase salt resistance of rice seedlings. The results showed that (1) the application of NO alleviated the inhibitory effects of salt stress on plant height and biomass accumulation, and increased the nitrogen content of rice leaf. (2) the accumulation of the sucrose and proline was markedly increased in salt stress after application of NO, and peroxidase activities was increased by 107% and 67.7% for Jinyuan85 and Liaojing763, respectively. (3) NO significantly increased the activities of glutamate dehydrogenase, sucrose synthase and sucrose phosphate synthase in both rice varieties under salt stress. (4) Additionally, NO regulated the expression levels of AMT, NIA and SUT genes, but these regulation effects are different with rice varieties and treatments. The results suggested that NO mainly increased the glutamate dehydrogenase and peroxidase activities and sucrose accumulation to enhance the nitrogen metabolism and antioxidative capacity, and alleviated the negative effects of salt stress on rice performance.

Assessment of Spatial and Temporal Trend of Groundwater Salinity in Jaffna Peninsula and Its Link to Paddy Land Abandonment

Salinization is an explicit global threat faced by coastal low lands. The increased seawater ingression into groundwater due to various climatic and anthropogenic factors affects functioning of ecosystems, biodiversity and the sustainability of coastal agriculture. This study was undertaken to investigate the changes in groundwater salinity in Jaffna Peninsula over a 20-year period and its relationship with paddy land abandonment. Permanently abandoned paddy areas were mapped using historical Landsat images, while groundwater salinity changes in 63 agricultural wells for the period 1999 to 2019 were analysed. The trend in salinity, including proximity to the coast, was examined. The results showed that approximately 8178 ha (43% of total paddy land) of paddy lands had been permanently abandoned while the groundwater salinity had increased by 1.6-fold over the last two decades. An increasing salinity trend with decreasing distance from the coast was observed. Presently, nearly 59% of the wells showed salinity levels that were unsuitable for crop irrigation. The results underline the need for urgent and effective management of groundwater resources in order to maintain the sustainability of the existing paddy lands and ensure availability of potable water for consumption along the coastal low land areas of Jaffna Peninsula.

Diversity analysis of selected rice landraces from West Bengal and their linked molecular markers for salinity tolerance

Study of genetic diversity in crop plants is essential for the selection of appropriate germplasm for crop improvement. As salinity posses a serious environmental challenge to rice production globally and especially in India, it is imperative that the study of large collections of germplasms be undertaken to search for salt tolerant stocks. In the present study, 64 indica germplasms were collected from different agro-climatic zones of West Bengal, India, from the Himalayan foothills in the northern part down to the southern saline belt of the state keeping in view the soil characteristics and other edaphic factors prevailing in the region. Salt tolerance parameters were used to screen the large set of germplasms in terms of root-shoot length, fresh-dry weight, chlorophyll content, Na+/K+ ratio and germination potential in presence of salt. Standard evaluation score or SES was calculated to find out tolerant to sensitive cultivar. Twenty-one SSR markers, some associated with the Saltol QTL and others being candidate gene based SSR (cgSSR) were used to study the polymorphism of collected germplasm. A wide diversity was detected among the collected germplasms at the phenotypic as well as molecular level. Of the 21 SSR markers, 15 markers were found to be polymorphic with 88 alleles. Based on phenotypic and biochemical results, 21 genotypes were identified as salinity tolerant, whereas 40 genotypes turned out to be salt susceptible. The present study shows that apart from the established salt tolerant lines, several other landraces like Bonkanta, Morisal, Ghiosh, Patni may be the source of salt tolerant donor in future breeding programs.

Tissue Tolerance Coupled With Ionic Discrimination Can Potentially Minimize the Energy Cost of Salinity Tolerance in Rice

Salinity is one of the major constraints in rice production. To date, development of salt-tolerant rice cultivar is primarily focused on salt-exclusion strategies, which incur greater energy cost. The present study aimed to evaluate a balancing strategy of ionic discrimination vis-à-vis tissue tolerance, which could potentially minimize the energy cost of salt tolerance in rice. Four rice genotypes, viz., FL478, IR29, Kamini, and AC847, were grown hydroponically and subjected to salt stress equivalent to 12 dS m-1 at early vegetative stage. Different physiological observations (leaf chlorophyll content, chlorophyll fluorescence traits, and tissue Na+ and K+ content) and visual scoring suggested a superior Na+-partitioning strategy operating in FL478. A very low tissue Na+/K+ ratio in the leaves of FL478 after 7 days of stress hinted the existence of selective ion transport mechanism in this genotype. On the contrary, Kamini, an equally salt-tolerant genotype, was found to possess a higher leaf Na+/K+ ratio than does FL478 under similar stress condition. Salt-induced expression of different Na+ and K+ transporters indicated significant upregulation of SOS, HKT, NHX, and HAK groups of transporters in both leaves and roots of FL478, followed by Kamini. The expression of plasma membrane and vacuolar H+ pumps (OsAHA1, OsAHA7, and OsV-ATPase) were also upregulated in these two genotypes. On the other hand, IR29 and AC847 showed greater salt susceptibility owing to excess upward transport of Na+ and eventually died within a few days of stress imposition. But in the "leaf clip" assay, it was found that both IR29 and Kamini had high tissue-tolerance and chlorophyll-retention abilities. On the contrary, FL478, although having higher ionic-discrimination ability, showed the least degree of tissue tolerance as evident from the LC50 score (amount of Na+ required to reduce the initial chlorophyll content to half) of 336 mmol g-1 as against 459 and 424 mmol g-1 for IR29 and Kamini, respectively. Overall, the present study indicated that two components (ionic selectivity and tissue tolerance) of salt tolerance mechanism are distinct in rice. Unique genotypes like Kamini could effectively balance both of these strategies to achieve considerable salt tolerance, perhaps with lesser energy cost.

Amendments to saline-sodic soils showed long-term effects on improving growth and yield of rice (Oryza sativa L.)

Background

Saline-sodic soils are widely distributed in arid and semi-arid regions around the world. High levels of salt and sodium inhibit the growth and development of crops. However, there has been limited reports on both osmotic potential in soil solutions (OP_ss) and characteristics of Na⁺ and K⁺ absorption in rice in saline-sodic soils under various amendments application.

Methods

A field experiment was conducted between 2009 and 2017 to analyze the influence of amendments addition to saline-sodic soils on rice growth and yield. Rice was grown in the soil with no amendment (CK), with desulfurization gypsum (DG), with sandy soil (SS), with farmyard manure (FM) and with the mixture of above amendments (M). The osmotic potential in soil solution, selective absorption of K⁺ over Na⁺ (SA), selective transport of K⁺ over Na⁺ (ST), the distribution of K⁺ and Na⁺and yield components in rice plants were investigated.

Results

The results indicated that amendments application have positive effects on rice yield. The M treatment was the best among the tested amendments with the highest rice grain yield. M treatment increased the OP_ss values significantly to relieve the inhibition of the water uptake by plants. Additionally, the M treatment significantly enhanced K⁺ concentration and impeded Na⁺ accumulation in shoots. SA values were reduced while ST values were increased for all amendments. In conclusion, a mixture of desulfurization gypsum, sandy soil and farmyard manure was the best treatment for the improvement of rice growth and yield in the Songnen Plain, northeast China.

Alleviation of Salt Stress in Upland Rice (Oryza sativa L. ssp. indica cv. Leum Pua) Using Arbuscular Mycorrhizal Fungi Inoculation

Arbuscular mycorrhizal fungi (AMF) symbionts not only promote the growth of host plant but also alleviate abiotic stresses. This study aimed to investigate the putative role of AMF in salt stress regulation of upland pigmented rice cv. Leum Pua (LP) comparing with Pokkali salt tolerant (positive check). In general, LP is a variety of glutinous rice that contains anthocyanin pigment in the black pericarp, due to which it possesses high antioxidant activities compared to non-pigmented rice. Pot experiment was conducted to evaluate the impact of inoculated AMF, Glomus etunicatum (GE), Glomus geosporum (GG), and Glomus mosseae (GM) strains, in the LP plantlets subjected to 0 (control) or 150 mM NaCl (salt stress) for 2 weeks in comparison with Pokkali (a salt tolerant rice cultivar), which was maintained as a positive check. Root colonization percentage under NaCl conditions ranged from 23 to 30%. Na⁺ content in the flag leaf tissues was increased to 18-35 mg g^-1 DW after exposure to 150 mM NaCl for 14 days in both inoculated and un-inoculated LP plants, whereas Na:K ratio was very low in cv. Pokkali. Interestingly, sucrose content in the flag leaf tissues of un-inoculated LP plants under salt stress was increased significantly by 50 folds over the control as an indicator of salt stress response, whereas it was unchanged in all AMF treatments. Fructose and free proline in GE inoculated plants under salt stress were accumulated over control by 5.75 and 13.59 folds, respectively, for osmotic adjustment of the cell, thereby maintaining the structure and functions of chlorophyll pigments, F_v/F_m, Φ_PSII, and stomatal function. Shoot height, flag leaf length, number of panicles, panicle length, panicle weight, and 100-grain weight in GE inoculated plants of cv. LP under salt stress were maintained similar to cv. Pokkali. Interestingly, cyanidin-3-glucoside (C3G) and peonidin-3-glucoside (P3G) in the pericarp of cv. LP were regulated by GE inoculation under salt stress conditions. In summary, AMF-inoculation in rice crop is a successful alternative approach to reduce salt toxicity, maintain the yield attributes, and regulate anthocyanins enrichment in the pericarp of grains.

Introgressed Saltol QTL Lines Improves the Salinity Tolerance in Rice at Seedling Stage

Rice is a staple food crop in Asia and plays a crucial role in the economy of this region. However, production of rice and its cultivating areas are under constant threat of soil salinity. A major QTL, Saltol, responsible for salinity tolerance at seedling stage has been mapped on chromosome 1 using Pokkali/IR29 Recombinant Inbred Lines (RIL) population. The present study was aimed to incorporate Saltol Quantitative Trait Loci (QTL) in two high yielding mega rice varieties i.e. Pusa44 and Sarjoo52 through Marker Assisted Backcross Breeding (MABB). To improve the seedling stage salinity tolerance in these cultivars, we introgressed the Saltol QTL from donor parent FL478 a derivative of Pokkali. A total of three backcrosses (BC₃) followed by selfing have led to successful introgression of Saltol QTL. Foreground selection at each breeding cycle was done using micro-satellite markers RM3412 and AP3206 to confirm Saltol QTL. The precise transfer of Saltol region was established using recombinant selection through flanking markers RM493 and G11a. Finally, 10 Saltol near isogenic lines (NILs) of Pusa44 and eight NILs of Sarjoo52 were successfully developed. These NILs (BC₃F₄) were evaluated for seedling stage salinity under hydroponic system. The NILs PU99, PU176, PU200, PU215, PU229, PU240, PU241, PU244, PU252, PU263 of Pusa44 and SAR17, SAR23, SAR35, SAR39, SAR77, SAR87, SAR123, SAR136 NILs of Sarjoo52 confirmed tolerance to salinity with low salt injury score of 3 or 5. Ratio of Na⁺/K⁺ content of Saltol NILs ranged from 1.26 to 1.85 in Pusa44 and 1.08 to 1.69 in Sarjoo52. The successfully developed NILs were further phenotyped stringently for morphological traits to estimate Phenotypic Recovery. Background selection of NILs along with parents was carried out with 50K SNP chip and recovered 94.83-98.38% in Pusa44 NILs and 94.51 to 98.31% in Sarjoo52 NILs of recurrent genome. The present study of MAB has accelerated the development of salt tolerant lines in the genetic background of Pusa44 and Sarjoo52. These NILs could be used for commercial cultivation in saline affected area.

Sustainability of Coastal Agriculture under Climate Change

Climatic and non-climatic stressors, such as temperature increases, rainfall fluctuations, population growth and migration, pollution, land-use changes and inadequate gender-specific strategies, are major challenges to coastal agricultural sustainability. In this paper, we discuss all pertinent issues related to the sustainability of coastal agriculture under climate change. It is evident that some climate-change-related impacts (e.g., temperature and rainfall) on agriculture are similarly applicable to both coastal and non-coastal settings, but there are other factors (e.g., inundation, seawater intrusion, soil salinity and tropical cyclones) that particularly impact coastal agricultural sustainability. Coastal agriculture is characterised by low-lying and saline-prone soils where spatial competition with urban growth is an ever-increasing problem. We highlight how coastal agricultural viability could be sustained through blending farmer perceptions, adaptation options, gender-specific participation and integrated coastal resource management into policy ratification. This paper provides important aspects of the coastal agricultural sustainability, and it can be an inspiration for further research and coastal agrarian planning.

Identification of Superior Alleles for Seedling Stage Salt Tolerance in the USDA Rice Mini-Core Collection

Salt stress is a major constraint to rice acreage and production worldwide. The purpose of this study was to evaluate the natural genetic variation available in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) for early vigor traits under salt stress and identify quantitative trait loci (QTLs) for seedling-stage salt tolerance via a genome-wide association study (GWAS). Using a hydroponic system, the seedlings of 162 accessions were subjected to electrical conductivity (EC) 6.0 dS m⁻¹ salt stress at the three-to-four leaf stage. After completion of the study, 59.4% of the accessions were identified as sensitive, 23.9% were identified as moderately tolerant, and 16.7% were identified as highly tolerant. Pokkali was the most tolerant variety, while Nerica-6 was the most sensitive. Adapting standard International Rice Research Institute (IRRI) protocols, eight variables associated with salt tolerance were determined. The GWAS of the URMC, using over three million single-nucleotide polymorphisms (SNPs), identified nine genomic regions associated with salt tolerance that were mapped to five different chromosomes. Of these, none were in the known Saltol QTL region, suggesting different probable genes and mechanisms responsible for salt tolerance in the URMC. The study uncovered genetic loci that explained a large portion of the variation in salt tolerance at the seedling stage. Fourteen highly salt-tolerant accessions, six novel loci, and 16 candidate genes in their vicinity were identified that may be useful in breeding for salt stress tolerance. Identified QTLs can be targeted for fine mapping, candidate gene verification, and marker-assisted breeding in future studies.

Membrane Lipid Remodeling in Response to Salinity

Salinity is one of the most decisive environmental factors threatening the productivity of crop plants. Understanding the mechanisms of plant salt tolerance is critical to be able to maintain or improve crop yield under these adverse environmental conditions. Plant membranes act as biological barriers, protecting the contents of cells and organelles from biotic and abiotic stress, including salt stress. Alterations in membrane lipids in response to salinity have been observed in a number of plant species including both halophytes and glycophytes. Changes in membrane lipids can directly affect the properties of membrane proteins and activity of signaling molecules, adjusting the fluidity and permeability of membranes, and activating signal transduction pathways. In this review, we compile evidence on the salt stress responses of the major membrane lipids from different plant tissues, varieties, and species. The role of membrane lipids as signaling molecules in response to salinity is also discussed. Advances in mass spectrometry (MS)-based techniques have largely expanded our knowledge of salt-induced changes in lipids, however only a handful studies have investigated the underlying mechanisms of membrane lipidome regulation. This review provides a comprehensive overview of the recent works that have been carried out on lipid remodeling of plant membranes under salt treatment. Challenges and future perspectives in understanding the mechanisms of salt-induced changes to lipid metabolisms are proposed.

Effect of salinity stress on bioactive compounds and antioxidant activity of wheat microgreen extract under organic cultivation conditions

This study was conducted to confirm the effects of salinity stress on bioactive compounds and antioxidant activity of wheat microgreen extract. The microgreens were cultivated for 8 days in organic media with different concentrations of Na [0 (control), 12.5, 25, 50, and 100 mM from sodium chloride] which was contained in a growth chamber with controlled temperature (20/15 °C, day/night), light (14/10 h, light/dark; intensity 150 μmol·m^-2·s^-1 with quantum dot light-emitting diodes), and humidity (60%). Treatment with increasing concentrations of Na resulted in an increase in the Na content of microgreens. Treatment with 12.5 mM of NaCl significantly maximized β-carotene (1.21 μg/mL), phenolic acid (41.70 μg/mL), flavonoid (165.47 μg/mL), and vitamin C (29.51 μg/mL) levels and the nitrite-scavenging activities (37.33%) in wheat microgreen extracts. In addition, the salt-stress caused due to treatment with 25 mM of NaCl resulted in the highest anthocyanin (51.43 μg/mL), 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (89.31%), and 2,2-diphenyl-1-picrylhydrazyl (63.28%) radical-scavenging activity. Therefore, attaining adequate levels of salt-stress may be useful for the industrial manufacturing of new products from wheat microgreen extract.

Evaluating rice for salinity using pot-culture provides a systematic tolerance assessment at the seedling stage

BACKGROUND

Rice (Oryza sativa L.) is one of the major staple food crops consumed globally. However, rice production is severely affected by high salinity levels, particularly at the seedling stage. A good solution would be the development of an efficient screening methodology to identify genotypes possessing genes for salt tolerance.

RESULT

A new salinity tolerance screening technique using rice seedlings in pot-culture was tested. This method controls soil heterogeneity by using pure sand as a growth medium and minimizes unexpected extreme weather conditions with a movable shelter. Seventy-four rice genotypes were screened at three salinity treatments including high salt stress (electrical conductivity (EC) 12 dSm^- 1), moderate salt stress (EC 6 dSm^- 1), and control (no salt stress), imposed 1 week after emergence. Several shoot and root morpho-physiological traits were measured at 37 days after sowing. A wide range of variability was observed among genotypes for measured traits with root traits being identified as the best descriptors for tolerance to salt stress conditions. Salt stress response indices (SSRI) were used to classify the 74 rice genotypes; 7 genotypes (9.46%) were identified as salt sensitive, 27 (36.48%) each as low and moderately salt tolerant, and 13 (17.57%) as highly salt tolerant. Genotypes FED 473 and IR85427 were identified as the most salt tolerant and salt sensitive, respectively. These results were further confirmed by principal component analysis (PCA) for accuracy and reliability.

CONCLUSION

Although tolerant genotypes still need to be confirmed in field studies and tolerance mechanisms identified at the molecular level, information gained from this study could help rice breeders and other scientists to accelerate breeding by selecting appropriate donor parents, progenies and potential genotypes at early growth stages necessary for salinity tolerance research.

Evaluating rice for salinity using pot-culture provides a systematic tolerance assessment at the seedling stage

BACKGROUND

Rice (Oryza sativa L.) is one of the major staple food crops consumed globally. However, rice production is severely affected by high salinity levels, particularly at the seedling stage. A good solution would be the development of an efficient screening methodology to identify genotypes possessing genes for salt tolerance.

RESULT

A new salinity tolerance screening technique using rice seedlings in pot-culture was tested. This method controls soil heterogeneity by using pure sand as a growth medium and minimizes unexpected extreme weather conditions with a movable shelter. Seventy-four rice genotypes were screened at three salinity treatments including high salt stress (electrical conductivity (EC) 12 dSm^- 1), moderate salt stress (EC 6 dSm^- 1), and control (no salt stress), imposed 1 week after emergence. Several shoot and root morpho-physiological traits were measured at 37 days after sowing. A wide range of variability was observed among genotypes for measured traits with root traits being identified as the best descriptors for tolerance to salt stress conditions. Salt stress response indices (SSRI) were used to classify the 74 rice genotypes; 7 genotypes (9.46%) were identified as salt sensitive, 27 (36.48%) each as low and moderately salt tolerant, and 13 (17.57%) as highly salt tolerant. Genotypes FED 473 and IR85427 were identified as the most salt tolerant and salt sensitive, respectively. These results were further confirmed by principal component analysis (PCA) for accuracy and reliability.

CONCLUSION

Although tolerant genotypes still need to be confirmed in field studies and tolerance mechanisms identified at the molecular level, information gained from this study could help rice breeders and other scientists to accelerate breeding by selecting appropriate donor parents, progenies and potential genotypes at early growth stages necessary for salinity tolerance research.

Salt Tolerance Improvement in Rice through Efficient SNP Marker-Assisted Selection Coupled with Speed-Breeding

Salinity critically limits rice metabolism, growth, and productivity worldwide. Improvement of the salt resistance of locally grown high-yielding cultivars is a slow process. The objective of this study was to develop a new salt-tolerant rice germplasm using speed-breeding. Here, we precisely introgressed the hst1 gene, transferring salinity tolerance from “Kaijin” into high-yielding “Yukinko-mai” (WT) rice through single nucleotide polymorphism (SNP) marker-assisted selection. Using a biotron speed-breeding technique, we developed a BC₃F₃ population, named “YNU31-2-4”, in six generations and 17 months. High-resolution genotyping by whole-genome sequencing revealed that the BC₃F₂ genome had 93.5% similarity to the WT and fixed only 2.7% of donor parent alleles. Functional annotation of BC₃F₂ variants along with field assessment data indicated that “YNU31-2-4” plants carrying the hst1 gene had similar agronomic traits to the WT under normal growth condition. “YNU31-2-4” seedlings subjected to salt stress (125 mM NaCl) had a significantly higher survival rate and increased shoot and root biomasses than the WT. At the tissue level, quantitative and electron probe microanalyzer studies indicated that “YNU31-2-4” seedlings avoided Na⁺ accumulation in shoots under salt stress. The “YNU31-2-4” plants showed an improved phenotype with significantly higher net CO₂ assimilation and lower yield decline than WT under salt stress at the reproductive stage. “YNU31-2-4” is a potential candidate for a new rice cultivar that is highly tolerant to salt stress at the seedling and reproductive stages, and which might maintain yields under a changing global climate.

1-Methylcyclopropene Modulates Physiological, Biochemical, and Antioxidant Responses of Rice to Different Salt Stress Levels

Salt stress in soil is a critical constraint that affects the production of rice. Salt stress hinders plant growth through osmotic stress, ionic stress, and a hormonal imbalance (especially ethylene), therefore, thoughtful efforts are needed to devise salt tolerance management strategies. 1-Methylcyclopropene (1-MCP) is an ethylene action inhibitor, which could significantly reduce ethylene production in crops and fruits. However, 1-MCPs response to the physiological, biochemical and antioxidant features of rice under salt stress, are not clear. The present study analyzed whether 1-MCP could modulate salt tolerance for different rice cultivars. Pot culture experiments were conducted in a greenhouse in 2016-2017. Two rice cultivars, Nipponbare (NPBA) and Liangyoupeijiu (LYP9) were used in this trial. The salt stress included four salt levels, 0 g NaCl/kg dry soil (control, CK), 1.5 g NaCl/ kg dry soil (Low Salt stress, LS), 4.5 g NaCl/kg dry soil (Medium Salt stress, MS), and 7.5 g NaCl/kg dry soil (Heavy Salt stress, HS). Two 1-MCP levels, 0 g (CT) and 0.04 g/pot (1-MCP) were applied at the rice booting stage in 2016 and 2017. The results showed that applying 1-MCP significantly reduced ethylene production in rice spikelets from LYP9 and NPBA by 40.2 and 23.9% (CK), 44.3 and 28.6% (LS), 28 and 25.9% (MS), respectively. Rice seedlings for NPBA died under the HS level, while application of 1-MCP reduced the ethylene production in spikelets for LYP9 by 27.4% compared with those that received no 1-MCP treatment. Applying 1-MCP improved the photosynthesis rate and SPAD value in rice leaves for both cultivars. 1-MCP enhanced the superoxide dismutase production, protein synthesis, chlorophyll contents (chl a, b, carotenoids), and decreased malondialdehyde, H2O2, and proline accumulation in rice leaves. Application of 1-MCP also modulated the aboveground biomass, and grain yield for LYP9 and NPBA by 19.4 and 15.1% (CK), 30.3 and 24% (LS), 26.4 and 55.4% (MS), respectively, and 34.5% (HS) for LYP9 compared with those that received no 1-MCP treatment. However, LYP9 displayed a better tolerance than NPBA. The results revealed that 1-MCP could be employed to modulate physiology, biochemical, and antioxidant activities in rice plants, at different levels of salt stress, as a salt stress remedy.

Marker-free transgenic rice plant overexpressing pea LecRLK imparts salinity tolerance by inhibiting sodium accumulation

KEY MESSAGE

PsLecRLK overexpression in rice provides tolerance against salinity stress and cause upregulation of SOS1 pathway genes, which are responsible for extrusion of excess Na+ ion under stress condition. Soil salinity is one of the most devastating factors threatening cultivable land. Rice is a major staple crop and immensely affected by soil salinity. The small genome size of rice relative to wheat and barley, together with its salt sensitivity, makes it an ideal candidate for studies on salt stress response caused by a particular gene. Under stress conditions crosstalk between organelles and cell to cell response is imperative. LecRLK is an important family, which plays a key role under stress conditions and regulates the physiology of the plant. Here we have functionally validated the PsLecRLK gene in rice for salinity stress tolerance and hypothesized the model for its working. Salt stress sensitive rice variety IR64 was used for developing marker-free transgenic with modified binary vector pCAMBIA1300 overexpressing PsLecRLK gene. Comparison of transgenic and wild-type (WT) plants showed better physiological and biochemical results in transgenic lines with a low level of ROS, MDA and ion accumulation and a higher level of proline, relative water content, root/shoot ration, enzymatic activities of ROS scavengers and upregulation of stress-responsive genes. Based on the relative expression of stress-responsive genes and ionic content, the working model highlights the role of PsLecRLK in the extrusion of Na+ ion from the cell. This extrusion of Na+ ion is facilitated by higher expression of SOS1 (Na+/K+ channel) in transgenic plants as compared to WT plants. Altered expression of stress-responsive genes and change in biochemical and physiological properties of the cell suggests an extensive reprogramming of the stress-responsive metabolic pathways by PsLecRLK under stress condition, which could be responsible for the salt tolerance capability.

Identification of the antioxidant defense genes which may provide enhanced salt tolerance in Oryza sativa L

Antioxidative mechanisms are important to protect cells from the hazardous effects of reactive oxygen species (ROS). Salt stress is one of the environmental stress factors that leads to accumulation of ROS at toxic levels. In this study, we analyzed the responses of two rice (Oryza sativa L.) cultivars against NaCl stress at enzymatic and transcriptional levels. In 14 day-old-seedlings, different antioxidant enzyme activities were observed. These findings were also supported by transcriptional analyses of the responsible genes. According to the results, Cyt-APX, CAT A, Cyt-GR1 and proline metabolism-related genes were differentially expressed between two rice varieties under different salt concentrations. Their regulational differences cause different salt sensitivities of the varieties. By this study, we provided an insight into understanding of the correlation between antioxidant defence genes and ROS enzymes under salt stress.

Exogenously Applied Nitric Oxide Enhances Salt Tolerance in Rice (Oryza sativa L.) at Seedling Stage

Salinity is one of the major abiotic factors that limit rice production worldwide. Previous trends show that salt concentration in rivers is increasing consistently, posing potentially adverse threats in the near future. Thus, crops currently being cultivated, particularly in small-scale farming systems, are under high threat from salinity. In this study, we investigated the mitigating effect of nitric oxide (NO) on salt stress in rice based on the assessment of changes in the transcript levels of different genes and the phenotypic response of rice genotypes. We observed that exogenously applied NO increased the expression levels of OsHIPP38, OsGR1, and OsP5CS2 in the susceptible genotype of rice, whereas in the tolerant genotype, the effect of NO was mainly in counteracting the salt-induced gene expression that diverts cellular energy for defense. Moreover, seedlings that were pretreated with NO showed high biomass production under salt stress conditions, indicating the positive role of NO against salt-induced leaf chlorosis and early senescence. The effect of NO-mediated enhancement was more pronounced in the salt tolerant genotype. Therefore, the use of NO with the integration of tolerant genes or genotypes will enhance salt tolerance levels in rice.

Modeling salinity effect on rice growth and grain yield with ORYZA v3 and APSIM-Oryza

Development and testing of reliable tools for simulating rice production in salt-affected areas are presented in this paper. New functions were implemented in existing crop models ORYZA v3 and the cropping systems modelling framework APSIM. Field experiments covering two years, two different sites, and three varieties were used to validate both improved models. We used the salt balance module in the systems model APSIM to simulate the observed daily soil salinity with acceptable accuracy (RMSEn <35%), whereas ORYZA v3 used measured soil salinity at a given interval of days as a model input. Both models presented similarly good accuracy in simulating aboveground biomass, leaf area index, and grain yield for IR64 over a gradient of salinity conditions. The model index of agreement ranged from 0.86 to 0.99. Variability of yield under stressed and non-stressed conditions was simulated with a RMSE, of 191 kg ha^-1 and 222 kg ha^-1 _, respectively, for ORYZA v3 and APSIM-Oryza, corresponding to an RMSE_n of 14.8% and 17.3%. These values are within the bounds of experimental error, therefore indicating acceptable model performance. The model test simulating genotypic variability of rice crop responses resulted in similar levels of acceptable model performance with RMSE_n ranging from 11.3 to 39.9% for observed total above ground biomass for IR64 and panicle biomass for IR29, respectively. With the improved models, more reliable tools are now available for use in risk assessment and evaluation of suitable management options for rice production in salt-affected areas. The approach presented may also be applied in improving other non-rice crop models to integrate a response to soil salinity - particularly in process-based models which capture stage-related stress tolerance variability and resource use efficiency.

A differential tolerance to mild salt stress conditions among six Italian rice genotypes does not rely on Na+ exclusion from shoots

Rice is very sensitive to salt stress at the seedling level, with consequent poor crop establishment. A natural variability in susceptibility to moderate saline environments was found in a group of six Italian temperate japonica rice cultivars, and the physiological determinants for salt tolerance were investigated. Cation (Na⁺, K⁺ and Mg⁺⁺) levels were determined in shoots from individual rice plantlets grown in the absence or in the presence of inhibitory, yet sublethal salt levels, and at increasing time after salt treatments. Significant variations were found among genotypes, but these were unrelated to the relative tolerance, which seems to result from neither mechanism(s) for reduced Na⁺ translocation to the aerial part, nor its increased retrieval from the xylem mediating Na⁺ exclusion from leaves. Accordingly, thiobarbituric acid reactive substance levels raised in leaf tissues of salt-treated seedlings, and osmo-induced proline accumulation was found in all genotypes. Data suggest that the difference in salt tolerance most likely depends on mechanisms for osmotic adjustment and/or antioxidative defence.