Relative salinity tolerance of rice cultivars native to North East India: a physiological, biochemical and molecular perspective

Transcriptional networks revealed late embryogenesis abundant genes regulating drought mitigation in aromatic Keteki Joha rice

Climate change has become increasingly intertwined with the occurrence and severity of droughts. As global temperatures rise due to greenhouse gas emissions, weather patterns are altered, leading to shifts in precipitation levels and distribution. These exacerbate the risk of drought in many regions, with potentially devastating consequences. A comprehensive transcriptome analysis was performed on Keteki Joha, an aromatic rice from North East India, with the aim of elucidating molecular responses to drought. Numerous genes linked to drought were activated, with both ABA-dependent and ABA-independent pathways playing crucial roles. Upregulated genes were enriched with gene ontology terms with response to abscisic acid and abscisic acid-activated signalling pathway, suggesting the existence of an ABA-dependent pathway for drought mitigation. The upregulated genes were also enriched with responses to stress, water, heat, jasmonic acid, and hydrogen peroxide, indicating the presence of an ABA-independent pathway alongside the ABA-dependent mechanism. Weighted Correlation Network Analysis (WGCNA) identified 267 genes that specifically govern drought mitigation in Keteki Joha. The late embryogenesis abundant (LEA) gene family emerges as the most overrepresented in both RNA sequencing data and WGCNA analysis, suggesting their dominant role in mitigating drought. Notably, 31 LEA genes were induced in seedlings and 32 in mature stages under drought stress. The LEA3-1, LEA14/WSI18, RAB16A, RAB16B, DHN1, DHN6, LEA1, LEA3, LEA17, and LEA33 exhibited and established co-expression with numerous other drought stress-related genes, indicating their inseparable role in alleviating drought. Consequently, LEA genes have been proposed to be primary and crucial responders to drought in Keteki Joha.

Meta-analysis and validation of genomic loci governing seedling and reproductive stage salinity tolerance in rice

Identification of concurrent genomic regions contributing tolerance to salinity at the seedling and reproductive stages were done using 45 quantitative trait loci (QTL) mapping studies reporting 915 individual QTLs. The QTL-data were used to perform a meta-analysis to predict, validate and analyze the Meta-QTLs governing component traits contributing to salinity tolerance. We predicted a total of 65 and 49 Meta-QTLs distributed across the genome governing seedling and reproductive stage salinity tolerance, respectively. Salinity stress (EC ~10.0 dSm^-1 ) was evaluated in a set of 32 genotypes grown hydroponically, from these eight extreme (highly tolerant and highly susceptible) genotypes were selected for validation of significant Meta-QTLs. Another set of eight previously known and reported (highly tolerant and highly susceptible) genotypes were evaluated under saline micro plot conditions (EC ~8.0 dSm^-1 ) and used for validation of significant Meta-QTLs for reproductive stage salinity tolerance. The microsatellite marker "RM5635" linked to MSQTL4.2 (~295.43 kb) was able to clearly differentiate contrasting genotypes for seedling stage salinity tolerance, whereas at the reproductive stage, none of the markers were able to validate the predicted Meta-QTL for salinity tolerance. Earlier reported, gene expression studies were used for candidate gene analysis of validated MSQTL4.2, which indicated the down regulation of Os04g0423100, a gene encoding Mono-oxygenase-FAD binding domain containing protein. The traits associated with this Meta-QTL were root and shoot sodium and potassium concentration and leaf chlorophyll content. The identified and validated genomic region assumes a great significant role in seedling stage salinity tolerance in rice, and it can be used for marker-assisted backcross breeding programs.

Expression levels of the Na+/K+ transporter OsHKT2;1 and vacuolar Na+/H+ exchanger OsNHX1, Na enrichment, maintaining the photosynthetic abilities and growth performances of indica rice seedlings under salt stress

Salt affected soil inhibits plant growth, development and productivity, especially in case of rice crop. Ion homeostasis is a candidate defense mechanism in the salt tolerant plants or halophyte species, where the salt toxic ions are stored in the vacuoles. The aim of this investigation was to determine the OsNHX1 (a vacuolar Na⁺/H⁺ exchanger) and OsHKT2;1 (Na⁺/K⁺ transporter) regulation by salt stress (200 mM NaCl) in two rice cultivars, i.e. Pokkali (salt tolerant) and IR29 (salt susceptible), the accumulation of Na⁺ in the root and leaf tissues using CoroNa Green^® staining dye and the associated physiological changes in test plants. Na⁺ content was largely increased in the root tissues of rice seedlings cv. Pokkali (15 min after salt stress) due to the higher expression of OsHKT2;1 gene (by 2.5 folds) in the root tissues. The expression of OsNHX1 gene in the leaf tissues was evidently increased in salt stressed seedlings of Pokkali, whereas it was unchanged in salt stressed seedlings of IR29. Na⁺ in the root tissues of both Pokkali and IR29 was enriched, when subjected to 200 mM NaCl for 12 h and easily detected in the leaf tissues of salt stressed plants exposed for 24 h, especially in cv. Pokkali. Moreover, the overexpression of OsNHX1 gene regulated the translocation of Na⁺ from root to leaf tissues, and compartmentation of Na⁺ into vacuoles, thereby maintaining the photosynthetic abilities in cv. Pokkali. Overall growth performance, maximum quantum yield (F_v/F_m), photon yield of PSII (Φ_PSII) and net photosynthetic rate (P_n) was improved in salt stressed leaves of Pokkali than those in salt stressed IR29.

Genotypic variation among 20 rice cultivars/landraces in response to cadmium stress grown locally in West Bengal, India

Cadmium (Cd) is a hazardous soil contaminant and causes environmental toxicity when present beyond the allowable limit in soil. It can alter growth and metabolism in both plants and animals even at very low concentration. Being sessile in nature, plants try to evade this harmful effect by adopting various defence mechanisms including activation of antioxidants and other metal homeostasis mechanisms. This study shows the varietal Cd stress tolerance capacity of rice cultivars commonly grown in West Bengal, which is a rice biodiversity region in India. Seven days old rice (Oryza sativa L.) seedlings were treated with 10 μM CdCl₂ for another 7days and different physiological and biochemical stress parameters were studied to compare the varietal stress responses. Principle component analysis (PCA) and root tolerance index (RTI) revealed that rice cultivars I.E.T-4786, Jamini and Netiya, Maharaj showed divergent stress responses towards susceptibility and tolerance. Histochemical localization of hydrogen peroxide (H₂O₂), superoxide (O₂˙^-) and pot experiment were performed in these four cultivars (I.E.T-4786-Jamini and Netiya-Maharaj) to elucidate the different Cd stress tolerance. Histochemical analysis, agronomic traits and grain Cd content analyses showed that I.E.T-4786 and Jamini were susceptible with no Cd accumulation in grain, whereas cultivars Netiya and Maharaj were stress tolerant and Cd accumulators. In addition, health risk assessment was monitored for dietary intake of Cd through Cd accumulating rice and non Cd accumulating rice genotypes were identified. Thus, the study identified the Cd tolerant and sensitive cultivars grown locally.

A New Approach for Estimating Soil Salinity Using A Low-Cost Soil Sensor In Situ: A Case Study in Saline Regions of China’s East Coast

Accurate and timely information on soil salinity is crucial for vegetation growth and agricultural productivity in coastal regions. This study investigates the potential of using Wifi POGO, an in situ electromagnetic sensor, for soil salinity assessment over saline coastal regions in eastern China. The sensor readings, soil moisture, and temperature-corrected apparent electrical conductivity (ECa) were used to generate models for EC1:5 (a surrogate for soil salinity) estimation. Two salty areas with distinct soil textures, sandy loam (Shuntai) and clay (Dongxin), were selected. This study revealed that the difference between soil salinity and the in situ measured soil ECa (i.e., EC1:5-ECa) had a strong curvilinear relationship with soil moisture. Such a relationship allows for the direct estimation of soil salinity from soil ECa with the aid of soil moisture information. Both ECa and soil moisture can be measured in situ using a Wifi POGO, a low-cost ground-based soil sensor. By using the leave-one-out cross-validation (LOOCV), the achieved root mean square error (RMSE) and relative RMSE (RRMSE) in EC1:5 estimation were 0.0109 S/m and 19.24% respectively in Shuntai, and 0.0157 S/m and 16.05%, in Dongxin. This new method offers a simple, cost-effective and reliable tool for assessing soil salinity in dynamic coastal regions.

Microbial-assisted and genomic-assisted breeding: a two way approach for the improvement of nutritional quality traits in agricultural crops

Both human and animals, for their nutritional requirements, mainly rely on the plant-based foods, which provide a wide range of nutrients. Minerals, proteins, vitamins are among the nutrients which are essential and need to be available in adequate amount in edible portion of the staple crops. Increasing nutritional content in staple crops either through agronomic biofortification or through conventional plant-breeding strategies continue to be a huge task for scientists around the globe. Although some success has been achieved in recent past, in most cases, we have fallen short of expected targets. To maximize the nutrient uptake and partitioning to different economic part of plants, scientists have employed and tailored several biofortification strategies. But in present agricultural and environmental concerns, these approaches are not much effective. Henceforth, we are highlighting the recent developments and promising aspects of microbial-assisted and genomic-assisted breeding as candidate biofortification approach, that have contributed significantly in increasing nutritional content in grains of different crops. The methods used to date to accomplish nutrient enrichment with recently emerging strategies that we believe could be the most promising and holistic approach for future biofortification program. Results are encouraging, but for future perspective, the existing knowledge about the strategies needs to be confined. Concerted scientific investment are required to widen up these biofortification strategies, so that it could play an important role in ensuring nutritional security of ever-growing population in growing agricultural and environmental constraints.

Evaluation and clustering on salt-tolerant ability in rice genotypes (Oryza sativa L. subsp. indica) using multivariate physiological indices

Salinity is a major abiotic stress that affects plant growth and development, especially in rice crop as it is a salt susceptible crop. Therefore, a wide range of rice genetic resources are screened in the germplasm banks to identify salt tolerant cultivars. The objective of this investigation was to develop effective indices for the classification of salt tolerant rice genotypes among Pathumthani 1, Khao Dawk Mali 105 (KDML 105), RD31, RD41, Suphanburi 1, RD43, RD49 and Riceberry. Rice seedlings were hydroponically grown with 10 dS m^-1 NaCl treatment or without NaCl treatment (to serve as control) (WP; 2 dS m^-1). Standard evaluation system peaked at a score of 9 in Pathumthani 1 and KDML 105, after 21 days of salt treatment, leading to leaf chlorosis, leaf burns and plant death. Chlorophyll a, chlorophyll b and total carotenoids were maintained better in the salt-stressed leaves of rice cvs. Riceberry and RD43, as compared to other cultivars. Salt stress induced a remarkable increase in the free proline accumulation (by 8.38 folds) in cv. Riceberry. Overall growth performance in rice cv. Riceberry was retained, whereas it declined in other cultivars. After 21 days of NaCl treatment at a concentration of 10 dS m^-1, eight rice cultivars were classified into 3 groups based on multivariate physio-morphological indices, Group I: salt-tolerant rice, including cv. Riceberry; Group II: moderately salt tolerant, consisting of RD31, RD41, Suphanburi 1, RD43 and RD49 cultivars; Group III: salt-sensitive cultivars, namely Pathumthani 1 and KDML 105.