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Wheat genotype Kharchia is a donor for salt tolerance in wheat breeding programs worldwide; however, the tolerance mechanism in Kharchia is yet to be deciphered completely. To avoid spending energy on accumulating organic osmolytes and to conserve resources for maintaining growth, plants deploy sodium (NaThe online version contains supplementary material available at 10.1007/s12298-022-01237-w.

The rise in atmospheric CO2 levels impacts humankind by threatening food and nutritional security. The strong correlation between crop yield and grain weight in cereals is an essential component of yield stability. Further, improving grain protein and mineral nutrient content is a crucial breeding target for cereal crops. The study was performed to understand the interactive effects of elevated CO2 (EC) and nitrogen (N) fertilization on grain ionome, grain yield parameters, grain morphology, and the expression of genes related to grain morphology. The changes in ionome and grain parameters were examined in response to two N levels optimal N (ON: 500 mg/pot) and high N (HN: 625 mg/pot) along with atmospheric CO2 enrichment [ambient (CO2) of 400 ±10 ppm and elevated (CO2) of 700 ±10 ppm]. Grain ionome (N, K, Ca and Fe) showed a general decrease in EC-grown wheat plants. The expression of genes related to grain length (TaGL3 and TaGL7) were upregulated, and those genes related to grain width (TaGW2 and TaGW6) were downregulated under EC in maturing spikelet of wheat. In the case of TaSnRK2, the expression was promoted by EC in HN treatment. The complex regulation of source and sink-associated gene transcript abundance indicates an EC mediated alteration in N and sugar signalling in wheat.

Nitrogen (N) recognized as a critical element for plant growth plays a fundamental role in rice cultivation. The N use efficiency (NUE) hovers around 30-35% in rice, suggesting a significant loss of N from the rice fields. Improving the NUE therefore would require genetic interventions and breeding. The cultivar improvement for N uptake and utilization is required to elevate NUE to further heights. Several quantitative trait loci (QTLs) for NUE under varying conditions and genetic backgrounds have been reported in rice. Consolidation of this distributed and unorganized information is necessary to identify critical genomic regions to be used for crop improvement. Therefore, a Meta-analysis from an assembly of 506 QTLs reported from 18 different studies was performed to identify the most significant genomic regions associated with NUE in rice. A total of 12 meta-QTLs (mQTLs) related to the traits such as NUE and grain yield per plant under N deficit conditions have been identified over four rice chromosomes namely 1, 3, 4, and 8. Evaluation of these mQTLs in a set of Indian rice germplasm revealed a significant association of the meta loci with N use parameters and showed wide distribution in the germplasm. Identification of mQTLs on different chromosomes together with their respective markers will help recruit them in marker-assisted selection (MAS) to develop N use efficient genotypes.

To maintain yield stability and environmental sustainability of rice cultivation, improvement in nitrogen use efficiency (NUE) is essential. We identified rice genotypes showing high NUE in control (N120) and N deficient (N0) field conditions by analyzing NUE parameters and different contributing traits. In the first season, genotypes BAM-3181, BAM-4797, BAM-3154, NL-26 IR-83929-B-B-291-3-1-1 (IR-3-1-1), APO and NERICA-L-42 showed high biomass, panicle yield and N utilization efficiency (NutE) at low N field conditions. Reproductive stage N assimilatory and signaling gene expression was correlated to the variation in NUtE. The sequence variation in N metabolism and signaling (NLP) genes were analyzed in selected genotypes (APO and NERICA-L-42). Significant non-synonymous SNPs were found in NPF2.2, PTR2, NGR9 (DEP1), Fd-GOGAT, NLP3, NLP4 and NLP5 genes of APO, NERICA-L-42 and w.r.to japonica genotype Nipponbare. The significant variation in reproductive stage gene expression and changes in amino acid sequence of NLP3, NLP4, NLP5 among rice genotypes differing in NUE is an unexplored and potent genome editing target for high NUE in rice. The non-synonymous SNPs identified in the study will be important genomic resources for improving rice NUE.

Plant's stomatal physiology and anatomical features are highly plastic and are influenced by diverse environmental signals including the concentration of atmospheric CO2 and nutrient availability. Recent reports suggest that the form of nitrogen (N) is a determinant of plant growth and nutrient nitrogen use efficiency (NUE) under elevated CO2 (EC). Previously, we found that high nitrate availability resulted in early senescence, enhanced reactive oxygen species (ROS), and reactive nitrogen species (RNS) production and also that mixed nutrition of nitrate and ammonium ions were beneficial than sole nitrate nutrition in wheat. In this study, the interactive effects of different N forms (nitrate, ammonium, mixed nutrition of nitrate, and ammonium) and EC on epidermal and stomatal morphology were analyzed. Wheat seedlings were grown at two different CO2 levels and supplied with media devoid of N (N0) or with nitrate-N (NN), mixed nutrition of ammonium and nitrate (MN), or only ammonium-N (AN). The stoma length increased significantly in nitrate nutrition with a consistent reduction in stoma width. Guard cell length was higher in EC treatment as compared to AC. The guard cell width was maximum in AN-grown plants at EC. Epidermal cell density and stomatal density were lower at EC. Nitrate nutrition increased the stomatal area at EC while the reverse was true for MN and AN. Wheat plants fertilized with AN showed a higher accumulation of superoxide radical (SOR) at EC, while in NN treatment, the accumulation of hydrogen peroxide (H2O2) was higher at EC. Reactive oxygen species, particularly H2O2, can trigger mitogen-activated protein kinase (MAPK) mediated signaling and its crosstalk with abscisic acid (ABA) signaling to regulate stomatal anatomy in nitrate-fed plants. The SOR accumulation in ammonium- and ammonium nitrate-fed plants and H2O2 in NN-fed plants might finely regulate the sensitivity of stomata to alter water/nutrient use efficiency and productivity under EC. The data reveals that the variation in anatomical attributes viz. cell length, number of cells, etc. affected the leaf growth responses to EC and forms of N nutrition. These attributes are fine targets for effective manipulation of growth responses to EC.

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.

Sugar beet is a salt-tolerant crop that can be explored for crop production in degraded saline soils. Seeds of multigerm genotypes LKC-2006 (susceptible) and LKC-HB (tolerant) were grown in 150 mM NaCl, from germination to 60 days after sowing, to decipher the mechanism of salinity tolerance at the vegetative stage. The biomass of the root and leaf were maintained in the tolerant genotype, LKC-HB, under saline conditions. Na+ /K+ ratios were similar in roots and leaves of LKC-HB, with lower values under salinity compared to LKC 2006. Infrared temperatures were 0.96°C lower in LKC-HB than in LKC-2006, which helped regulate the leaf water status under stressed conditions. Pulse-chase experiment showed that 14 C photosynthate was preferentially allocated towards the development of new leaves in the tolerant genotype. The sugar profile of leaves and roots showed accumulation of raffinose in leaves of LKC-HB, indicating a plausible role in imparting salinity tolerance by serving as an osmolyte or scavenger. The molecular analysis of the genes responsible for raffinose synthesis revealed an 18-fold increase in the expression of BvRS2 in the tolerant genotype, suggesting its involvement in raffinose synthesis. Our study accentuated that raffinose accumulation in leaves is vital for inducing salinity tolerance and maintenance of shoot dry weight in sugar beet.

Tissue and canopy-level evidence suggests that elevated carbon dioxide (EC) inhibits shoot nitrate assimilation in plants and thereby affects nitrogen (N) and protein content of the economic produce. It is speculated that species or genotypes relying more on root nitrate assimilation can adapt better under EC due to the improved/steady supply of reductants required for nitrate assimilation. A study was conducted to examine the effect of EC on N assimilation and associated gene expression in wheat seedlings. Wheat genotypes, BT-Schomburgk (BTS) with comparatively high leaf nitrate reductase (NR) activity and Gluyas Early (GE) with high root NR activity were grown in hydroponic culture for 30 days with two different nitrate levels (0.05 mM and 5 mM) in the climate controlled growth chambers maintained at either ambient (400 ± 10 μmol mol−1) or EC (700 ± 10 μmol mol−1) conditions. Exposure to EC downregulated the activity of enzyme NR and glutamate synthase (GOGAT) in leaf tissues, whereas in roots, activities of both the enzymes were upregulated by exposure to EC. In addition, EC downregulated N assimilation and signalling gene expression under high N availability. Root N assimilation was less affected in comparison with shoot N assimilation; thereby, the proportion of root contribution towards total assimilation was higher. The results suggest that EC could alter and re-programme N assimilation and signalling in wheat seedlings. The genotype and tissue-specific effects of EC on N assimilation also warrants the need for identification of suitable genotypes and revision of fertiliser regime for tapping the beneficial effects of EC conditions.

In drought prone areas, often farmers use less nitrogen, and thus the crop is subjected to combined stress (low N + osmotic stress). Since understanding the regulation of genes involved in nitrate signalling, uptake and assimilation under water-deficit (osmotic stress) is important for improving yield under the combined stress environments, this study analysed the regulation of genes coding for N responses under low N, osmotic stress (OS) and combined stress conditions in seedlings of a wheat. The results revealed that HD2967, a mega wheat variety, was more tolerant to short-term N starvation, OS and combined stress as compared with C306, a drought tolerant check. Interestingly, it was found that low N stress can also lead to accumulation of ABA in wheat seedlings. Real-time RT-qPCR analysis revealed that in addition to low N stress, OS also regulated expression of nitrate signalling genes (TaCIPK8, TaCIPK23, TaNLP4, TaSPL9, TabHLH1 and TaNAC4), HATS gene TaNRT2.1, LATS genes (TaNRT6.5 and TaNPF7.1), nitrate and nitrite assimilation genes and ammonium assimilation genes at least in one tissue of one of the genotypes. Combined stress was found to have significant interaction in regulation genes for nitrate signalling, uptake and assimilation. TabZIP1 and TaPIMP1 TF were identified as new players in low N response in wheat. Thus, osmotic stress and combined stress modulates the genes for N responses, and genotypic variation exists for this in wheat. The common expression pattern of N response genes found under low N and OS may probably regulated, at least in part, by ABA-dependent pathway, as ABA accumulation was induced by both OS and low N stresses. Functional analysis of the osmotic stress regulated genes coding for N response will help enhance tolerance of wheat to combined stress conditions.

In plants, reactive oxygen species accumulate to a toxic level under various abiotic stresses. Many antioxidant defense systems require NADPH as a principal reducing energy equivalent. However, the source of NADPH and the molecular mechanisms associated with the maintenance of cytoplasmic redox balance are still unknown. The present study describes Vigna NADH kinase (VlNADHK), an enzyme involved in NADPH synthesis and prefers NADH as a diphospho-nicotinamide nucleotide donor. We analyzed the enzymatic activity of a putative cytoplasmic NADH kinase during waterlogging in contrasting mung bean genotypes Vigna luteola (tolerant) and Vigna radiata cv. T44 (susceptible) under pot-culture condition. The tolerant cultivar showed higher enzymatic activity under waterlogging as well as after recovery. Similarly, the transcript level of waterlogging-induced NADHK expression was also studied and found to be upregulated in response to waterlogging in the roots of V. luteola and T44. PCR amplicons of partial and full-length sequences were cloned and sequenced from V. luteola. To the best of our knowledge, this is the first time an ATP-dependent NADH kinase gene has been recognized as a component of waterlogging stress tolerance in legumes. Our study indicated that this cytoplasmic NADH kinase is a primary source of the cytosolic NADPH and might have a role in waterlogging tolerance in legumes.

The rapid escalation in atmospheric carbon dioxide (CO2) is an important cause of global climate change that determines global crop productivity. Under elevated CO2 (EC), there is an initial increase in the rate of photosynthesis (PN) that is frequently accompanied by a decrease of PN and an overall decline in nitrogen (N) and protein concentration. Increasing CO2 concentrations results in a general decrease in the nutritional quality of plant products and thus impacts the food and dietary requirements of the global population. EC often results in a significant increase in the nonstructural carbohydrates and total sugar content while reducing grain proteins and cooking quality. Crops grown under EC also exhibits an average reduction of 8% in 25 minerals, including calcium, potassium, zinc, and iron. Exposure to EC also decreases the ratio of minerals to carbohydrates leading to irreversible impacts on human health, reduction in immunity, malnutrition and stunted growth in children, rise in maternal and child deaths, and also obesity due to the carbohydrate-rich diet. The mechanistic understanding of reduction in crop and grain quality under EC is limited. The dilution of N metabolites and minerals due to higher carbon accumulation, restriction in nutrient uptake due to lower transpiration rate, and reductant availability are the foremost reasons. Recent evidence also suggests the regulatory role of reactive oxygen and nitrogen species in EC-mediated changes in N metabolism and uptake. The current understanding advocates the prominence of identifying CO2 responsive crop genotypes and using genotype-specific fertilizer management for meeting food and nutritional security needs under future EC scenarios.

Wheat crop grown under elevated CO

Bread wheat (

The reversible protein phosphorylation and dephosphorylation mediated by protein kinases and phosphatases regulate different biological processes and their response to environmental cues, including nitrogen (N) availability. Nitrate assimilation is under the strict control of phosphorylation—dephosphorylation mediated post-translational regulation. The protein phosphatase family with approximately 150 members in Arabidopsis and around 130 members in rice is a promising player in N uptake and assimilation pathways. Protein phosphatase 2A (PP2A) enhances the activation of nitrate reductase (NR) by deactivating SnRK1 and reduces the binding of inhibitory 14–3–3 proteins on NR. The functioning of nitrate transporter NPF6.3 is regulated by phosphorylation of CBL9 (Calcineurin B like protein 9) and CIPK23 (CBL interacting protein kinase 23) module. Phosphorylation by CIPK23 inhibits the activity of NPF6.3, whereas protein phosphatases (PP2C) enhance the NPF6.3-dependent nitrate sensing. PP2Cs and CIPK23 also regulate ammonium transporters (AMTs). Under either moderate ammonium supply or high N demand, CIPK23 is bound and inactivated by PP2Cs. Ammonium uptake is mediated by nonphosphorylated and active AMT1s. Whereas, under high ammonium availability, CIPK23 gets activated and phosphorylate AMT1;1 and AMT1;2 rendering them inactive. Recent reports suggest the critical role of protein phosphatases in regulating N use efficiency (NUE). In rice, PP2C9 regulates NUE by improving N uptake and assimilation. Comparative leaf proteome of wild type and PP2C9 over-expressing transgenic rice lines showed 30 differentially expressed proteins under low N level. These proteins are involved in photosynthesis, N metabolism, signalling, and defence.

The response of salt tolerant wheat genotype (Kharchia 65), and sensitive cultivars (HD2687, HD2009, WL711) to vegetative stage salinity stress (for 4 weeks) were studied at 1.1 (control), 9.1 (S1) and 14.2 (S2) dSm-1 salinity levels. Based on relative change in Membrane stability, PSII efficiency, retention of chlorophyll and carotenoid contents, Kharchia 65 showed better tolerance to salinity than other genotypes considered. To understand the role of different component mechanisms, expression of genes involved in ion exclusion, antioxidant defence and compatible osmolyte synthesis were analysed. Expression of SOS1 (plasma membrane Na+/H+ antiporter), NHX (vacuolar Na+/H+ antiporter), Ionic (sodium exclusion) and tissue tolerance (Sodium compartmentation, compatible solute accumulation and antioxidant defence) mechanisms were analysed in leaves of the genotypes after 4 weeks of salinity stress. Expression assay and the content of respective constituents indicated that apart from the well-known ion exclusion ability, Kharchia 65 also showed high level of tissue tolerance resulting in high early vigour and maintenance of growth rate afterwards. In Kharchia 65, sensing of salinity stress at plasma membrane activates NADPH Oxidase (RBOH) genes and generate ROS at apoplast. Apoplastic ROS triggers calcium influx and activates calcium signaling genes of SOS pathway (SOS1 and NHX). ROS generated from organelles chloroplast, peroxisome and mitochondria triggers cellular oxidative burst. ROS and calcium activates MAPK genes and downstream transcription factors, NAC and bZIP. MAPK signaling induces cellular antioxidant and compatible osmolyte biosynthesis and imparts tissue tolerance to salinity.

Sugar beet is a salt-tolerant crop that can be explored for crop production in degraded saline soils. Seeds of multigerm genotypes LKC-2006 (susceptible) and LKC-HB (tolerant) were grown in 150 mM NaCl, from germination to 60 days after sowing, to decipher the mechanism of salinity tolerance at the vegetative stage. The biomass of the root and leaf were maintained in the tolerant genotype, LKC-HB, under saline conditions. Na

The nitrogen (N) and protein concentration of wheat crop and grain often decline as a result of exposure of the crop to elevated CO

Wheat is an important staple food crop of the world and it accounts for 18–20% of human dietary protein. Recent reports suggest that CO2 elevation (CE) reduces grain protein and micronutrient content. In our earlier study, it was found that the enhanced production of nitric oxide (NO) and the concomitant decrease in transcript abundance as well as activity of nitrate reductase (NR) and high affinity nitrate transporters (HATS) resulted in CE-mediated decrease in N metabolites in wheat seedlings. In the current study, two bread wheat genotypes Gluyas Early and B.T. Schomburgk differing in nitrate uptake and assimilation properties were evaluated for their response to CE. To understand the impact of low (LN), optimal (ON) and high (HN) nitrogen supply on plant growth, phenology, N and C metabolism, ROS and RNS signaling and yield, plants were evaluated under short term (hydroponics experiment) and long term (pot experiment) CE. CE improved growth, altered N assimilation, C/N ratio, N use efficiency (NUE) in B.T. Schomburgk. In general, CE decreased shoot N concentration and grain protein concentration in wheat irrespective of N supply. CE accelerated phenology and resulted in early flowering of both the wheat genotypes. Plants grown under CE showed higher levels of nitrosothiol and ROS, mainly under optimal and high nitrogen supply. Photorespiratory ammonia assimilating genes were down regulated by CE, whereas, expression of nitrate transporter/NPF genes were differentially regulated between genotypes by CE under different N availability. The response to CE was dependent on N supply as well as genotype. Hence, N fertilizer recommendation needs to be revised based on these variables for improving plant responses to N fertilization under a future CE scenario.

The NIN-LIKE PROTEIN (NLP) family of transcription factors were identified as nitrate-responsive cis-element (NRE)-binding proteins, which function as transcriptional activators in the nitrate-regulated expression of downstream genes. This study was aimed at genome-wide analysis of NLP gene family in rice and the expression profiling of NLPs in response to nitrogen (N) supply and deficiency in rice genotypes with contrasting N use efficiency (NUE). Based on in silico analysis, 6 NLP genes (including alternative splice forms 11 NLPs) were identified from rice. Expression of NLPs was promoted by nitrate supply as well as N deficiency (NLP1, NLP3, NLP4 and NLP5). Four rice genotypes APO (high NUE under sufficient N), IR83929-B-B-291-3-1-1 (IR-3-1-1), Nerica-L-42 (NL-42) (High NUE at low N), and Pusa Basmati 1 (PB1, low NUE) to correlate traits governing NUE and expression of NLPs. Analysis of rate of nitrate uptake and expression of N assimilatory and uptake genes established that IR-3-1-1 has high uptake and assimilation efficiency, translating into high NUE, whereas PB1 is efficient in uptake only when N availability is high. Along with the transcriptional upregulation of NLPs, genotype IR-3-1-1, displayed highest expression of OsNRT1.1B gene, the closest rice homologue of nitrate transceptor AtNRT1.1 and plays major role in nitrate uptake, translocation and signaling in rice. The results showed that high NUE rice genotypes has both high Nitrogen uptake efficiency (NUpE) and Nitrogen utilization efficiency (NUtE), resulting from the effective and coordinated signal transduction network involving the rice homologue of nitrate transceptor OsNRT1.1B, the probable primary nitrate response (PNR) regulator OsNLP1 and the master response regulator OsNLP3, a homologue of AtNLP6/7.

Tyrosine phosphorylation constitutes up to 5% of the total phophoproteome. However, only limited studies are available on protein tyrosine kinases (PTKs) that catalyze protein tyrosine phosphorylation in plants. In this study, domain analysis of the 27 annotated PTK genes in rice genome led to the identification of 18 PTKs with tyrosine kinase domain. The kinase domain of rice PTKs shared high homology with that of dual specificity kinase BRASSINOSTEROID- INSENSITIVE 1 (BRI1) of Arabidopsis. In phylogenetic analysis, rice PTKs clustered with receptor-like cytoplasmic kinases-VII (RLCKs-VII) of Arabidopsis. mRNAseq analysis using Genevestigator revealed that rice PTKs except PTK9 and PTK16 express at moderate to high level in most tissues. PTK16 expression was highly abundant in panicle at flowering stage. mRNAseq data analysis led to the identification of drought, heat, salt, and submergence stress regulated PTK genes in rice. PTK14 was upregulated under all stresses. qRT-PCR analysis also showed that all PTKs except PTK10 were significantly upregulated in root under osmotic stress. Tissue specificity and abiotic stress mediated differential regulation of PTKs suggest their potential role in development and stress response of rice. The candidate dual specificity PTKs identified in this study paves way for molecular analysis of tyrosine phosphorylation in rice.