Plants have developed complex mechanisms to perceive, transduce, and respond to environmental signals, such as light, which are essential for acquiring and allocating resources, including nitrogen (N). This review delves into the complex interaction between light signals and N metabolism, emphasizing light-mediated regulation of N uptake and assimilation. Firstly, we examine the details of light-mediated regulation of N uptake and assimilation, focusing on the light-responsive activity of nitrate reductase (NR) and nitrate transporters. Secondly, we discuss the influence of light on N-dependent developmental plasticity, elucidating how N availability regulates crucial developmental transitions such as flowering time, shoot branching, and root growth, as well as how light modulates these processes. Additionally, we consider the molecular interaction between light and N signalling, focusing on photoreceptors and transcription factors such as HY5, which are necessary for N uptake and assimilation under varying light conditions. A recent understanding of the nitrate signalling and perception of low N is also highlighted. The in silico transcriptome analysis suggests a reprogramming of N signalling genes by shade, and identifies NLP7, bZIP1, CPK30, CBL1, LBD37, LBD38, and HRS1 as crucial molecular regulators integrating light-regulated N metabolism.

A high-yielding and well-adapted wheat variety for central and peninsular India HD2932 was improved for three types of wheat rusts by introgressing genes Lr19/Sr25, Lr24/Sr24 and Yr10 and a new variety HD3407 (Unnat HD2932) was developed. The linked genes, Lr19/Sr25 and Lr24/Sr24, were derived from Thinopyrum (syn. Agropyron), whereas Yr10 was derived from Moro wheat (Triticum aestivum L.). NILs (> 90

Emmer wheat germplasm has received little attention with regard to exploring its genetic diversity toward enhancing utilization. Agro-morphological characterization was performed on 192 emmer wheat accessions during the winter season of 2019–2020, and subsequently 96 accessions were selected for morphological and molecular diversity analysis during the winter season of 2020–2021. Genetic diversity and population structure of 96 diverse Triticum dicoccum genotypes conserved in the National Genebank of India were estimated using 56 microsatellite (simple sequence repeat) markers. The number of alleles per locus ranged from one to six, with an average of 1.68 alleles. A total of 93 alleles were detected, with the highest polymorphic information content value (0.9912) observed for the Xcfd20 marker. Based on ‘STRUCTURE’ analysis, 96 dicoccum accessions were divided into two subpopulations. The analysis of molecular variance revealed that genetic differentiation among subpopulations was low and within subpopulations was high. A cluster analysis based on Jaccard’s dissimilarity index identified two clusters which were in congruence with the population structure. Indigenous and exotic collections were categorized into distinct subclusters within the same cluster with some overlapping suggesting limited genomic differentiation between these collections. Based on the present study, it is evident that cultivated emmer wheat showed low genetic diversity and a narrow genetic base. This might be due to limited cultivation in small pockets and emphasizes a need to broaden the genetic base of emmer wheat genetic resources for enhanced utilization.

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 different NUE parameters. Reproductive stage N assimilatory and signalling gene expression correlated to the variation in N utilization efficiency (NutE) variation. The sequence variation in N metabolism and signaling (NLP) genes was analyzed in selected genotypes (Apo (Indica) and Nerica-L-42 (Oryza glaberrima*Indica)). 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 the amino acid sequence of NLP3, NLP4, and NLP5 among rice genotypes differing in NUtE is a new and potent genome editing target improving rice NUE. The non-synonymous SNPs identified in the study will be important genomic resources for improving rice NUE.

Triticum militinae (2n = 4X = 28, AtAtGG), belonging to the secondary gene pool of wheat, is known to carry resistance to many diseases. Though some disease resistance genes were reported from T. timopheevii, the closest wild relative of T. militinae, there are no reports from T. militinae. Twenty-one T. militinae Derivatives (TMD lines) developed at the Division of Genetics, IARI, New Delhi, were evaluated for leaf and stripe rusts at seedling and adult plant stages. Eight TMD lines (6–4, 6–5, 11–6, 12–4, 12–8, 12–12, 13–7 and 13–9) showed seedling resistance to both leaf and stripe rusts while six TMD lines (7–5, 7–6, 11–5, 13–1, 13–3 and 13–4) showed seedling resistance to leaf rust but adult plant resistance to stripe rust and three TMD lines (9–1, 9–2 and 15) showed seedling resistance to leaf rust but susceptibility to stripe rust. Three TMD lines (2–7, 2–8 and 6–1) with adult plant resistance to leaf and stripe rusts were found to carry the known gene Lr34/Yr18. Ten TMD lines (7–5, 7–6, 9–1, 9–2, 11–5, 11–6, 12–12, 12–4, 12–8, and 15) with seedling resistance to leaf rust, showing absence of known genes Lr18 and Lr50 with linked markers requires further confirmation by the test of allelism studies. As not a single stripe rust resistance gene has been reported from T. militinae or its close relative T. timpopheevii, all the 8 TMD lines (6–4, 6–5, 11–6,12–4, 12–8, 12–12, 13–7 and 13–9) identified of carrying seedling resistance to stripe rust and 3 TMD lines (13–1, 13–3 and 13–4) identified of carrying adult plant resistance to stripe rust are expected to carry unknown genes. Also, all the TMD lines were found to be cytologically stable and thus can be used in inheritance and mapping studies.

Calcium ion (Ca2+) is the most ubiquitous signalling molecule and is sensed by different classes of Ca2+ sensor proteins. Recent evidences underscore the role of calcium signalling in plant response to nitrogen/nitrate supply. Recently we found that under nitrate deficiency, a short-term supply of calcium could improve the plant biomass, nitrate assimilation, anthocyanin accumulation and expression of nitrate uptake and signalling genes. Long-term calcium supply, on the other hand, was not beneficial. Calcineurin B-like (CBL) proteins are one of the vital plant Ca2+ sensory protein family which is essential for stress perception and signaling. To understand the dynamics of CBL-mediated stress signalling in bread wheat, we identified CBL genes in bread wheat (Triticum aestivum) and its progenitors, namely Triticum dicoccoides, Triticum urartu and Aegilops tauschii with the aid of newly available whole-genome sequence. The expression of different CBLs and the changes in root Ca2+ localization in response to nitrate provision or deficiency were analysed. Expression of the CBLs were studied in two bread wheat genotypes with comparatively higher (B.T. Schomburgk, BTS) and lower (Gluyas early, GE) nitrate responsiveness and nitrogen use efficiency. High N promoted the expression of CBLs in seedling leaves while in roots the expression was promoted by N deficiency. At the 5 days after anthesis stage, nitrate starvation downregulated the expression of CBLs while nitrate supply enhanced the expression. At anthesis stage, expression of CBL6 was significantly promoted by HN in panicles of both the genotypes, the highest expression was recorded in BTS. Expression of CBL6 was significantly upregulated by short term nitrate treatment also suggesting its role in Primary nitrate response (PNR) in wheat. There was a significant down regulation of CBL6 expression post nitrate starvation, making it a probable regulator of nitrogen starvation response (NSR) as well. In seedling roots, the tissue localization of Ca2+ was increased both by high and low nitrate treatments, albeit at different magnitudes. Our results suggest that calcium signalling might be a major signalling pathway governing nitrogen responsiveness and CBL6 might be playing pivotal role in NSR and PNR in wheat.

Molybdenum (Mo) is an important trace element for higher plants and plays an important regulatory role in developmental processes, photosynthesis, nitrogen (N) metabolism, hormone signaling, and stress tolerance. Molybdenum is an important element for more than 40 enzymes, four of which have been extensively studied in plants and include nitrate reductase (NR), and nitrogenase which is involved in nitrogen fixation and assimilation, respectively, xanthine dehydrogenase/oxidase (XDH), which plays an important role in purine catabolism, aldehyde oxidase (AO), which plays an essential part in the synthesis of indole-3 acetic acid (IAA), abscisic acid (ABA), and sulfite oxidase (SO) which has a role in sulfur metabolism. Molybdenum application increased the synthesis of nitric oxide (NO) through regulating NR and NO as a signal molecule regulates a series of growth modules including primary root growth, root meristem growth, root hair development, and lateral root formation. Therefore, it could be speculated that Mo application might improve root system growth through NO accumulation 326and NR regulation. Molybdate is the dominant form of Mo available to plants. Although Mo participates in various redox reactions, it is required at very low levels and the required amount of Mo is considered to be one of the lowest among the essential micronutrients. There are several possible ways by which Mo could enhance the development of stress tolerance in plant cells; Mo may increase the anti-oxidative defense by increasing the activity of the anti-oxidative enzymes. Molybdenum also activates AO and thereby increasing the ABA content. ABA accumulation can trigger bZIP transcription factors (TFs) and downstream stress signaling.

Near-isogenic lines (NILs) are useful genetic resources for basic genetic studies and further understanding of associated molecular mechanisms. The NILs can be developed through standard methods like backcross breeding or advanced generation segregating lines. The present study aimed the development of NILs for leaf rust resistance from the advanced generation segregating lines with residual heterozygosity. Advanced generations segregating lines/heterogeneous inbred families (HIFs) segregating for contrasting infection types (IT;1 and 3) for leaf rust were identified from the recombinant inbred lines (RILs) between cross of T. timopheevii derived introgression line Selection G12, a resistant parent and a susceptible parent Agra local. The molecular analysis using polymorphic SSR markers between parents indicated a high level of similarity with 97.07 and 96.49% resemblance among the contrasting NIL pairs from HIF1 and HIF5, respectively. These NILs may serve as valuable resources for conducting fine mapping and expression analysis of leaf rust resistance in wheat and, therefore, will help to identify candidate gene(s) for leaf rust resistance in Selection G12.

The important roles of plant microRNAs (miRNAs) in adaptation to nitrogen (N) deficiency in different crop species especially cereals (rice, wheat, maize) have been under discussion since last decade with little focus on potential wild relatives and landraces. Indian dwarf wheat ( Triticum sphaerococcum Percival) is an important landrace native to the Indian subcontinent. Several unique features, especially high protein content and resistance to drought and yellow rust, make it a very potent landrace for breeding. Our aim in this study is to identify the contrasting Indian dwarf wheat genotypes based on nitrogen use efficiency (NUE) and nitrogen deficiency tolerance (NDT) traits and the associated miRNAs differentially expressed under N deficiency in selected genotypes. Eleven Indian dwarf wheat genotypes and a high NUE bread wheat genotype (for comparison) were evaluated for NUE under control and N deficit field conditions. Based on NUE, selected genotypes were further evaluated under hydroponics and miRNome was compared by miRNAseq under control and N deficit conditions. Among the identified, differentially expressed miRNAs in control and N starved seedlings, the target gene functions were associated with N metabolism, root development, secondary metabolism and cell-cycle associated pathways. The key findings on miRNA expression, changes in root architecture, root auxin abundance and changes in N metabolism reveal new information on the N deficiency response of Indian dwarf wheat and targets for genetic improvement of NUE.

The mega wheat variety HD2967 was improved for leaf and stripe rust resistance by marker-assisted backcross breeding. After its release in 2011, HD2967 became susceptible to stripe rust and moderately susceptible to leaf rust. The leaf rust resistance gene LrTrk was transferred into HD2967 from the durum wheat genotype Trinakria. Then, HD2967 was crossed with Trinakria to produce F1 plant foreground selection for LrTrk and background selection for the recurrent parent genotype was carried out in BC1F1, BC2F1 and BC2F2 generations. Foreground selection was carried out with the linked marker Xgwm234, while polymorphic SSR markers between parents were used for background selection. Background selection resulted in the rapid recovery of the recurrent parent genome. A morphological evaluation of 6 near isogenic lines (NILs)-2 resistant to leaf and stripe rust, and 4 resistant to leaf rust only-showed no significant differences in yields among NILs and the recurrent parent HD2967. All of the 6 NILs showed the presence of 2NS/2AS translocation, carrying the linked genes Lr37/Sr38/Yr17 present in HD2967 and the targeted leaf rust resistance gene LrTrk. Two NILs also showed additional resistance to stripe rust. Therefore, these NILs with rust resistance and an at par yielding ability of H2967 can replace the susceptible cultivar HD2967 to reduce yield losses due to disease.

Abstract 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.

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 (Na+) ions to maintain turgor. The enhanced ability to tolerate excess ion accumulation and ion toxicity is designated as tissue tolerance. In this study, salt-tolerant wheat genotype (Kharchia 65) and sensitive cultivars (HD2687, HD2009, WL711) were exposed to vegetative stage salinity stress (for four weeks). Kharchia 65 showed better tissue tolerance to salinity than the other genotypes based on different physiological parameters. Gene expression and abundance of chloroplast localized antioxidant enzymes and compatible osmolyte synthesis were upregulated by salinity in Kharchia 65. In Kharchia 65, the higher abundance of NADPH Oxidase (RBOH) transcripts and localization of reactive oxygen species (ROS) suggested an apoplastic ROS burst. Expression of calcium signaling genes of SOS pathway, MAPK6, bZIP6 and NAC4 were also upregulated by salinity in Kharchia 65. Considering that Kharchia local is the donor of salt tolerance trait in Kharchia 65, the publically available Kharchia local transcriptome data were analyzed. Our results and the in-silico transcriptome analysis also confirmed that higher basal levels and the stress-induced rise in the expression of plastidic isoforms of antioxidant enzymes and osmolyte biosynthesis genes provide tissue tolerance in Kharchia 65. Thus, in salinity tolerant genotype Kharchia 65, ROS burst mediated triggering of calcium signaling improves Na+ exclusion and tissue tolerance to Na+.

Wheat crop grown under elevated CO2 (EC) often have a lowered grain nitrogen (N) and protein concentration along with an altered grain ionome. The mechanistic understanding on the impact of CO2 x N interactions on the grain ionome and the expression of genes regulating grain ionome is scarce in wheat. In the present study, the interactive effect of EC and N dosage on grain yield, grain protein, grain ionome, tissue nitrate, and the expression of genes contributing to grain ionome (TaNAM-B1 and TaYSL6) are described. Three bread wheat genotypes were evaluated under two CO2 levels (Ambient CO2 (AC) of 400 ± 10 ppm and elevated CO2 (EC) of 700 ± 10 ppm) and two N levels (Low (LN) and Optimum N (ON). In EC, wheat genotypes HD2967 and HI 1500 recorded a significant decrease in grain nitrate content, while leaf and stem nitrate showed a significant increase. BT. Schomburgk (BTS), showed a significant increase in unassimilated nitrate and a decline in grain N and grain protein under EC. There was a general decline of grain ionome (N, P, K, Ca, Fe) in EC, except for grain Na content. The expression of genes TaNAM-B1 and TaYSL6 associated with protein and micronutrient remobilization to grains during senescence were affected by both EC and N treatments. For instance, in flag leaves of BTS, the expression of TaNAM-B1 and TaYSL6 were lower in EC-LN compared to AC-LN. In maturing spikes, transcript abundance of TaNAM-B1 and TaYSL6 were lower in EC in BTS. The altered transcript abundance of TaYSL6 and TaNAM-B1 in source and sink supports the change in grain ionome and suggests an N dependent transcriptional reprogramming in EC.

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.

Bread wheat (Triticum aestivum L.; Ta) is the staple cereal crop for the majority of the world's population. Leaf rust disease caused by the obligate fungal pathogen, Puccinia triticina L., is a biotrophic pathogen causing significant economic yield damage. The alteration in the redox homeostasis of the cell caused by various kinds of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in response to pathogenic infections is controlled by redox regulators. Thioredoxin (Trx) is one of the redox regulators with low molecular weight and is thermostable. Through a genome-wide approach, forty-two (42) wheat Trx genes (TaTrx) were identified across the wheat chromosome groups A, B, and D genomes containing 12, 16, and 14 Trx genes, respectively. Based on in silico expression analysis, 15 TaTrx genes were selected and utilized for further experimentation. These 15 genes were clustered into six groups by phylogenetic analysis. MicroRNA (miRNA) target analysis revealed eight different miRNA-targeted TaTrx genes. Protein-protein interaction (PPI) analysis showed TaTrx proteins interact with thioredoxin reductase, peroxiredoxin, and uncharacterized proteins. Expression profiles resulting from quantitative real-time PCR (qRT-PCR) revealed four TaTrx genes (TaTrx11-5A, TaTrx13-5B, TaTrx14-5D, and TaTrx15-3B) were significantly induced in response to leaf rust infection. Localization of ROS and its content estimation and an assay of antioxidant enzymes and expression analysis suggested that Trx have been involved in ROS homeostasis at span 24HAI-72HAI during the leaf rust resistance.

Micro RNAs (miRNAs) regulate their target genes, that are crucial for plant adaptation to perturbations in environmental variables and nutrient availability by the changes in their own abundance. The greatest limiting factors for the growth of plants are the changing environment and a scarcity of inputs. Nitrogen (N) is an essential nutrient for plant growth as it is a constituent of proteins and photosynthetic pigments, two of plants' most important components. Consequently, the identification of N stress-responsive miRNAs represents a significant research milestone. Several miRNAs related to nutrient stress and accompanying signalling pathways have been discovered in the past decade. This review focuses on the miRNAs associated with nutrient deficiency, their potential targets, and how their expression varies in response to different nutrient stresses, with a focus on N stress. Increased levels of miR169a, for example, induce down-regulation of NFYA family members, repressing NPF6.3 and NRT2.1 expression and decreasing nitrate ion accumulation. Another miRNA, miR167, regulates auxin Response Factors ARF6 and ARF8. The miR167 and its target ARF8 are engaged in lateral root development in response to nitrate. Root growth is likewise linked to miR164 and its target NAC1. The expression of miR164 is upregulated under low-nitrate conditions. N deprivation also increases the expression of miR826 and miR5090, which inhibits the AOP2 gene, which is implicated in glucosinolate biosynthesis. Plants overexpressing miR826 and miR5090 have lower glucosinolate levels, higher biomass accumulation, more lateral roots, higher chlorophyll content, reduced anthocyanin content, and higher NRT2.1 expression, all of which result in better N stress tolerance. This review could provide a thorough understanding of such miRNAs and their functions. Finally, the generation of transgenic plants, mutants, or artificial miRNAs (amiRNAs) can serve as the way forward for generating stress-tolerant and nutrient-efficient plants.

HD 3298 is a biofortified wheat variety having high iron (43.1 ppm) and protein (12.12 %) content with tolerance to terminal heat stress. This variety has a higher yield potential of 47.4 q ha-1 under very late sown conditions. It possesses a high level of resistance against stripe rust, leaf rust, and other important diseases. It has better agronomic attributes and has better adaption to sowing time from timely to very late. This variety has a perfect Glu score (10) with excellent grain quality parameters.

Nitric oxide (NO) modulates plant response to biotic and abiotic stresses by S-nitrosylation-mediated protein post-translational modification. Nitrate reductase (NR) and S-nitrosoglutathione reductase (GSNOR) enzymes are essential for NO synthesis and the maintenance of Nitric oxide/S-nitroso glutathione (NO/GSNO) homeostasis, respectively. S-nitrosoglutathione, formed by the S-nitrosylation reaction of NO with glutathione, plays a significant physiological role as the mobile reservoir of NO. The genome-wide analysis identified nine NR (NIA) and three GSNOR genes in the wheat genome. Phylogenic analysis revealed that the nine NIA genes +were clustered into four groups and the 3 GSNOR s into two groups. qRT-PCR expression profiling of NIAs and GSNORs was done in Chinese spring (CS), a leaf rust susceptible wheat line showing compatible interaction, and Transfer (TR), leaf rust-resistant wheat line showing incompatible interaction, post-inoculation with leaf rust pathotype 77–5 (121-R-63). All the NIA genes showed upregulation during incompatible interaction in comparison with the compatible reaction. The GSNOR genes showed a variable pattern of expression: the TaGSNOR1 showed little change, whereas TaGSNOR2 showed higher expression during the incompatible response. TaGSNOR3 showed a rise of expression both in compatible and incompatible reactions. Before inoculation and after 72 h of pathogen inoculation, NO localization was studied in both compatible and incompatible reactions. The S-nitrosothiol accumulation, NR, and glutathione reductase activity showed a consistent increase in the incompatible interactions. The results demonstrate that both NR and GSNOR plays significant role in defence against the leaf rust pathogen in wheat by modulating NO homeostasis or signalling.

In recent years, the development of RNA-guided genome editing (CRISPR-Cas9 technology) has revolutionized plant genome editing. Under nutrient deficiency conditions, different transcription factors and regulatory gene networks work together to maintain nutrient homeostasis. Improvement in the use efficiency of nitrogen (N), phosphorus (P) and potassium (K) is essential to ensure sustainable yield with enhanced quality and tolerance to stresses. This review outlines potential targets suitable for genome editing for understanding and improving nutrient use (NtUE) efficiency and nutrient stress tolerance. The different genome editing strategies for employing crucial negative and positive regulators are also described. Negative regulators of nutrient signalling are the potential targets for genome editing, that may improve nutrient uptake and stress signalling under resource-poor conditions. The promoter engineering by CRISPR/dead (d) Cas9 (dCas9) cytosine and adenine base editing and prime editing is a successful strategy to generate precise changes. CRISPR/dCas9 system also offers the added advantage of exploiting transcriptional activators/repressors for overexpression of genes of interest in a targeted manner. CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) are variants of CRISPR in which a dCas9 dependent transcription activation or interference is achieved. dCas9-SunTag system can be employed to engineer targeted gene activation and DNA methylation in plants. The development of nutrient use efficient plants through CRISPR-Cas technology will enhance the pace of genetic improvement for nutrient stress tolerance of crops and improve the sustainability of agriculture.