Early molecular events associated with nitrogen deficiency in rice seedling roots

Transcription factor OsSHR2 regulates rice architecture and yield per plant in response to nitrogen

MAIN CONCLUSION

Mutation of OsSHR2 adversely impacted root and shoot growth and impaired plant response to N conditions, further reducing the yield per plant. Nitrogen (N) is a crucial factor that regulates the plant architecture. There is still a lack of research on it. In our study, it was observed that the knockout of the SHORTROOT 2 (OsSHR2) which was induced by N deficiency, can significantly affect the regulation of plant architecture response to N in rice. Under N deficiency, the mutation of OsSHR2 significantly reduced root growth, and impaired the sensitivity of the root meristem length to N deficiency. The mutants were found to have approximately a 15% reduction in plant height compared to wild type. But mutants showed a significant increase in tillering at post-heading stage, approximately 26% more than the wild type, particularly in high N conditions. In addition, due to reduced seed setting rate and 1000-grain weight, mutant yield was significantly decreased by approximately 33% under low N fertilizer supply. The mutation also changed the distribution of N between the vegetative and reproductive organs. Our findings suggest that the transcription factor OsSHR2 plays a regulatory role in the response of plant architecture and yield per plant to N in rice.

Integrated metabolome and transcriptome analysis reveals the regulatory mechanism of low nitrogen-driven biosynthesis of saponins and flavonoids in Panax notoginseng

BACKGROUND

Nitrogen (N) is an important macronutrient involved in the biosynthesis of primary and secondary metabolites in plants. However, the metabolic regulatory mechanism of low-N-induced triterpenoid saponin and flavonoid accumulation in rhizomatous medicinal Panax notoginseng (Burk.) F. H. Chen remains unclear.

METHODS

To explore the potential regulatory mechanism and metabolic basis controlling the response of P. notoginseng to N deficiency, the transcriptome and metabolome were analysed in the roots.

RESULTS

The N content was significantly reduced in roots of N0-treated P. notoginseng (0 kg·N·667 m-2). The C/N ratio was enhanced in the N-deficient P. notoginseng. N deficiency promotes the accumulation of amino acids (L-proline, L-leucine, L-isoleucine, L-norleucine, L-arginine, and L-citrulline) and sugar (arabinose, xylose, glucose, fructose, and mannose), thus providing precursor metabolites for the biosynthesis of flavonoids and triterpenoid saponins. Downregulation of key structural genes (PAL, PAL3, ACC1, CHS2, PPO, CHI3, F3H, DFR, and FGT), in particular with the key genes of F3H, involved in the flavonoid biosynthesis pathway possibly induced the decrease in flavonoid content with increased N supply. Notoginsenoside R1, ginsenoside Re, Rg1, Rd, F1, R1 + Rg1 + Rb1 and total triterpenoid saponins were enhanced in the N0 groups than in the N15 (15 kg·N·667 m-2) plants. Higher phosphoenolpyruvate (an intermediate of glycolyticwith pathway metabolism) and serine (an intermediate of photorespiration) levels induced by N deficiency possibly promote saponin biosynthesis through mevalonic acid (MVA) and methylerythritol (MEP) pathways. Genes (MVD2, HMGS, HMGR1, HMGR2, DXR, and HMGR1) encoding the primary enzymes HMGS, HMGR, DXR, and MVD in the MVA and MEP pathways were significantly upregulated in the N0-treated P. notoginseng. The saponin biosynthesis genes DDS, DDS, CYP716A52, CYP716A47, UGT74AE2, and FPS were upregulated in the N-deficient plants. Upregulation of genes involved in saponin biosynthesis promotes the accumulation of triterpenoid saponins in the N0-grown P. notoginseng.

CONCLUSIONS

N deficiency enhances primary metabolisms, such as amino acids and sugar accumulation, laying the foundation for the synthesis of flavonoids and triterpenoid saponins in P. notoginseng. F3H, DDS, FPS, HMGR, HMGS and UGT74AE2 can be considered as candidates for functional characterisation of the N-regulated accumulation of triterpenoid saponins and flavonoids in future.

Identification of responsive genes to multiple abiotic stresses in rice (Oryza sativa): a meta-analysis of transcriptomics data

Abiotic stresses limit the quantity and quality of rice grain production, which is considered a strategic crop in many countries. In this study, a meta-analysis of different microarray data at seedling stage was performed to investigate the effects of multiple abiotic stresses (drought, salinity, cold situation, high temperature, alkali condition, iron, aluminum, and heavy metal toxicity, nitrogen, phosphorus, and potassium deficiency) on rice. Comparative analysis between multiple abiotic stress groups and their control groups indicated 561 differentially expressed genes (DEGs), among which 422 and 139 genes were up-regulated and down-regulated, respectively. Gene Ontology analysis showed that the process of responding to stresses and stimuli was significantly enriched. In addition, pathways such as metabolic process and biosynthesis of secondary metabolites were identified by KEGG pathway analysis. Weighted correlation network analysis (WGCNA) uncovered 17 distinct co-expression modules. Six modules were significantly associated with genes involved in response to abiotic stresses. Finally, to validate the results of the meta-analysis, five genes, including TIFY9 (JAZ5), RAB16B, ADF3, Os01g0124650, and Os05g0142900 selected for qRT-PCR analysis. Expression patterns of selected genes confirmed the results of the meta-analysis. The outcome of this study could help introduce candidate genes that may be beneficial for use in genetic engineering programs to produce more tolerant crops or as markers for selection.

The Genetic Dissection of Nitrogen Use-Related Traits in Flax (Linum usitatissimum L.) at the Seedling Stage through the Integration of Multi-Locus GWAS, RNA-seq and Genomic Selection

Nitrogen (N), the most important macro-nutrient for plant growth and development, is a key factor that determines crop yield. Yet its excessive applications pollute the environment and are expensive. Hence, studying nitrogen use efficiency (NUE) in crops is fundamental for sustainable agriculture. Here, an association panel consisting of 123 flax accessions was evaluated for 21 NUE-related traits at the seedling stage under optimum N (N+) and N deficiency (N-) treatments to dissect the genetic architecture of NUE-related traits using a multi-omics approach integrating genome-wide association studies (GWAS), transcriptome analysis and genomic selection (GS). Root traits exhibited significant and positive correlations with NUE under N- conditions (r = 0.33 to 0.43, p < 0.05). A total of 359 QTLs were identified, accounting for 0.11% to 23.1% of the phenotypic variation in NUE-related traits. Transcriptomic analysis identified 1034 differentially expressed genes (DEGs) under contrasting N conditions. DEGs involved in N metabolism, root development, amino acid transport and catabolism and others, were found near the QTLs. GS models to predict NUE stress tolerance index (NUE_STI) trait were tested using a random genome-wide SNP dataset and a GWAS-derived QTLs dataset. The latter produced superior prediction accuracy (r = 0.62 to 0.79) compared to the genome-wide SNP marker dataset (r = 0.11) for NUE_STI. Our results provide insights into the QTL architecture of NUE-related traits, identify candidate genes for further studies, and propose genomic breeding tools to achieve superior NUE in flax under low N input.

Genome-wide identification of DUF506 gene family in Oryzasativa and expression profiling under abiotic stresses

The domain of unknown function 560 (DUF560), also known as the PDDEXK_6 family, is a ubiquitous plant protein that has been confirmed to play critical roles in Arabidopsis root development as well as ABA and abiotic responses. However, genome-wide identification and expression pattern analysis in rice (Oryza sativa) still need to be improved. Based on the phylogenetic relationship, 10 OsDUF506 genes were identified and classified into four subfamilies. Segmental duplication was essential to the expansion of OsDUF506s, which were subjected to purifying selective pressure. Except for OsDUF50609 and OsDUF50610, the OsDUF506s shared colinear gene pairs with five monocot species, showing that they were conserved in evolution. Furthermore, the conserved domains, gene structures, SNPs distribution, and targeting miRNAs were systematically investigated. Massive cis-regulatory elements were discovered in promoter regions, implying that OsDUF506s may be important in hormone regulation and abiotic stress response. Therefore, we analyzed plant hormone-induced transcriptome data and performed qRT-PCR on eight OsDUF506s under drought, cold, and phosphorus-deficient stresses. The results revealed that most OsDUF506s respond to ABA and JA treatment, as well as drought and cold conditions. In conclusion, our findings provided insights into the evolution and function of OsDUF506s, which could benefit crop breeding in the future.

Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.)

BACKGROUND

Domains of unknown function (DUF) proteins are a number of uncharacterized and highly conserved protein families in eukaryotes. In plants, some DUFs have been predicted to play important roles in development and response to abiotic stress. Among them, DUF568-containing protein family is plant-specific and has not been described previously. A basic analysis and expression profiling was performed, and the co-expression and interaction networks were constructed to explore the functions of DUF568 family in rice.

RESULTS

The phylogenetic tree showed that the 8, 9 and 11 DUF568 family members from rice, Arabidopsis and maize were divided into three groups. The evolutionary relationship between DUF568 members in rice and maize was close, while the genes in Arabidopsis were more distantly related. The cis-elements prediction showed that over 82% of the elements upstream of OsDUF568 genes were responsive to light and phytohormones. Gene expression profile prediction and RT-qPCR experiments revealed that OsDUF568 genes were highly expressed in leaves, stems and roots of rice seedling. The expression of some OsDUF568 genes varied in response to plant hormones (abscisic acid, 6-benzylaminopurine) and abiotic stress (drought and chilling). Further analysis of the co-expression and protein-protein interaction networks using gene ontology showed that OsDUF568 - related genes were enriched in cellular transports, metabolism and processes.

CONCLUSIONS

In summary, our findings suggest that the OsDUF568 family may be a vital gene family for the development of rice roots, leaves and stems. In addition, the OsDUF568 family may participate in abscisic acid and cytokinin signaling pathways, and may be related to abiotic stress resistance in these vegetative tissues of rice.

Effect of Dopamine on Growth, Some Biochemical Attributes, and the Yield of Crisphead Lettuce under Nitrogen Deficiency

Nitrogen (N) represents the most important nutrient for plant growth and productivity, but extreme and ineffective usage of N fertilizer results in boosted plant production expenditures and environmental contamination. For the world’s sustainable food production and environmental profits, there has been increased research interest in reducing the use of N fertilization along with improving plant N deficiency (ND) tolerance. Dopamine (DA), a potential antioxidant, mediates several physio-biochemical processes in plants under normal or stressful conditions. However, their roles in increasing ND tolerance in crisphead lettuce are not well-documented. We investigate the role of DA concentration (0.50 and 100 µM) on the growth and yield of crisphead lettuce plants under ND. Under normal conditions (100% recommended N fertilizer dose), DA (50 and 100 μM) application significantly enhanced growth, chlorophyll concentration, N%, antioxidant enzymes activity, as well as yield and its components, decreased nitrate accumulation and oxidative biomarkers compared to untreated plants (0 μM DA). ND significantly decreased plant growth and yield attributes as well as evoked oxidative impairment and nitrate accumulation as compared to 100% recommended N fertilizer dose in the absence of DA. However, within ND conditions, the application of DA concentrations significantly mitigated ND-induced oxidative burst and improved plant growth, chlorophyll concentration, N%, nitrate concentration, peroxidase, catalase, superoxide dismutase, total soluble solid, vitamin C, dry matter %, and total sugars, over 0 μM DA treated plants. Current findings highlighted that exogenous application of 100 μM DA could reinforce the crisphead lettuce plant’s resilience to ND by minimizing reactive oxygen species accumulation and promoting enzymatic antioxidants alongside growth, yield, and quality improvement. The beneficial effects of DA in lessening ND’s drastic impacts on crisphead lettuce resulted from upregulating antioxidant enzyme activity, impairment of oxidative biomarkers, and maintaining chlorophyll levels. The current findings open pioneering prospects to reduce nitrogen fertilization by DA application without any drastic effect on plant productivity. But further research is needed to fully understand DA effects and their mechanisms in inducing ND tolerance in different plant species, including crisphead lettuce.

Identification of quantitative trait loci controlling nitrogen use efficiency-related traits in rice at the seedling stage under salt condition by genome-wide association study

Rice cultivation is facing both salt intrusion and overuse of nitrogen fertilizers. Hence, breeding new varieties aiming to improve nitrogen use efficiency (NUE), especially under salt conditions, is indispensable. We selected 2,391 rice accessions from the 3K Rice Genomes Project to evaluate the dry weight under two N concentrations [2.86 mM - standard N (SN), and 0.36 mM - low N (LN)] crossed with two NaCl concentrations [0 (0Na) and 60 mM (60Na)] at the seedling stage. Genome-wide association studies for shoot, root, and plant dry weight (DW) were carried out. A total of 55 QTLs - 32, 16, and 7 in the whole, indica, and japonica panel - associated with one of the tested traits were identified. Among these, 27 QTLs co-localized with previously identified QTLs for DW-related traits while the other 28 were newly detected; 24, 8, 11, and 4 QTLs were detected in SN-0Na, LN-0Na, SN-60Na, and LN-60Na, respectively, and the remaining 8 QTLs were for the relative plant DW between treatments. Three of the 11 QTLs in SN-60Na were close to the regions containing three QTLs detected in SN-0Na. Eleven candidate genes for eight important QTLs were identified. Only one of them was detected in both SN-0Na and SN-60Na, while 5, 0, 3, and 2 candidate genes were identified only once under SN-0Na, LN-0Na, SN-60Na, and LN-60Na, respectively. The identified QTLs and genes provide useful materials and genetic information for future functional characterization and genetic improvement of NUE in rice, especially under salt conditions.

Weighted gene co-expression network analysis of nitrogen (N)-responsive genes and the putative role of G-quadruplexes in N use efficiency (NUE) in rice

Rice is an important target to improve crop nitrogen (N) use efficiency (NUE), and the identification and shortlisting of the candidate genes are still in progress. We analyzed data from 16 published N-responsive transcriptomes/microarrays to identify, eight datasets that contained the maximum number of 3020 common genes, referred to as N-responsive genes. These include different classes of transcription factors, transporters, miRNA targets, kinases and events of post-translational modifications. A Weighted gene co-expression network analysis (WGCNA) with all the 3020 N-responsive genes revealed 15 co-expression modules and their annotated biological roles. Protein-protein interaction network analysis of the main module revealed the hub genes and their functional annotation revealed their involvement in the ubiquitin process. Further, the occurrences of G-quadruplex sequences were examined, which are known to play important roles in epigenetic regulation but are hitherto unknown in N-response/NUE. Out of the 3020 N-responsive genes studied, 2298 contained G-quadruplex sequences. We compared these N-responsive genes containing G-quadruplex sequences with the 3601 genes we previously identified as NUE-related (for being both N-responsive and yield-associated). This analysis revealed 389 (17%) NUE-related genes containing G-quadruplex sequences. These genes may be involved in the epigenetic regulation of NUE, while the rest of the 83% (1811) genes may regulate NUE through genetic mechanisms and/or other epigenetic means besides G-quadruplexes. A few potentially important genes/processes identified as associated with NUE were experimentally validated in a pair of rice genotypes contrasting for NUE. The results from the WGCNA and G4 sequence analysis of N-responsive genes helped identify and shortlist six genes as candidates to improve NUE. Further, the hitherto unavailable segregation of genetic and epigenetic gene targets could aid in informed interventions through genetic and epigenetic means of crop improvement.

Expression levels of nitrogen assimilation-related genes, physiological responses, and morphological adaptations of three indica rice (Oryza sativa L. ssp. indica) genotypes subjected to nitrogen starvation conditions

Nitrogen (N) is an essential nutrient available to the plants in form of nitrate and ammonium. It is a macronutrient important for the plant growth and development, especially in cereal crops, which consume it for the production of amino acids, proteins/enzymes, nucleic acids, cell wall complexes, plant hormones, and vitamins. In rice production, 17 kg N uptake is required to produce 1 ton of rice. Considering this, many techniques have been developed to evaluate leaf greenness or SPAD value for assessing the amount of N application in the rice cultivar to maximize the grain yield. The aim of the present study was to investigate the morpho-physiological characteristics and relative expression level of N assimilation in three different rice genotypes (MT2, RD31, KDML105) under 1.00 × (full N), 0.50 × , 0.25 × (N depletion), and 0.00 × (N deficiency) at seedling stage and the morpho-physiological traits and the grain yield attributes under 1.00 × (full N) and 0.25 × (N depletion) were compared. Leaf chlorosis and growth inhibition in rice seedlings under N deficiency were evidently observed. Shoot height, number of leaves, shoot fresh weight, shoot dry weight, and root fresh weight in KDML105 under N deficiency were decreased by 27.65%, 42.11%, 65.44%, 47.90%, and 54.09% over the control (full N). Likewise, leaf greenness was lowest in KDML105 under N deficiency (78.57% reduction over the full N), leading to low photosynthetic abilities. In addition, expression of nitrogen assimilation-related genes, OsNR1, OsGln1;1, and OsGln2, in KDML105 under N depletion were increased within 3 h and then declined after the long incubation period, whereas those were unchanged in cvs. MT2 and RD31. Similarly, relative expression level of OsNADH-GOGAT, OsFd-GOGAT, and OsAspAt1 in KDML105 was peaked when subjected to 0.50 × N for 6 h and then declined after the long incubation period. Moreover, overall growth characters and physiological changes in cv. RD31 at vegetative stage under 0.25 × N were retained better than those in cvs. KDML105 and MT2, resulting in high yield at the harvesting process. In summary, N assimilated-related genes in rice seedlings under N depletion were rapidly regulated within 3-6 h, especially cv. KDML105 and MT2, then downregulated, resulting in physiological changes, growth inhibition, and yield reduction.

Transcriptome analysis of the phosphate starvation response sheds light on strigolactone biosynthesis in rice

Phosphorus (P) is a major element required for plant growth and development. To cope with P shortage, plants activate local and long-distance signaling pathways, such as an increase in the production and exudation of strigolactones (SLs). The role of the latter in mitigating P deficiency is, however, still largely unknown. To shed light on this, we studied the transcriptional response to P starvation and replenishment in wild-type rice and a SL mutant, dwarf10 (d10), and upon exogenous application of the synthetic SL GR24. P starvation resulted in major transcriptional alterations, such as the upregulation of P TRANSPORTER, SYG1/PHO81/XPR1 (SPX) and VACUOLAR PHOSPHATE EFFLUX TRANSPORTER. Gene Ontology (GO) analysis of the genes induced by P starvation showed enrichment in phospholipid catabolic process and phosphatase activity. In d10, P deficiency induced upregulation of genes enriched for sesquiterpenoid production, secondary shoot formation and metabolic processes, including lactone biosynthesis. Furthermore, several genes induced by GR24 treatment shared the same GO terms with P starvation-induced genes, such as oxidation reduction, heme binding and oxidoreductase activity, hinting at the role that SLs play in the transcriptional reprogramming upon P starvation. Gene co-expression network analysis uncovered a METHYL TRANSFERASE that displayed co-regulation with known rice SL biosynthetic genes. Functional characterization showed that this gene encodes an enzyme catalyzing the conversion of carlactonoic acid to methyl carlactonoate. Our work provides a valuable resource to further studies on the response of crops to P deficiency and reveals a tool for the discovery of SL biosynthetic genes.

Long term nitrogen deficiency alters expression of miRNAs and alters nitrogen metabolism and root architecture in Indian dwarf wheat (Triticum sphaerococcum Perc.) genotypes

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.

Genome-Wide Meta-Analysis of QTLs Associated with Root Traits and Implications for Maize Breeding

Root system architecture (RSA), also known as root morphology, is critical in plant acquisition of soil resources, plant growth, and yield formation. Many QTLs associated with RSA or root traits in maize have been identified using several bi-parental populations, particularly in response to various environmental factors. In the present study, a meta-analysis of QTLs associated with root traits was performed in maize using 917 QTLs retrieved from 43 mapping studies published from 1998 to 2020. A total of 631 QTLs were projected onto a consensus map involving 19,714 markers, which led to the prediction of 68 meta-QTLs (MQTLs). Among these 68 MQTLs, 36 MQTLs were validated with the marker-trait associations available from previous genome-wide association studies for root traits. The use of comparative genomics approaches revealed several gene models conserved among the maize, sorghum, and rice genomes. Among the conserved genomic regions, the ortho-MQTL analysis uncovered 20 maize MQTLs syntenic to 27 rice MQTLs for root traits. Functional analysis of some high-confidence MQTL regions revealed 442 gene models, which were then subjected to in silico expression analysis, yielding 235 gene models with significant expression in various tissues. Furthermore, 16 known genes viz., DXS2, PHT, RTP1, TUA4, YUC3, YUC6, RTCS1, NSA1, EIN2, NHX1, CPPS4, BIGE1, RCP1, SKUS13, YUC5, and AW330564 associated with various root traits were present within or near the MQTL regions. These results could aid in QTL cloning and pyramiding in developing new maize varieties with specific root architecture for proper plant growth and development under optimum and abiotic stress conditions.

Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions

Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system’s response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice.

Plant nitrogen availability and crosstalk with phytohormones signallings and their biotechnology breeding application in crops

Nitrogen (N), one of the most important nutrients, limits plant growth and crop yields in sustainable agriculture system, in which phytohormones are known to play essential roles in N availability. Hence, it is not surprising that massive studies about the crosstalk between N and phytohormones have been constantly emerging. In this review, with the intellectual landscape of N and phytohormones crosstalk provided by the bibliometric analysis, we trace the research story of best-known crosstalk between N and various phytohormones over the last 20 years. Then, we discuss how N regulates various phytohormones biosynthesis and transport in plants. In reverse, we also summarize how phytohormones signallings modulate root system architecture (RSA) in response to N availability. Besides, we expand to outline how phytohormones signallings regulate uptake, transport, and assimilation of N in plants. Further, we conclude advanced biotechnology strategies, explain their application, and provide potential phytohormones-regulated N use efficiency (NUE) targets in crops. Collectively, this review provides not only a better understanding on the recent progress of crosstalk between N and phytohormones, but also targeted strategies for improvement of NUE to increase crop yields in future biotechnology breeding of crops.

Effects of Nitrogen Deficiency on the Metabolism of Organic Acids and Amino Acids in Oryza sativa

Organic acids metabolism and nitrogen (N) metabolism in rice seedlings and the relationship between them are not fully understood. In this study, rice (Oryza sativa L. ssp. Indica) variety "Huanghuazhan" was used as the experimental material, and three N levels (5 mM, 1 mM, and 0 mM NH₄NO₃) were set by the hydroponic method for different levels of N treatment. Our results showed that the increased content of malate in rice leaves caused by reducing N level was related to the increased synthesis of malate (the activity of leaf PEPC increased)and the decreased degradation of malate (the activity of leaf NADP-ME decreased), while the increased contents of citrate and isocitrate in rice leaves caused by reducing N level might not be caused by the increased biosynthesis, but due to the decrease in degradation of citrate and isocitrate (the activities of leaf CS, ACO, and NADP-IDH decreased). The increased content of malate in rice roots caused by reducing N level might be related to the increased biosynthesis and the decreased degradation of root malate (the activities of root NAD-MDH and PEPC increased, while the activity of NADP-ME decreased). Compared to the control (5 mM NH₄NO₃), the increased content of citrate in rice roots caused by reducing N level might be related to the increased biosynthesis rather than the decreased degradation of citrate, due to the higher activities of CS and ACO in rice roots under 0 mM N and 1mM N treatment when compared to that of the control ones. At the same time, the increased content of isocitrate in roots was related to the increased isomerization of isocitrate (the activity of root ACO increased) and the decreased degradation of isocitrate (the activity of root NADP-IDH decreased). With the reducing N level, the activities of N metabolism-related enzymes, such as nitrate reductase (NR), glutamine synthetase (GS), and glutamate synthase (GOGAT), decreased in rice leaves and roots, resulting in the decreased contents of total free amino acids (TFAAs) and soluble proteins in rice seedlings, and finally led to the growth inhibition. Our results showed that the dynamics of organic acids metabolism caused by reducing N level were different in rice leaves and roots. In conclusion, there was a close correlation between organic acids metabolism and N metabolism in rice leaves and roots under N-limited conditions; furthermore, such a correlation was more obvious in rice leaves than that of roots.

Regulation of ppGpp Synthesis and Its Impact on Chloroplast Biogenesis during Early Leaf Development in Rice

Guanosine tetraphosphate (ppGpp) is known as an alarmone that mediates bacterial stress responses. In plants, ppGpp is synthesized in chloroplasts from GTP and ATP and functions as a regulator of chloroplast gene expression to affect photosynthesis and plant growth. This observation indicates that ppGpp metabolism is closely related to chloroplast function, but the regulation of ppGpp and its role in chloroplast differentiation are not well understood. In rice, ppGpp directly inhibits plastidial guanylate kinase (GKpm), a key enzyme in GTP biosynthesis. GKpm is highly expressed during early leaf development in rice, and the GKpm-deficient mutant, virescent-2 (v2), develops chloroplast-deficient chlorotic leaves under low-temperature conditions. To examine the relationship between GTP synthesis and ppGpp homeostasis, we generated transgenic rice plants over-expressing RSH3, a protein known to act as a ppGpp synthase. When RSH3 was overexpressed in v2, the leaf chlorosis was more severe. Although the RSH3 overexpression in the wild type caused no visible effects, pulse amplitude modulation fluorometer measurements indicated that photosynthetic rates were reduced in this line. This finding implies that the regulation of ppGpp synthesis in rice is involved in the maintenance of the GTP pool required to regulate plastid gene expression during early chloroplast biogenesis. We further investigated changes in the expressions of RelA/SpoT Homolog (RSH) genes encoding ppGpp synthases and hydrolases during the same period. Comparing the expression of these genes with the cellular ppGpp content suggests that the basal ppGpp level is determined by the antagonistic action of multiple RSH enzymatic activities during early leaf development in rice.

Insights into nitrogen metabolism in the wild and cultivated lettuce as revealed by transcriptome and weighted gene co-expression network analysis

Large amounts of nitrogen fertilizers applied during lettuce (Lactuca sativa L.) production are lost due to leaching or volatilization, causing severe environmental pollution and increased costs of production. Developing lettuce varieties with high nitrogen use efficiency (NUE) is the eco-friendly solution to reduce nitrogen pollution. Hence, in-depth knowledge of nitrogen metabolism and assimilation genes and their regulation is critical for developing high NUE varieties. In this study, we performed comparative transcriptomic analysis of the cultivated lettuce (L. sativa L.) and its wild progenitor (L. serriola) under high and low nitrogen conditions. A total of 2,704 differentially expressed genes were identified. Key enriched biological processes included photosynthesis, oxidation-reduction process, chlorophyll biosynthetic process, and cell redox homeostasis. The transcription factors (TFs) belonging to the ethylene responsive factor family and basic helix-loop-helix family were among the top differentially expressed TFs. Using weighted gene co-expression network analysis we constructed nine co-expression modules. Among these, two modules were further investigated because of their significant association with total nitrogen content and photosynthetic efficiency of photosystem II. Three highly correlated clusters were identified which included hub genes for nitrogen metabolism, secondary metabolites, and carbon assimilation, and were regulated by cluster specific TFs. We found that the expression of nitrogen transportation and assimilation genes varied significantly between the two lettuce species thereby providing the opportunity of introgressing wild alleles into the cultivated germplasm for developing lettuce cultivars with more efficient use of nitrogen.

Nitrogen deficiency- and sucrose-induced anthocyanin biosynthesis is modulated by HISTONE DEACETYLASE15 in Arabidopsis

Anthocyanin accumulation is a hallmark response to nitrogen (N) deficiency in Arabidopsis. Although the regulation of anthocyanin biosynthesis has been extensively studied, the roles of chromatin modification in this process are largely unknown. In this study we show that anthocyanin accumulation induced by N deficiency is modulated by HISTONE DEACETYLASE15 (HDA15) in Arabidopsis seedlings. The hda15-1 T-DNA insertion mutant accumulated more anthocyanins than the wild-type when the N supply was limited, and this was caused by up-regulation of anthocyanin biosynthetic and regulatory genes in the mutant. The up-regulated genes also had increased levels of histone acetylation in the mutant. The accumulation of anthocyanins induced by sucrose and methyl jasmonate, but not that induced by H2O2 and phosphate starvation, was also greater in the hda15-1 mutant. While sucrose increased histone acetylation in the hda15-1 mutant in genes in a similar manner to that caused by N deficiency, methyl jasmonate only enhanced histone acetylation in the genes involved in anthocyanin biosynthesis. Our results suggest that different stresses act through distinct regulatory modules to activate anthocyanin biosynthesis, and that HDA15-mediated histone modification modulates the expression of anthocyanin biosynthetic and regulatory genes to avoid overaccumulation in response to N deficiency and other stresses.

Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.)

Maize is a heavy consumer of fertilizer nitrogen (N) which not only results in the high cost of cultivation but may also lead to environmental pollution. Therefore, there is a need to develop N-use efficient genotypes, a prerequisite for which is a greater understanding of N-deficiency stress adaptation. In this study, comparative transcriptome analysis was performed using leaf and root tissues from contrasting inbred lines, viz., DMI 56 (tolerant to N stress) and DMI 81 (susceptible to N stress) to delineate the differentially expressed genes (DEGs) under low-N stress. The contrasting lines were grown hydroponically in modified Hoagland solution having either sufficient- or deficient-N, followed by high-throughput RNA-sequencing. A total of 8 sequencing libraries were prepared and 88–97% of the sequenced raw reads were mapped to the reference B73 maize genome. Genes with a p value ≤ 0.05 and fold change of ≥ 2.0 or ≤ − 2 were considered as DEGs in various combinations performed between susceptible and tolerant genotypes. DEGs were further classified into different functional categories and pathways according to their putative functions. Gene Ontology based annotation of these DEGs identified three different functional categories: biological processes, molecular function, and cellular component. The KEGG and Mapman based analysis revealed that most of the DEGs fall into various metabolic pathways, biosynthesis of secondary metabolites, signal transduction, amino acid metabolism, N-assimilation and metabolism, and starch metabolism. Some of the key genes involved in N uptake (high-affinity nitrate transporter 2.2 and 2.5), N assimilation and metabolism (glutamine synthetase, asparagine synthetase), redox homeostasis (SOD, POX), and transcription factors (MYB36, AP2-EREBP) were found to be highly expressed in the tolerant genotype compared to susceptible one. The candidate genes identified in the present study might be playing a pivotal role in low-N stress adaptation in maize and hence could be useful in augmenting further research on N metabolism and development of N-deficiency tolerant maize cultivars.

Arginine Increases Tolerance to Nitrogen Deficiency in Malus hupehensis via Alterations in Photosynthetic Capacity and Amino Acids Metabolism

Arginine plays an important role in the nitrogen (N) cycle because it has the highest ratio of N to carbon among amino acids. In recent years, there has been increased research interest in improving the N use of plants, reducing the use of N fertilizer, and enhancing the tolerance of plants to N deficiency. Here, the function of arginine in the growth of apple (Malus hupehensis) under N deficiency was explored. The application of 100 μmol L-1 arginine was effective for alleviating N-deficiency stress. Exogenous arginine promoted the absorption and use of N, phosphorus (P), and potassium (K) under low N stress. The net photosynthetic rate, maximal photochemical efficiency of photosystem II, and chlorophyll content were higher in treated plants than in control plants. Exogenous arginine affected the content of many metabolites, and the content of many amino acids with important functions was significantly increased, such as glutamate and ornithine, which play an important role in the urea cycle. Half of the metabolites were annotated to specialized metabolic pathways, including the synthesis of phenolic substances, flavonoids, and other substances with antioxidant activity. Our results indicate that arginine promotes the plant photosynthetic capacity and alters amino acid metabolism and some antioxidants including phenolic substances and flavonoids to improve the tolerance of apple to N deficiency, possibly through the improvement of arginine content, and the absorption of mineral.

Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice

Nitrogen (N) and Water (W) - two resources critical for crop productivity - are becoming increasingly limited in soils globally. To address this issue, we aim to uncover the gene regulatory networks (GRNs) that regulate nitrogen use efficiency (NUE) - as a function of water availability - in Oryza sativa, a staple for 3.5 billion people. In this study, we infer and validate GRNs that correlate with rice NUE phenotypes affected by N-by-W availability in the field. We did this by exploiting RNA-seq and crop phenotype data from 19 rice varieties grown in a 2x2 N-by-W matrix in the field. First, to identify gene-to-NUE field phenotypes, we analyzed these datasets using weighted gene co-expression network analysis (WGCNA). This identified two network modules ("skyblue" & "grey60") highly correlated with NUE grain yield (NUEg). Next, we focused on 90 TFs contained in these two NUEg modules and predicted their genome-wide targets using the N-and/or-W response datasets using a random forest network inference approach (GENIE3). Next, to validate the GENIE3 TF→target gene predictions, we performed Precision/Recall Analysis (AUPR) using nine datasets for three TFs validated in planta. This analysis sets a precision threshold of 0.31, used to "prune" the GENIE3 network for high-confidence TF→target gene edges, comprising 88 TFs and 5,716 N-and/or-W response genes. Next, we ranked these 88 TFs based on their significant influence on NUEg target genes responsive to N and/or W signaling. This resulted in a list of 18 prioritized TFs that regulate 551 NUEg target genes responsive to N and/or W signals. We validated the direct regulated targets of two of these candidate NUEg TFs in a plant cell-based TF assay called TARGET, for which we also had in planta data for comparison. Gene ontology analysis revealed that 6/18 NUEg TFs - OsbZIP23 (LOC_Os02g52780), Oshox22 (LOC_Os04g45810), LOB39 (LOC_Os03g41330), Oshox13 (LOC_Os03g08960), LOC_Os11g38870, and LOC_Os06g14670 - regulate genes annotated for N and/or W signaling. Our results show that OsbZIP23 and Oshox22, known regulators of drought tolerance, also coordinate W-responses with NUEg. This validated network can aid in developing/breeding rice with improved yield on marginal, low N-input, drought-prone soils.

Role of protein phosphatases in the regulation of nitrogen nutrition in plants

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.

Understanding rice growth-promoting potential of Enterobacter spp. isolated from long-term organic farming soil in India through a supervised learning approach

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Diazotrophic bacteria were screened and characterized from long-term organic rice fields of Sikkim

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Screened the diazotrophic bacteria for nitrogen fixing ability and plant growth promoting traits

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Enterobacter was commonly found in paddy soils of Sikkim

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Enterobacter species were significantly enhanced the above and below ground responses in rice plants

This study addresses the plant beneficial enterobacteria present in rice rhizosphere and their efficiency for enhancing nitrogen uptake in rice plant. Using culturable approaches, the population of total diazotrophs present in rhizosphere samples collected from different organic rice fields of Sikkim were studied and recorded in the range between 4.62 to 4.97 log₁₀ CFU/g soil. All the isolated commonly occurred diazotrophic bacterial isolates were screened based on their ability to fix nitrogen in milligram per gram of sugar consumed under in-vitro condition with the reference check. In addition to nitrogen fixation, plant growth promoting traits such as production of indole-3-acetic acid and gibberellic acid were estimated using spectrophotometric approaches and compared against Bacillus subtilis as reference multi-potent plant growth promoting strain. In-vivo evaluation of these diazotrophic species in rice found improvement in both above and below ground responses in rice plant evaluated by estimating changes in chlorophyll concentration, plant biomass, root architecture, nitrogen uptake, microbial biomass and associated biochemical activity of soil. Further, the selected isolates were identified through DNA targeted analysis of 16S rRNA gene present in diazotrophs and which identified that the isolates belonged to the Enterobacter genus. Statistical models were prepared for deciphering the dynamics of plant growth improvement due to selective enrichment of rhizosphere bacteria and found significant (p<0.05) correlation between soil and plant parameters. This study concludes that Enterobacter spp. present in organic paddy soils of Sikkim having good nitrogen fixing abilities and whose selective enrichment in rhizosphere improved nitrogen uptake and plant growth promotion in rice plant.

Identifying stress responsive genes using overlapping communities in co-expression networks

Background

This paper proposes a workflow to identify genes that respond to specific treatments in plants. The workflow takes as input the RNA sequencing read counts and phenotypical data of different genotypes, measured under control and treatment conditions. It outputs a reduced group of genes marked as relevant for treatment response. Technically, the proposed approach is both a generalization and an extension of WGCNA. It aims to identify specific modules of overlapping communities underlying the co-expression network of genes. Module detection is achieved by using Hierarchical Link Clustering. The overlapping nature of the systems’ regulatory domains that generate co-expression can be identified by such modules. LASSO regression is employed to analyze phenotypic responses of modules to treatment.

Results

The workflow is applied to rice (Oryza sativa), a major food source known to be highly sensitive to salt stress. The workflow identifies 19 rice genes that seem relevant in the response to salt stress. They are distributed across 6 modules: 3 modules, each grouping together 3 genes, are associated to shoot K content; 2 modules of 3 genes are associated to shoot biomass; and 1 module of 4 genes is associated to root biomass. These genes represent target genes for the improvement of salinity tolerance in rice.

Conclusions

A more effective framework to reduce the search-space for target genes that respond to a specific treatment is introduced. It facilitates experimental validation by restraining efforts to a smaller subset of genes of high potential relevance.

Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species

Tomato is one of the most produced crop plants on earth and growing in the fields and greenhouses all over the world. Breeding with known traits of wild species can enhance stress tolerance of cultivated crops. In this study, we investigated responses of the transcriptome as well as primary and secondary metabolites in leaves of a cultivated and a wild tomato to several abiotic stresses such as nitrogen deficiency, chilling or warmer temperatures, elevated light intensities and combinations thereof. The wild species responded different to varied temperature conditions compared to the cultivated tomato. Nitrogen deficiency caused the strongest responses and induced in particular the secondary metabolism in both species but to much higher extent in the cultivated tomato. Our study supports the potential of a targeted induction of valuable secondary metabolites in green residues of horticultural production, that will otherwise only be composted after fruit harvest. In particular, the cultivated tomato showed a strong induction in the group of mono caffeoylquinic acids in response to nitrogen deficiency. In addition, the observed differences in stress responses between cultivated and wild tomato can lead to new breeding targets for better stress tolerance.

Rice amino acid transporter-like 6 (OsATL6) is involved in amino acid homeostasis by modulating the vacuolar storage of glutamine in roots

Glutamine is a product of ammonium (NH₄⁺ ) assimilation catalyzed by glutamine synthetase (GS) and glutamate synthase (GOGAT). The growth of NH₄⁺ -preferring paddy rice (Oryza sativa L.) depends on root NH₄⁺ assimilation and the subsequent root-to-shoot allocation of glutamine; however, little is known about the mechanism of glutamine storage in roots. Here, using transcriptome and reverse genetics analyses, we show that the rice amino acid transporter-like 6 (OsATL6) protein exports glutamine to the root vacuoles under NH₄⁺ -replete conditions. OsATL6 was expressed, along with OsGS1;2 and OsNADH-GOGAT1, in wild-type (WT) roots fed with sufficient NH₄ Cl, and was induced by glutamine treatment. We generated two independent Tos17 retrotransposon insertion mutants showing reduced OsATL6 expression to determine the function of OsATL6. Compared with segregants lacking the Tos17 insertion, the OsATL6 knock-down mutant seedlings exhibited lower root glutamine content but higher glutamine concentration in the xylem sap and greater shoot growth under NH₄⁺ -replete conditions. The transient expression of monomeric red fluorescent protein-fused OsATL6 in onion epidermal cells confirmed the tonoplast localization of OsATL6. When OsATL6 was expressed in Xenopus laevis oocytes, glutamine efflux from the cell into the acidic bath solution increased. Under sufficient NH₄⁺ supply, OsATL6 transiently accumulated in sclerenchyma and pericycle cells, which are located adjacent to the Casparian strip, thus obstructing the apoplastic solute path, and in vascular parenchyma cells of WT roots before the peak accumulation of GS1;2 and NADH-GOGAT1 occurred. These findings suggest that OsATL6 temporarily stores excess glutamine, produced by NH₄⁺ assimilation, in root vacuoles before it can be translocated to the shoot.

Overexpression of OsERF83, a Vascular Tissue-Specific Transcription Factor Gene, Confers Drought Tolerance in Rice

Abiotic stresses severely affect plant growth and productivity. To cope with abiotic stresses, plants have evolved tolerance mechanisms that are tightly regulated by reprogramming transcription factors (TFs). APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors are known to play an important role in various abiotic stresses. However, our understanding of the molecular mechanisms remains incomplete. In this study, we identified the role of OsERF83, a member of the AP2/ERF transcription factor family, in response to drought stress. OsERF83 is a transcription factor localized to the nucleus and induced in response to various abiotic stresses, such as drought and abscisic acid (ABA). Overexpression of OsERF83 in transgenic plants (OsERF83^OX) significantly increased drought tolerance, with higher photochemical efficiency in rice. OsERF83^OX was also associated with growth retardation, with reduced grain yields under normal growth conditions. OsERF83 is predominantly expressed in the vascular tissue of all organs. Transcriptome analysis revealed that OsERF83 regulates drought response genes, which are related to the transporter (OsNPF8.10, OsNPF8.17, OsLH1), lignin biosynthesis (OsLAC17, OsLAC10, CAD8D), terpenoid synthesis (OsTPS33, OsTPS14, OsTPS3), cytochrome P450 family (Oscyp71Z4, CYP76M10), and abiotic stress-related genes (OsSAP, OsLEA14, PCC13-62). OsERF83 also up-regulates biotic stress-associated genes, including PATHOGENESIS-RELATED PROTEIN (PR), WALL-ASSOCIATED KINASE (WAK), CELLULOSE SYNTHASE-LIKE PROTEIN E1 (CslE1), and LYSM RECEPTOR-LIKE KINASE (RLK) genes. Our results provide new insight into the multiple roles of OsERF83 in the cross-talk between abiotic and biotic stress signaling pathways.

The N uptake-associated physiological processes at late growth stage in wheat (Triticum aestivum) under N deprivation combined with deficit irrigation condition

Elucidating physiological mechanisms underlying the plant N uptake benefits breeding of high N use efficiency (NUE) crop cultivars. In this study, we investigated the growth and N uptake-associated processes in wheat under N deprivation and deficit irrigation, using two contrasting NUE cultivars. Compared with sufficient-N (SN), deficient-N (DN) treatment reduced plant biomass, N accumulation, and yields in two cultivars (high NUE Shinong 086 and N deprivation-sensitive Jimai 585), suggesting that N deprivation negatively regulates plant growth and N uptake. Shinong 086 was better on growth and N uptake-associated traits than Jimai 585 due to the improved root biomass across soil profile, which was consistent with the decrease of available N contents in soil layers. These results suggested that the improved root system architecture (RAS) enhances plant acquirement for soil N under N- and water-deprivation condition, contributing to the plant N uptake and yield formation capacities. Transcriptome investigation revealed that numerous genes were differentially expressed (DE) in the N-deprived Shinong 086 plants, which involve the regulation of complicate biochemical pathways. These results suggested that the modified RAS and N uptake in high NUE plants are accomplished underlying the regulation of numerous DE genes. TaWRKY20, a gene in ZFP transcription factor family, was functionally characterized for the role in mediating plant N uptake. Overexpression of it conferred plants improved growth and N uptake under DN due to its regulation on TaNRT2.1 and TaNRT2.2, two nitrate transporter genes. Our investigation provides insights in high NUE mechanisms in wheat under N deprivation.

OsJAZ11 regulates phosphate starvation responses in rice

OsJAZ11 regulates phosphate homeostasis by suppressing jasmonic acid signaling and biosynthesis in rice roots. Jasmonic Acid (JA) is a key plant signaling molecule which negatively regulates growth processes including root elongation. JAZ (JASMONATE ZIM-DOMAIN) proteins function as transcriptional repressors of JA signaling. Therefore, targeting JA signaling by deploying JAZ repressors may enhance root length in crops. In this study, we overexpressed JAZ repressor OsJAZ11 in rice to alleviate the root growth inhibitory action of JA. OsJAZ11 is a low phosphate (Pi) responsive gene which is transcriptionally regulated by OsPHR2. We report that OsJAZ11 overexpression promoted primary and seminal root elongation which enhanced Pi foraging. Expression studies revealed that overexpression of OsJAZ11 also reduced Pi starvation response (PSR) under Pi limiting conditions. Moreover, OsJAZ11 overexpression also suppressed JA signaling and biosynthesis as compared to wild type (WT). We further demonstrated that the C-terminal region of OsJAZ11 was crucial for stimulating root elongation in overexpression lines. Rice transgenics overexpressing truncated OsJAZ11ΔC transgene (i.e., missing C-terminal region) exhibited reduced root length and Pi uptake. Interestingly, OsJAZ11 also regulates Pi homeostasis via physical interaction with a key Pi sensing protein, OsSPX1. Our study highlights the functional connections between JA and Pi signaling and reveals JAZ repressors as a promising candidate for improving low Pi tolerance of elite rice genotypes.

Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.)

BACKGROUND

Nitrogen (N) and phosphorus (P) are macronutrients essential for crop growth and productivity. In cultivated fields, N and P levels are rarely sufficient, contributing to the gap between realized and potential production. Fertilizer application increases nutrient availability, but is not available to all farmers, nor are current rates of application sustainable or environmentally desirable. Transcriptomic studies of cereal crops have revealed dramatic responses to either low N or low P single stress treatments. In the field, however, levels of both N and P may be suboptimal. The interaction between N and P starvation responses remains to be fully characterized.

RESULTS

We characterized growth and root and leaf transcriptomes of young maize plants under nutrient replete, low N, low P or combined low NP conditions. We identified 1555 genes to respond to our nutrient treatments, in one or both tissues. A large group of genes, including many classical P starvation response genes, were regulated antagonistically between low N and P conditions. An additional experiment over a range of N availability indicated that a mild reduction in N levels was sufficient to repress the low P induction of P starvation genes. Although expression of P transporter genes was repressed under low N or low NP, we confirmed earlier reports of P hyper accumulation under N limitation.

CONCLUSIONS

Transcriptional responses to low N or P were distinct, with few genes responding in a similar way to the two single stress treatments. In combined NP stress, the low N response dominated, and the P starvation response was largely suppressed. A mild reduction in N availability was sufficient to repress the induction of P starvation associated genes. We conclude that activation of the transcriptional response to P starvation in maize is contingent on N availability.

Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture

The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.

A genome wide transcriptional study of Populus alba x P. tremula var. glandulosa in response to nitrogen deficiency stress

Poplar 84 K (Populus alba x P. tremula var. glandulosa) is a good resource for genetic engineering due to its rapid growth and wide adaptability, and it is also an excellent ornamental tree species. In this study, we used 84 K plantlets grown in the nitrogen-limited medium as experimental materials to explore the molecular mechanism in 84 K leaves under nitrogen deficiency. A total of 5,868 differentially expressed genes (DEGs) were identified using the transcriptional information from RNA-seq data. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment results revealed that the DEGs were mainly involved in energy metabolism and anthocyanin biosynthesis. We then identified differentially expressed transcription factors (TFs) and constructed TF centered gene co-expression networks for chlorophyll and anthocyanin biosynthesis pathway genes. Twenty potential regulators were finally identified. We speculated the transcription factors that control the pigmentation in leaves with the MYB-bHLH-WD40 (MBW) pigment regulatory model. Such identification will clarify the genetic basis of the secondary metabolism in 84 K, and being a source of candidate genes for future plant genetic engineering. Our work broadens the researchers' understanding of the regulation of anthocyanin synthesis in trees and provides new perspectives for ornamental 84 K poplar breeding.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01012-3.

Nitrogen Signaling Genes and SOC1 Determine the Flowering Time in a Reciprocal Negative Feedback Loop in Chinese Cabbage (Brassica rapa L.) Based on CRISPR/Cas9-Mediated Mutagenesis of Multiple BrSOC1 Homologs

Precise flowering timing is critical for the plant life cycle. Here, we examined the molecular mechanisms and regulatory network associated with flowering in Chinese cabbage (Brassica rapa L.) by comparative transcriptome profiling of two Chinese cabbage inbred lines, “4004” (early bolting) and “50” (late bolting). RNA-Seq and quantitative reverse transcription PCR (qPCR) analyses showed that two positive nitric oxide (NO) signaling regulator genes, nitrite reductase (BrNIR) and nitrate reductase (BrNIA), were up-regulated in line “50” with or without vernalization. In agreement with the transcription analysis, the shoots in line “50” had substantially higher nitrogen levels than those in “4004”. Upon vernalization, the flowering repressor gene Circadian 1 (BrCIR1) was significantly up-regulated in line “50”, whereas the flowering enhancer genes named SUPPRESSOR OF OVEREXPRESSION OF CONSTANCE 1 homologs (BrSOC1s) were substantially up-regulated in line “4004”. CRISPR/Cas9-mediated mutagenesis in Chinese cabbage demonstrated that the BrSOC1-1/1-2/1-3 genes were involved in late flowering, and their expression was mutually exclusive with that of the nitrogen signaling genes. Thus, we identified two flowering mechanisms in Chinese cabbage: a reciprocal negative feedback loop between nitrogen signaling genes (BrNIA1 and BrNIR1) and BrSOC1s to control flowering time and positive feedback control of the expression of BrSOC1s.

Nitrogen Deficiency and Synergism between Continuous Light and Root Ammonium Supply Modulate Distinct but Overlapping Patterns of Phytohormone Composition in Xylem Sap of Tomato Plants

Continuous light (CL) or a predominant nitrogen supply as ammonium (NH4+) can induce leaf chlorosis and inhibit plant growth. The similarity in injuries caused by CL and NH4+ suggests involvement of overlapping mechanisms in plant responses to these conditions; however, these mechanisms are poorly understood. We addressed this topic by conducting full factorial experiments with tomato plants to investigate the effects of NO3- or NH4+ supply under diurnal light (DL) or CL. We used plants at ages of 26 and 15 days after sowing to initiate the treatments, and we modulated the intensity of the stress induced by CL and an exclusive NH4+ supply from mild to strong. Under DL, we also studied the effect of nitrogen (N) deficiency and mixed application of NO3- and NH4+. Under strong stress, CL and exclusive NH4+ supply synergistically inhibited plant growth and reduced chlorophyll content. Under mild stress, when no synergetic effect between CL and NH4+ was apparent on plant growth and chlorophyll content, we found a synergetic effect of CL and NH4+ on the accumulation of several plant stress hormones, with an especially strong effect for jasmonic acid (JA) and 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene, in xylem sap. This modulation of the hormonal composition suggests a potential role for these plant hormones in plant growth responses to the combined application of CL and NH4+. No synergetic effect was observed between CL and NH4+ for the accumulation of soluble carbohydrates or of mineral ions, indicating that these plant traits are less sensitive than the modulation of hormonal composition in xylem sap to the combined CL and NH4+ application. Under diurnal light, NH4+ did not affect the hormonal composition of xylem sap; however, N deficiency strongly increased the concentrations of phaseic acid (PA), JA, and salicylic acid (SA), indicating that decreased N concentration rather than the presence of NO3- or NH4+ in the nutrient solution drives the hormone composition of the xylem sap. In conclusion, N deficiency or a combined application of CL and NH4+ induced the accumulation of JA in xylem sap. This accumulation, in combination with other plant hormones, defines the specific plant response to stress conditions.

Down regulation of transcripts involved in selective metabolic pathways as an acclimation strategy in nitrogen use efficient genotypes of rice under low nitrogen

To understand the molecular mechanism of nitrogen use efficiency (NUE) in rice, two nitrogen (N) use efficient genotypes and two non-efficient genotypes were characterized using transcriptome analyses. The four genotypes were evaluated for 3 years under low and recommended N field conditions for 12 traits/parameters of yield, straw, nitrogen content along with NUE indices and 2 promising donors for rice NUE were identified. Using the transcriptome data generated from GS FLX 454 Roche and Illumina HiSeq 2000 of two efficient and two non-efficient genotypes grown under field conditions of low N and recommended N and their de novo assembly, differentially expressed transcripts and pathways during the panicle development were identified. Down regulation was observed in 30% of metabolic pathways in efficient genotypes and is being proposed as an acclimation strategy to low N. Ten sub metabolic pathways significantly enriched with additional transcripts either in the direction of the common expression or contra-regulated to the common expression were found to be critical for NUE in rice. Among the up-regulated transcripts in efficient genotypes, a hypothetical protein OsI_17904 with 2 alternative forms suggested the role of alternative splicing in NUE of rice and a potassium channel SKOR transcript (LOC_Os06g14030) has shown a positive correlation (0.62) with single plant yield under low N in a set of 16 rice genotypes. From the present study, we propose that the efficient genotypes appear to down regulate several not so critical metabolic pathways and divert the thus conserved energy to produce seed/yield under long-term N starvation.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02631-5.

Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production

Genome-wide transcriptome profiling is a powerful tool for identifying key genes and pathways involved in plant development and physiological processes. This review summarizes studies that have used transcriptome profiling mainly in rice to focus on responses to macronutrients such as nitrogen, phosphorus and potassium, and spatio-temporal root profiling in relation to the regulation of root system architecture as well as nutrient uptake and transport. We also discuss strategies based on meta- and co-expression analyses with different attributed transcriptome data, which can be used for investigating the regulatory mechanisms and dynamics of nutritional responses and adaptation, and speculate on further advances in transcriptome profiling that could have potential application to crop breeding and cultivation.

Effect of sodium chloride on the expression of genes involved in the salt tolerance of Bacillus sp. strain “SX4” isolated from salinized greenhouse soil

Salt stress is one of the important adverse conditions affecting bacterium growth. How bacteria isolated from greenhouse soil cope with salt stress and regulate the genes responsible for salt tolerance are still unclear. We conducted RNA transcriptome profiling of genes contributing to the salt tolerance of a Bacillus sp. strain (“SX4”) obtained from salinized soil. Results showed that NaCl effectively regulated the growth of “SX4” in terms of cell length and colony-forming unit number decrease. A total of 121 upregulated and 346 downregulated genes were detected under salt stress with reference to the control. The largest numbers of differential expression genes were 17 in carbon metabolism, 13 in the biosynthesis of amino acids, 10 in a two-component system, and 10 in ABC transporter pathways for adapting to salt stress. Our data revealed that cation, electron and transmembrane transport, and catalytic activity play important roles in the resistance of bacterial cells to salt ions. Single-nucleotide polymorphism and the mutation of base pair T:A to C:G play potential roles in the adaptation of “SX4” to high NaCl concentrations. The findings from this study provide new insights into the molecular mechanisms of strain “SX4” and will be helpful in promoting the application of salt-tolerant bacteria.

Heterotrimeric G-protein α subunit (RGA1) regulates tiller development, yield, cell wall, nitrogen response and biotic stress in rice

G-proteins are implicated in plant productivity, but their genome-wide roles in regulating agronomically important traits remain uncharacterized. Transcriptomic analyses of rice G-protein alpha subunit mutant (rga1) revealed 2270 differentially expressed genes (DEGs) including those involved in C/N and lipid metabolism, cell wall, hormones and stress. Many DEGs were associated with root, leaf, culm, inflorescence, panicle, grain yield and heading date. The mutant performed better in total weight of filled grains, ratio of filled to unfilled grains and tillers per plant. Protein–protein interaction (PPI) network analysis using experimentally validated interactors revealed many RGA1-responsive genes involved in tiller development. qPCR validated the differential expression of genes involved in strigolactone-mediated tiller formation and grain development. Further, the mutant growth and biomass were unaffected by submergence indicating its role in submergence response. Transcription factor network analysis revealed the importance of RGA1 in nitrogen signaling with DEGs such as Nin-like, WRKY, NAC, bHLH families, nitrite reductase, glutamine synthetase, OsCIPK23 and urea transporter. Sub-clustering of DEGs-associated PPI network revealed that RGA1 regulates metabolism, stress and gene regulation among others. Predicted rice G-protein networks mapped DEGs and revealed potential effectors. Thus, this study expands the roles of RGA1 to agronomically important traits and reveals their underlying processes.

Signaling Responses to N Starvation: Focusing on Wheat and Filling the Putative Gaps With Findings Obtained in Other Plants. A Review

Wheat is one of the most important food crops worldwide. In recent decades, fertilizers, especially nitrogen (N), have been increasingly utilized to maximize wheat productivity. However, a large proportion of N is not used by plants and is in fact lost into the environment and causes serious environmental pollution. Therefore, achieving a low N optimum via efficient physiological and biochemical processes in wheat grown under low-N conditions is highly important for agricultural sustainability. Although N stress-related N capture in wheat has become a heavily researched subject, how this plant adapts and responds to N starvation has not been fully elucidated. This review summarizes the current knowledge on the signaling mechanisms activated in wheat plants in response to N starvation. Furthermore, we filled the putative gaps on this subject with findings obtained in other plants, primarily rice, maize, and Arabidopsis. Phytohormones have been determined to play essential roles in sensing environmental N starvation and transducing this signal into an adjustment of N transporters and phenotypic adaptation. The critical roles played by protein kinases and critical kinases and phosphatases, such as MAPK and PP2C, as well as the multifaceted functions of transcription factors, such as NF-Y, MYB, DOF, and WRKY, in regulating the expression levels of their target genes (proteins) for low-N tolerance are also discussed. Optimization of root system architecture (RSA) via root branching and thinning, improvement of N acquisition and assimilation, and fine-tuned autophagy are pivotal strategies by which plants respond to N starvation. In light of these findings, we attempted to construct regulatory networks for RSA modification and N uptake, transport, assimilation, and remobilization.

Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice

Nitrogen-use efficiency (NUE) is a function of N-response and yield that is controlled by many genes and phenotypic parameters that are poorly characterized. This study compiled all known yield-related genes in rice and mined them from the N-responsive microarray data to find 1,064 NUE-related genes. Many of them are novel genes hitherto unreported as related to NUE, including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases. They were further shortlisted to 62 NUE-candidate genes following hierarchical methods, including quantitative trait locus (QTL) co-localization, functional evaluation in the literature, and protein-protein interactions (PPIs). They were localized to chromosomes 1, 3, 5, and 9, of which chromosome 1 with 26 genes emerged as a hotspot for NUE spanning 81% of the chromosomes. Further, co-localization of the NUE genes on NUE-QTLs resolved differences in the earlier studies that relied mainly on N-responsive genes regardless of their role in yield. Functional annotations and PPIs for all the 1,064 NUE-related genes and also the shortlisted 62 candidates revealed transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal function among the prominent processes. In silico expression analysis confirmed differential expression of the 62 NUE-candidate genes in a tissue/stage-specific manner. Experimental validation in two contrasting genotypes revealed that high NUE rice shows better photosynthetic performance, transpiration efficiency and internal water-use efficiency in comparison to low NUE rice. Feature Selection Analysis independently identified one-third of the common genes at every stage of hierarchical shortlisting, offering 6 priority targets to validate for improving the crop NUE.

Diverse Roles of MAX1 Homologues in Rice

Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.

Raman Spectroscopy Enables Non-invasive and Confirmatory Diagnostics of Salinity Stresses, Nitrogen, Phosphorus, and Potassium Deficiencies in Rice

Proper management of nutrients in agricultural systems is critically important for maximizing crop yields while simultaneously minimizing the health and environmental impacts of pollution from fertilizers. These goals can be achieved by timely confirmatory diagnostics of nutrient deficiencies in plants, which enable precise administration of fertilizers and other supplementation in fields. Traditionally, nutrient diagnostics are performed by wet-laboratory analyses, which are both time- and labor-consuming. Unmanned aerial vehicle (UAV) and satellite imaging have offered a non-invasive alternative. However, these imaging approaches do not have sufficient specificity, and they are only capable of detecting symptomatic stages of nutrient deficiencies. Raman spectroscopy (RS) is a non-invasive and non-destructive technique that can be used for confirmatory detection and identification of both biotic and abiotic stresses on plants. Herein, we show the use of a hand-held Raman spectrometer for highly accurate pre-symptomatic diagnostics of nitrogen, phosphorus, and potassium deficiencies in rice (Oryza sativa). Moreover, we demonstrate that RS can also be used for pre symptomatic diagnostics of medium and high salinity stresses. A Raman-based analysis is fast (1 s required for spectral acquisition), portable (measurements can be taken directly in the field), and label-free (no chemicals are needed). These advantages will allow RS to transform agricultural practices, enabling precision agriculture in the near future.

Rice NIN-LIKE PROTEIN 1 rapidly responds to nitrogen deficiency and improves yield and nitrogen use efficiency

Nitrogen (N) is indispensable for crop growth and yield, but excessive agricultural application of nitrogenous fertilizers has generated severe environmental problems. A desirable and economical solution to cope with these issues is to improve crop nitrogen use efficiency (NUE). Plant NUE has been a focal point of intensive research worldwide, yet much still has to be learned about its genetic determinants and regulation. Here, we show that rice (Oryza sativa L.) NIN-LIKE PROTEIN 1 (OsNLP1) plays a fundamental role in N utilization. OsNLP1 protein localizes in the nucleus and its transcript level is rapidly induced by N starvation. Overexpression of OsNLP1 improves plant growth, grain yield, and NUE under different N conditions, while knockout of OsNLP1 impairs grain yield and NUE under N-limiting conditions. OsNLP1 regulates nitrate and ammonium utilization by cooperatively orchestrating multiple N uptake and assimilation genes. Chromatin immunoprecipitation and yeast one-hybrid assays showed that OsNLP1 can directly bind to the promoter of these genes to activate their expression. Therefore, our results demonstrate that OsNLP1 is a key regulator of N utilization and represents a potential target for improving NUE and yield in rice.

Genome-Wide Association Study and Identification of Candidate Genes for Nitrogen Use Efficiency in Barley (Hordeum vulgare L.)

Nitrogen (N) fertilizer is largely responsible for barley grain yield potential and quality, yet excessive application leads to environmental pollution and high production costs. Therefore, efficient use of N is fundamental for sustainable agriculture. In the present study, we investigated the performance of 282 barley accessions through hydroponic screening using optimal and low NH4NO3 treatments. Low-N treatment led to an average shoot dry weight reduction of 50%, but there were significant genotypic differences among the accessions. Approximately 20% of the genotypes showed high (>75%) relative shoot dry weight under low-N treatment and were classified as low-N tolerant, whereas 20% were low-N sensitive (≤55%). Low-N tolerant accessions exhibited well-developed root systems with an average increase of 60% in relative root dry weight to facilitate more N absorption. A genome-wide association study (GWAS) identified 66 significant marker trait associations (MTAs) conferring high nitrogen use efficiency, four of which were stable across experiments. These four MTAs were located on chromosomes 1H(1), 3H(1), and 7H(2) and were associated with relative shoot length, relative shoot and root dry weight. Genes corresponding to the significant MTAs were retrieved as candidate genes, including members of the asparagine synthetase gene family, several transcription factor families, protein kinases, and nitrate transporters. Most importantly, the high-affinity nitrate transporter 2.7 (HvNRT2.7) was identified as a promising candidate on 7H for root and shoot dry weight. The identified candidate genes provide new insights into our understanding of the molecular mechanisms driving nitrogen use efficiency in barley and represent potential targets for genetic improvement.

Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency

Understanding the molecular mechanisms controlling the accumulation of grain storage proteins in response to nitrogen (N) and sulfur (S) nutrition is essential to improve cereal grain nutritional and functional properties. Here, we studied the grain transcriptome and metabolome responses to postanthesis N and S supply for the diploid wheat einkorn (Triticum monococcum). During grain filling, 848 transcripts and 24 metabolites were differentially accumulated in response to N and S availability. The accumulation of total free amino acids per grain and the expression levels of 241 genes showed significant modifications during most of the grain filling period and were upregulated in response to S deficiency. Among them, 24 transcripts strongly responded to S deficiency and were identified in coexpression network analyses as potential coordinators of the grain response to N and S supply. Sulfate transporters and genes involved in sulfate and Met metabolism were upregulated, suggesting regulation of the pool of free amino acids and of the grain N-to-S ratio. Several genes highlighted in this study might limit the impact of S deficiency on the accumulation of grain storage proteins.

Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency

BACKGROUND

Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family may involve in nitrate uptake and transport. Here, we identified PTR gene family in rice and analyzed their expression profile in near-isogenic lines.

RESULTS

We identified 96, 85 and 78 PTR genes in Nipponbare, R498 and Oryza glaberrima, and the phylogenetic trees were similar in Asian cultivated rice and African cultivated rice. The number of PTR genes was higher in peanut (125) and soybean (127). The 521 PTR genes in rice, maize, sorghum, peanut, soybean and Arabidopsis could be classified into 4 groups, and their distribution was different between monocots and dicots. In Nipponbare genome, the 25 PTR genes were distributed in 5 segmental duplication regions on chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 10. The PTR genes in rice have 0-11 introns and 1-12 exons, and 16 of them have the NPF (NRT1/PTR family) domain. The results of RNA-seq showed that the number of differentially expressed genes (DEGs) between NIL15 and NIL19 at three stages were 928, 1467, and 1586, respectively. Under low N conditions, the number of differentially expressed PTR genes increased significantly. The RNA-seq data was analyzed using WGCNA to predict the potential interaction between genes. We classified the genes with similar expression pattern into one module, and obtained 25 target modules. Among these modules, three modules may be involved in rice N uptake and utilization, especially the brown module, in which hub genes were annotated as protein kinase that may regulate rice N metabolism.

CONCLUSIONS

In this study, we comprehensively analyzed the PTR gene family in rice. 96 PTR genes were identified in Nippobare genome and 25 of them were located on five large segmental duplication regions. The Ka/Ks ratio indicated that many PTR genes had undergone positive selection. The RNA-seq results showed that many PTR genes were involved in rice nitrogen use efficiency (NUE), and protein kinases might play an important role in this process. These results provide a fundamental basis to improve the rice NUE via molecular breeding.

Overexpression of OsMYB305 in Rice Enhances the Nitrogen Uptake Under Low-Nitrogen Condition

Excessive nitrogen fertilizer application causes severe environmental degradation and drives up agricultural production costs. Thus, improving crop nitrogen use efficiency (NUE) is essential for the development of sustainable agriculture. Here, we characterized the roles of the MYB transcription factor OsMYB305 in nitrogen uptake and assimilation in rice. OsMYB305 encoded a transcriptional activator and its expression was induced by N deficiency in rice root. Under low-N condition, OsMYB305 overexpression significantly increased the tiller number, shoot dry weight and total N concentration. In the roots of OsMYB305-OE rice lines, the expression of OsNRT2.1, OsNRT2.2, OsNAR2.1, and OsNiR2 was up-regulated and 15NO3 - influx was significantly increased. In contrast, the expression of lignocellulose biosynthesis-related genes was repressed so that cellulose content decreased, and soluble sugar concentration increased. Certain intermediates in the glycolytic pathway and the tricarboxylic acid cycle were significantly altered and NADH-GOGAT, Pyr-K, and G6PDH were markedly elevated in the roots of OsMYB305-OE rice lines grown under low-N condition. Our results revealed that OsMYB305 overexpression suppressed cellulose biosynthesis under low-nitrogen condition, thereby freeing up carbohydrate for nitrate uptake and assimilation and enhancing rice growth. OsMYB305 is a potential molecular target for increasing NUE in rice.

Comparing the growth-promoting potential of Paenibacillus lentimorbus and Bacillus amyloliquefaciens in Oryza sativa L. var. Sarju-52 under suboptimal nutrient conditions

An adequate supply of mineral nutrients is crucial to obtain optimum productivity in agriculture. The present investigation was carried to find the inoculation effect of plant growth-promoting rhizobacteria (PGPR), i.e., Paenibacillus lentimorbus B-30488 (B-30488), Bacillus amyloliquefaciens SN13 (SN13) and their consortium for the growth of rice var. Sarju-52, grown under suboptimal nutrient conditions. The study revealed that the individual PGPR treatments showed comparatively better performance than consortia in morphological, physiological, biochemical, and nutrient analysis. Towards understanding the complex mechanism(s), untargeted metabolite profiling was performed using GC-MS, showed alteration of metabolites in rice seedlings facing suboptimal nutrient conditions and inoculated with PGPR. Metabolites such as oleic acid, mannitol, and ethyl iso-allocol were accumulated significantly under starved conditions. Under suboptimal nutrient conditions, sugars such as ribose, glucose, fructose, trehalose, palmitic acid, and myristic acid were accumulated significantly in PGPR inoculated seedlings. The significantly altered pathways due to PGPR inoculation under suboptimal nutrient conditions mainly belongs to carbohydrate and fatty acid metabolism. Interestingly, it was observed that among all the treatments, inoculation with SN13 performed comparatively better than other treatments. Further, in SN13 inoculated samples the qRT-PCR analysis of transcription factors and metabolism-related genes were validated that indicates PGPR deploy metabolic re-programming in rice var. Sarju-52 to enhance its nutrient use efficiency, tolerance, and growth under suboptimum nutrient conditions.

CBL-INTERACTING PROTEIN KINASE 9 regulates ammonium-dependent root growth downstream of IDD10 in rice (Oryza sativa)

BACKGROUND AND AIMS

INDETERMINATE DOMAIN 10 (IDD10) is a key transcription factor gene that activates the expression of a large number of NH4+-responsive genes including AMMONIUM TRANSPORTER 1;2 (AMT1;2). Primary root growth of rice (Oryza sativa) idd10 mutants is hypersensitive to NH4+. The involvement of CALCINEURIN B-LIKE INTERACTING PROTEIN KINASE (CIPK) genes in the action of IDD10 on NH4+-mediated root growth was investigated.

METHODS

Quantitative reverse transcription-PCR was used to analyse NH4+- and IDD10-dependent expression of CIPK genes. IDD10-regulated CIPK target genes were identified using electrophoretic mobility shift assays, chromatin immunoprecipitation and transient transcription assays. Root growth rate, ammonium content and 15N uptake of cipk mutants were measured to determine their sensitivity to NH4+ and to compare these phenotypes with those of idd10. The genetic relationship between CIPK9 OX and idd10 was investigated by crosses between the CIPK9 and IDD10 lines.

KEY RESULTS

AMT1;2 was overexpressed in idd10 to determine whether NH4+-hypersensitive root growth of idd10 resulted from limitations in NH4+ uptake or from low cellular levels of NH4+. High NH4+ levels in idd10/AMT1;2 OX did not rescue the root growth defect. Next, the involvement of CIPK genes in NH4+-dependent root growth and interactions between IDD10 and CIPK genes was investigated. Molecular analysis revealed that IDD10 directly activated transcription of CIPK9 and CIPK14. Expression of CIPK8, 9, 14/15 and 23 was sensitive to exogenous NH4+. Further studies revealed that cipk9 and idd10 had almost identical NH4+-sensitive root phenotypes, including low efficiency of 15NH4+ uptake. Analysis of plants containing both idd10 and CIPK9 OX showed that CIPK9 OX could rescue the NH4+-dependent root growth defects of idd10.

CONCLUSIONS

CIPK9 was involved in NH4+-dependent root growth and appeared to act downstream of IDD10. This information will be useful in future explorations of NH4+ signalling in plants.