Light signalling regulates plant growth and stress resistance, whereas its mechanism in controlling saline-alkaline tolerance (SAT) remains largely unknown. This study identified that light signalling, primarily mediated by Phytochrome B (PhyB), inhibited ammonium transporter 1 (AMT1) to negatively regulate SAT. Our previous findings have shown that PhyB can impede the transcription factors indeterminate domain 10 (IDD10) and brassinazole resistant 1 (BZR1) to reduce NH4 + uptake, thereby modulating SAT and sheath blight (ShB) resistance in rice. However, inhibition of IDD10 and BZR1 in the phyB background did not fully suppress NH4 + uptake, suggesting that other signalling pathways regulated AMT1 downstream of PhyB. Further analysis revealed that PhyB interacted with Calcineurin B-like protein-interacting protein kinase 31 (CIPK31), which positively regulated AMT1 expression. CIPK31 also interacted with Teosinte Branched1/Cycloidea/PCF19 (TCP19), a key regulator of nitrogen use efficiency (NUE). However, PhyB neither degraded CIPK31 nor directly interacted with TCP19. Instead, PhyB inhibited the CIPK31-TCP19 interaction, releasing TCP19, which repressed AMT1;2 directly and AMT1;1 and AMT1;3 indirectly, thereby inhibiting NH4 + uptake and SAT while reducing ShB resistance. Additionally, Phytochrome Interacting Factor-Like 15 (PIL15) interacted with TCP19. Different from TCP19, PIL15 directly activated AMT1;2 to promote SAT, suggesting a balancing mechanism for NH4 + uptake downstream of PhyB. Furthermore, PIL15 interacted with IDD10 and BZR1 to form a transcriptional complex that collaboratively activated AMT1;2 expression. Overall, this study provides novel insights into how PhyB signalling regulates NH4 + uptake and coordinates SAT and ShB resistance in rice.

Disease occurrence severely affects crop yield production; however, the signaling pathway controlling yield and immunity are antagonistic that made plant breeding even difficult [1].Plant trait of tiller, e.g., tiller number, is the key architectural factor that is directly associated with yield production [2].The previous transcriptome study using sheath blight (ShB) susceptible cultivar (Lemont) and resistant cultivar (Teqing) identified that 2048 genes including Grassy tiller 1 (GT1) differentially expressed upon inoculation of Rhizoctonia solani AG1-IA (Fig. 1a) [3].RT-qPCR analysis confirmed that GT1 expression level was drastically lower in Teqing than in Lemont (Fig. 1b).Our previous study also showed that GT1 expression is significantly induced by R. solani AG1-IA [4].qRT-PCR results verified that R. solani-inoculation significantly induced GT1 expression after 12, 36 and 48 h, and the highest induction was detected after 36 h of inoculation (Fig. 1c).These results demonstrated that disease-related GT1 was significantly activated by R. solani.Transcriptome analysis using GT1 RNAi plants determined that sugar will

Hydroxyurea (HU) is a known suppressor of ribonucleotide reductase enzyme through enhanced hydrogen peroxide (H2O2) production, causing oxidative damage to DNA in plants. Kinetin (KI) has emerged as an important phytohormone in regulating development processes and antioxidant protection effects against environmental stresses. Therefore, this study aimed to investigate the potential and regulating mechanism of KI application on tolerance of Oryza sativa to HU-induced oxidative stress. Three-day-old rice seedlings were grown in 1/2 MS medium for seven days following different treatments: control, HU (1 mM), KI (40 nM), and HU + KI. The results showed that, compared to control, HU treatment significantly reduced the growth (e.g., dry weight and root length: 36

Phytochromes are red/far-red light receptors that regulate various aspects of plant growth, development, and stress responses. The precise mechanism by which phytochrome B (PhyB)-mediated light signaling influences plant defense and development remains unclear. In this study, we showed that PhyB enhances rice (Oryza sativa) blast disease resistance, tillering, and grain size compared to wild-type plants. Notably, PhyB interacted with and degraded grassy tiller 1 (GT1), a negative regulator of tiller development. Knockdown of GT1 in a phyB background partially rescued the diminished tillering of phyB. However, GT1 negatively regulates rice resistance to blast, suggesting that PhyB degradation of GT1 promotes tillering but not blast resistance. Previously, PhyB was found to interact with and degrade phytochrome-interacting factor 15 (PIL15), a key regulator of seed development that reduces rice resistance to blast and seed size. pil15 mutation in phyB mutants rescued phyB seed size and blast resistance, suggesting that PhyB might interact with and degrade PIL15 to negatively regulate blast resistance and seed size. PIL15 directly activated sugar will be eventually exported transporter 2a (SWEET2a). sweet2a mutants were less susceptible to blast disease compared to wild type. Collectively, these data demonstrate that PhyB promotes rice yield and blast resistance by inhibiting the transcription factors GT1 and PIL15 and downstream signaling. Red and far-red receptor-mediated signaling inhibits multiple downstream transcription factors and concurrently enhances blast disease resistance, tillering, and grain size in rice.

Phytochrome B (PhyB), a red-light receptor, plays important roles in diverse biological processes in plants; however, its function in NH4 + uptake and stress responses of plants is unclear. Here, we observed that mutation in indeterminate domain 10 (IDD10), which encodes a key transcription factor in NH4 + signaling, led to NH4 + -sensitive root growth in light but not in the dark. Genetic combinations of idd10 and phy mutants demonstrated that phyB, but not phyA or phyC, suppressed NH4 + -sensitive root growth of idd10. PhyB mutants and PhyB overexpressors (PhyB OXs) accumulated more and less NH4 + , respectively, compared with wild-type plants. Real time quantitative polymerase chain reaction (RT-qPCR) revealed that PhyB negatively regulated NH4 + -mediated induction of Ammonium transporter 1;2 (AMT1;2). AMT1 RNAi plants with suppressed AMT1;1, AMT1;2, and AMT1;3 expression exhibited shorter primary roots under NH4 + conditions. This suggested that NH4 + uptake might be positively associated with root growth. Further, PhyB interacted with and inhibited IDD10 and brassinazole-resistant 1 (BZR1). IDD10 interacted with BZR1 to activate AMT1;2. NH4 + uptake is known to promote resistance of rice (Oryza sativa) to sheath blight (ShB) and saline-alkaline stress. Inoculation of Rhizoctonia solani demonstrated that PhyB and IDD10 negatively regulated and AMT1 and BZR1 positively regulated resistance of rice to ShB. In addition, PhyB negatively regulated and IDD10 and AMT1 positively regulated resistance of rice to saline-alkaline stress. This suggested that PhyB-IDD10-AMT1;2 signaling regulates the saline-alkaline response, whereas the PhyB-BZR1-AMT1;2 pathway modulates ShB resistance. Collectively, these data prove that mutation in the PhyB gene enhances the resistance of rice to ShB and saline-alkaline stress by increasing NH4 + uptake.

INTRODUCTION:Rhizoctonia solani, the causative agent of the sheath blight disease (ShB), invades rice to obtain nutrients, especially sugars; however, the molecular mechanism via which R. solani hijacks sugars from rice remains unclear.OBJECTIVES:In this study, rice-R. solani interaction model was used to explore whether pathogen effector proteins affect plant sugar absorption during infection.METHODS:Yeast one-hybrid assay was used to identify Activator of SWEET2a (AOS2) from R. solani. Localization and invertase secretion assays showed that nuclear localization and secreted function of AOS2. Hexose transport assays verified the hexose transporter activity of SWEET2a and SWEET3a. Yeast two-hybrid assays, Bimolecular fluorescence complementation (BiFC) and transactivation assay were conducted to verify the AOS2-WRKY53-Grassy tiller 1 (GT1) transcriptional complex and its activation of SWEET2a and SWEET3a. Genetic analysis is used to detect the response of GT1, WRKY53, SWEET2a, and SWEET3a to ShB infestation. Also, the soluble sugar contents were measured in the mutants and overexpression plants before and after the inoculation of R. solani.RESULTS:The present study found that R. solani protein AOS2 activates rice SWEET2a and localized in the nucleus of tobacco cells and secreted in yeast. AOS2 interacts with rice transcription factor WRKY53 and GT1 to form a complex that activates the hexose transporter gene SWEET2a and SWEET3a and negatively regulate rice resistance to ShB.CONCLUSION:These data collectively suggest that AOS2 secreted by R. solani interacts with rice WRKY53 and GT1 to form a transcriptional complex that activates SWEETs to efflux sugars to apoplast; R. solani acquires more sugars and subsequently accelerates host invasion.

Hydroxyurea (HU) is the replication stress known to carry out cell cycle arrest by inhibiting ribonucleotide reductase (RNR) enzyme upon generating excess hydrogen peroxide (H2O2) in plants. Phytohormones undergo synergistic and antagonistic interactions with reactive oxygen species (ROS) and redox signaling to protect plants against biotic and abiotic stress. Therefore, in this study, we investigated the protective role of Indole-3-acetic acid (IAA) in mitigating HU-induced toxicity in rice seedlings. The results showed that IAA augmentation improved the growth of the seedlings and biomass production by maintaining photosynthesis metabolism under HU stress. This was associated with reduced H2O2 and malondialdehyde (MDA) contents and improved antioxidant enzyme [superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT), and peroxidase (POD)] activity that was significantly affected under HU stress. Furthermore, we showed that the HU stress-induced DNA damage leads to the activation of uridine 5′-diphosphate-glucosyltransferase (UGT), which mediates auxin homeostasis by catalyzing IAA-glucose conjugation in rice. This IAA-glucose conjugation upregulates the RNR, transcription factor 2 (E2F2), cyclin-dependent kinase (CDK), and cyclin (CYC) genes that are vital for DNA replication and cell division. As a result, perturbed IAA homeostasis significantly enhanced the key phytohormones, such as abscisic acid (ABA), salicylic acid (SA), cytokinin (CTK), and gibberellic acid (GA), that alter plant architecture by improving growth and development. Collectively, our results contribute to a better understanding of the physiological and molecular mechanisms underpinning improved growth following the HU + IAA combination, activated by phytohormone and ROS crosstalk upon hormone conjugation via UGT.

Sheath blight (ShB) significantly threatens rice yield production. However, the underlying mechanism of ShB defence in rice remains largely unknown. Here, we identified a highly ShB-susceptible mutant Ds-m which contained a mutation at the ammonium transporter 1;1 (AMT1;1) D358 N. AMT1;1 D358 N interacts with AMT1;1, AMT1;2 and AMT1;3 to inhibit the ammonium transport activity. The AMT1 RNAi was more susceptible and similar to the AMT1;1 D358 N mutant; however, plants with higher NH4+ uptake activity were less susceptible to ShB. Glutamine synthetase 1;1 (GS1;1) mutant gs1;1 and overexpressors (GS1;1 OXs) were more and less susceptible to ShB respectively. Furthermore, AMT1;1 overexpressor (AMT1;1 OX)/gs1;1 and gs1;1 exhibited a similar response to ShB, suggesting that ammonium assimilation rather than accumulation controls the ShB defence. Genetic and physiological assays further demonstrated that plants with higher amino acid or chlorophyll content promoted rice resistance to ShB. Interestingly, the expression of ethylene-related genes was higher in AMT1;1 OX and lower in RNAi mutants than in wild-type. Also, ethylene signalling positively regulated rice resistance to ShB and NH4+ uptake, suggesting that ethylene signalling acts downstream of AMT and also NH4+ uptake is under feedback control. Taken together, our data demonstrated that the AMT1 promotes rice resistance to ShB via the regulation of diverse metabolic and signalling pathways.

Rice (Oryza sativa) production is damaged to a great extent by sheath blight disease (ShB). However, the defense mechanism in rice against this disease is largely unknown. Previous transcriptome analysis identified a significantly induced eukaryotic protein phosphatase 2A catalytic subunit 1 (PP2A-1) after the inoculation of Rhizoctonia solani. Five genes encoding PP2A exist in rice genome, and these five genes are ubiquitously expressed in different tissues and stages. Inoculation of R. solani showed that the genome edited pp2a-1 mutants using the CRISPR/Cas9 were more susceptible to ShB than the wild-type control, but other PP2A gene mutants exhibited similar response to ShB compared to wild-type plants. In parallel, PP2A-1 expression level was higher in the activation tagging line, and PP2A-1 overexpression inhibited plant height and promoted the resistance to ShB. PP2A-1-GFP was localized in the cytoplasm and nucleus. In addition, R. solani-dependent induction kinetics of pathogen-related genes PBZ1 and PR1b was lower in pp2a-1 mutants but higher in PP2A-1 activation line compared to those in the wild-type. In conclusion, our analysis shows that PP2A-1 is a member of protein phosphatase, which regulates rice resistance to ShB. This result broadens the understanding of the defense mechanism against ShB and provides a potential target for rice breeding for disease resistance.

Rice blast disease caused by infection with Magnaporthe oryzae, a hemibiotrophic fungal pathogen, significantly reduces the yield production. However, the rice defense mechanism against blast disease remains elusive. To identify the genes involved in the regulation of rice defense to blast disease, dissociation (Ds) transposon tagging mutant lines were analyzed in terms of their response to M. oryzae isolate Guy11. Among them, CBL-interacting protein kinase 31 (CIPK31) mutants were more susceptible than wild-type plants to blast. The CIPK31 transcript was found to be insensitive to Guy11 infection, and the CIPK31-GFP was localized to the cytosol and nucleus. Overexpression of CIPK31 promoted rice defense to blast. Further analysis indicated that CIPK31 interacts with Calcineurin B-like 2 (CBL2) and CBL6 at the plasma membrane, and cbl2 mutants are more susceptible to blast compared with wild-type plants, suggesting that calcium signaling might partially through the CBL2-CIPK31 signaling regulate rice defense. Yeast two-hybrid results showed that AKT1-like (AKT1L), a potential potassium (K+) channel protein, interacted with CIPK31, and the K+ level was significantly lower in the cipk31 mutants than in the wild-type control. In addition, exogenous potassium application increased rice resistance to blast, suggesting that CIPK31 might interact with AKT1L to increase K+ uptake, thereby promoting resistance to blast. Taken together, the results presented here demonstrate that CBL2-CIPK31-AKT1L is a new signaling pathway that regulates rice defense to blast disease.

Tillering is one of the most important determinants of biomass and yield in rice ( Oryza sativa L.). The capacity of plants to develop tillers from primordial meristems or buds is determined not only by the genotype but also by environmental cues. Here, we characterized the function of rice grassy tiller1 ( OsGT1 ) and its interaction with other genetic and biological factors involved in tiller bud outgrowth in rice by generating OsGT1 RNA interference (RNAi) and overexpression (OX) lines. The tiller number was increased in OsGT1 -RNAi mutants but strongly suppressed in OsGT1 -OX lines. Expression analysis of OsGT1 in rice phyB mutants and in genotypes carrying various genetic combinations of GT1 RNAi and phyB demonstrated that OsGT1 is not involved in phyB -mediated suppression of tiller development in rice. Expression analysis of fine culm1 ( fc1 ), a rice tb1 homolog, and molecular assays demonstrated that FC1 enhances the expression of OsGT1 by directly binding to its promoter. Comparison of the transcriptomic profiles of fc1 and OsGT1 -RNAi mutants revealed differentially expressed genes (DEGs) common to both genotypes. Finally, analysis of tillering phenotypes of OX and RNAi seedlings treated with various phytohormones implied a possible role of OsGT1 in strigolactone-mediated tiller outgrowth. Overall, this study enhances our understanding of the diverse mechanisms of tiller development in grasses.

The AMT1 family comprises major ammonium transporters in rice roots. In this study, we utilized AMT1 RNAi mutants ( amt1 ) to explore how AMT1 affects NH 4 + - and NO 3 – -mediated morphological development and NH 4 + -responsive gene expression in roots. In the presence of NH 4 + , amt1 showed inhibition of NO 3 – - dependent lateral root development. The inhibitory action of NH 4 + on lateral root growth was independent of the NO 3 – concentrations supplied to amt1 roots. The results of split root assays indicated that NH 4 + exerts systemic action in inhibiting NO 3 – -dependent lateral root development in amt1 . Further study with NAA and NOA, a potent auxin flux inhibitor, suggested that perturbation of membrane dynamics might not be the primary cause of the inhibitory action of NH 4 + on NO 3 – -mediated lateral root growth in amt1 mutants. RNA-seq analysis of NH 4 + -responsive genes showed that approximately half of DEGs observed in wild-type roots were not detected in the DEGs of amt1 roots. Gene ontology enrichment analysis suggested that the expression of specific functional gene groups were affected by amt1 during the early response to NH 4 + . Auxin-responsive gene expression and root gravity responses were altered in amt1 . This study demonstrated that AMT1 affects the interactions not only between ammonium and nitrate in lateral root growth but also between auxin and NH 4 + in rice roots.

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 N-15 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 (NH4+)-N-15 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.

NH 4 + is an important nitrogen resource for rice plants in paddy soil. Therefore, it is likely that NH 4 + -triggered plant growth interacts with phytohormone-mediated developmental mechanisms. Our previous transcriptomic analysis revealed that many genes involved in auxin signaling and efflux are sensitive to NH 4 + . In the current study, we found that NH 4 + treatment causes a delayed gravity response in rice roots. To further elucidate the interlocking relationship between NH 4 + and auxin signaling during root development, we utilized mutants and overexpressors of a key NH 4 + signaling transcription factor INDETERMINATE DOMAIN 10 ( IDD10 ), encoding a transcription factor that regulates the expression of NH 4 + uptake and N-assimilation genes. We obtained several lines of evidence that auxin affects NH 4 + -mediated gene expression and root development in rice plants via IDD10. First, the gravity response was delayed in idd10 roots and accelerated in IDD10 overexpressor ( IDD10 OX ) roots in the absence and (especially) presence of NH 4 + . Second, idd10 plants showed strong root coiling only in the presence of NH 4 + . However, treatment of 1-N-naphthylphthalamic acid (NPA), a polar auxin transport inhibitor suppressed the NH 4 + -specific root phenotype of idd10 . Third, the expression of NH 4 + -responsive auxin-related genes was affected in idd10 and IDD10 overexpressors. Finally, IDD10 expression was induced by IAA and suppressed by NPA. These findings suggest that the gene expression patterns and phenotypes triggered by NH 4 + are influenced by the actions of auxin during root development, pointing to a regulatory circuit between NH 4 + and auxin signaling that functions in root development in rice.

The SWEET (sugars will eventually be exported transporter) family is a newly characterized group of sugar transporters. In plants, the key roles of SWEETs in phloem transport, nectar secretion, pollen nutrition, stress tolerance, and plant-pathogen interactions have been identified. SWEET family genes have been characterized in many plant species, but a comprehensive analysis of SWEET members has not yet been performed in wheat. Here, 59 wheat SWEETs (hereafter TaSWEETs) were identified through homology searches. Analyses of phylogenetic relationships, numbers of transmembrane helices (TMHs), gene structures, and motifs showed that TaSWEETs carrying 3-7 TMHs could be classified into four clades with 10 different types of motifs. Examination of the expression patterns of 18 SWEET genes revealed that a few are tissue-specific while most are ubiquitously expressed. In addition, the stem rust-mediated expression patterns of SWEET genes were monitored using a stem rust-susceptible cultivar, 'Little Club' (LC). The resulting data showed that the expression of five out of the 18 SWEETs tested was induced following inoculation. In conclusion, we provide the first comprehensive analysis of the wheat SWEET gene family. Information regarding the phylogenetic relationships, gene structures, and expression profiles of SWEET genes in different tissues and following stem rust disease inoculation will be useful in identifying the potential roles of SWEETs in specific developmental and pathogenic processes.

NH4+ is important for the growth and the yield production of paddy-soil grown rice. However, the mechanism of NH4+ signaling is largely unknown. Previously, we performed a microarray analysis to examine genomic responses and signaling pathways in rice roots exposed to NH4+, and interestingly found that transcription of a large number of genes including kinase, phosphatase, and transcription factors were sensitive to NH4+. In this study, we further analyzed transcription factors respond to NH4+, and identified an NH4+-repressed bHLH transcription factor involved in NH4+ acquisition process. bHLH is a nuclear protein and has transcription-activation activity in yeast and plants. RNAi-mediated suppression of bHLH and bHLH overexpression (bHLH OX) resulted in the accumulation of lower and higher NH4+ contents in transgenic rice roots, respectively. NH4+-mediated induction of AMT1;1 and AMT1;2 is lower in bHLH RNAi, but higher in bHLH OX as compared to in wild-type plant roots. However, bHLH does not directly activate AMT1;1 and AMT1;2 transcriptions. IDD10 expression is not altered in bHLH RNAi plant roots, and bHLH maintained similar expression level in idd10 mutant roots compared to in wild-type plant roots. Furthermore, NH4+ contents in idd10;bHLH RNAi double mutant roots were much lower than in each single mutant and wild-type plant roots, indicating that IDD10 and bHLH independently regulates NH4+ uptake. Taken together, these results provide a new regulatory path by which bHLH regulates NH4+ uptake in rice.

Lamina inclination is a key agronomical character that determines plant architecture and is sensitive to auxin and brassinosteroids (BRs). Loose Plant Architecture1 (LPA1) in rice (Oryza sativa) and its Arabidopsis homologues (SGR5/AtIDD15) have been reported to control plant architecture and auxin homeostasis. This study explores the role of LPA1 in determining lamina inclination in rice. LPA1 acts as a positive regulator to suppress lamina bending. Genetic and biochemical data indicate that LPA1 suppresses the auxin signalling that interacts with C-22-hydroxylated and 6-deoxo BRs, which regulates lamina inclination independently of OsBRI1. Mutant lpa1 plants are hypersensitive to indole-3-acetic acid (IAA) during the lamina inclination response, which is suppressed by the brassinazole (Brz) inhibitor of C-22 hydroxylase involved in BR synthesis. A strong synergic effect is detected between lpa1 and d2 (the defective mutant for catalysis of C-23-hydroxylated BRs) during IAA-mediated lamina inclination. No significant interaction between LPA1 and OsBRI1 was identified. The lpa1 mutant is sensitive to C-22-hydroxylated and 6-deoxo BRs in the d61-1 (rice BRI1 mutant) background. We present evidence verifying that two independent pathways function via either BRs or BRI1 to determine IAA-mediated lamina inclination in rice. RNA sequencing analysis and qRT-PCR indicate that LPA1 influences the expression of three OsPIN genes (OsPIN1a, OsPIN1c and OsPIN3a), which suggests that auxin flux might be an important factor in LPA1-mediated lamina inclination in rice.

Nitrogen (N) is the most important macronutrient for plant growth and grain yields. For rice crops, nitrate and ammonium are the major N sources. To explore the genomic responses to ammonium supplements in rice roots, we used 17-day-old seedlings grown in the absence of external N that were then exposed to 0.5mM (NH4)2SO4 for 3h. Transcriptomic profiles were examined by microarray experiments. In all, 634 genes were up-regulated at least two-fold by the N-supplement when compared with expression in roots from untreated control plants. Gene Ontology (GO) enrichment analysis revealed that those upregulated genes are associated with 23 GO terms. Among them, metabolic processes for diverse amino acids (i.e., aspartate, threonine, tryptophan, glutamine, l-phenylalanine, and thiamin) as well as nitrogen compounds are highly over-represented, demonstrating that our selected genes are suitable for studying the N-response in roots. This enrichment analysis also indicated that nitrogen is closely linked to diverse transporter activities by primary metabolites, including proteins (amino acids), lipids, and carbohydrates, and is associated with carbohydrate catabolism and cell wall organization. Integration of results from omics analysis of metabolic pathways and transcriptome data using the MapMan tool suggested that the TCA cycle and pathway for mitochondrial electron transport are co-regulated when rice roots are exposed to ammonium. We also investigated the expression of N-responsive marker genes by performing a comparative analysis with root samples from plants grown under different NH4(+) treatments. The diverse responses to such treatment provide useful insight into the global changes related to the shift from an N-deficiency to an enhanced N-supply in rice, a model crop plant.

Fibrous roots of sweetpotato (Ipomoea batatas (L.) Lam.) usually develop into both pencil and storage roots. To understand protein function in root development, a proteomic analysis was conducted on the pencil and storage roots of the light orange-fleshed sweetpotato cultivar, Yulmi. Two-dimensional gel electrophoresis showed that expression of 30 protein spots differed between pencil and storage roots: 15 proteins were up-regulated or expressed in pencil roots and 15 in storage roots. Differentially expressed proteins spots were investigated using matrix-assisted laser desorption/ionization time of flight mass spectrometry, and 10 proteins from pencil roots were identified as binding protein isoform A, catechol oxidase, peroxidases, ascorbate peroxidase, endochitinase, flavanone 3-hydroxylase and unknown proteins. Of the proteins up-regulated in, or restricted to, storage roots, 13 proteins were identified as protein disulfide isomerase, anionic peroxidase, putative ripening protein, sporamin B, sporamin A and sporamin A precursor. An analysis of enzyme activity revealed that catechol oxidase and peroxidase as the first and last enzymes of the lignin biosynthesis pathway, and ascorbate peroxidase had higher activities in pencil than in storage roots. The total concentration of phenolic compounds was also far higher in pencil than in storage roots, and lignin accumulated only in pencil roots. These results provide important insight into sweetpotato proteomics, and imply that lignin biosynthesis and stress-related proteins are up-regulated or uniquely expressed in pencil roots. The results indicate that the reduction of carbon flow toward phenylpropanoid biosynthesis and its delivery to carbohydrate metabolism is a major event in storage root formation.