Proteomic analysis revealed nitrogen-mediated metabolic, developmental, and hormonal regulation of maize (Zea mays L.) ear growth

Polyamines mediate the inhibitory effect of drought stress on nitrogen reallocation and utilization to regulate grain number in wheat

Drought stress poses a serious threat to grain formation in wheat. Nitrogen (N) plays crucial roles in plant organ development; however, the physiological mechanisms by which drought stress affects plant N availability and mediates the formation of grains in spikes of winter wheat are still unclear. In this study, we determined that pre-reproductive drought stress significantly reduced the number of fertile florets and the number of grains formed. Transcriptome analysis demonstrated that this was related to N metabolism, and in particular, the metabolism pathways of arginine (the main precursor for synthesis of polyamine) and proline. Continuous drought stress restricted plant N accumulation and reallocation rates, and plants preferentially allocated more N to spike development. As the activities of amino acid biosynthesis enzymes and catabolic enzymes were inhibited, more free amino acids accumulated in young spikes. The expression of polyamine synthase genes was down-regulated under drought stress, whilst expression of genes encoding catabolic enzymes was enhanced, resulting in reductions in endogenous spermidine and putrescine. Treatment with exogenous spermidine optimized N allocation in young spikes and leaves, which greatly alleviated the drought-induced reduction in the number of grains per spike. Overall, our results show that pre-reproductive drought stress affects wheat grain numbers by regulating N redistribution and polyamine metabolism.

DIENELACTONE HYDROLASE LIKE PROTEIN1 negatively regulates the KAI2-ligand pathway in Marchantia polymorpha

Karrikins are smoke-derived butenolides that induce seed germination and photomorphogenesis in a wide range of plants.1,2,3 KARRIKIN INSENSITIVE2 (KAI2), a paralog of a strigolactone receptor, perceives karrikins or their metabolized products in Arabidopsis thaliana.4,5,6,7 Furthermore, KAI2 is thought to perceive an unidentified plant hormone, called KAI2 ligand (KL).8,9 KL signal is transduced via the interaction between KAI2, MORE AXILLARY GROWTH2 (MAX2), and SUPPRESSOR of MORE AXILLARY GROWTH2 1 LIKE family proteins (SMXLs), followed by the degradation of SMXLs.4,7,10,11,12,13,14 This signaling pathway is conserved both in A. thaliana and the bryophyte Marchantia polymorpha.14 Although the KL signaling pathway is well characterized, the KL metabolism pathways remain poorly understood. Here, we show that DIENELACTONE HYDROLASE LIKE PROTEIN1 (DLP1) is a negative regulator of the KL pathway in M. polymorpha. The KL signal induces DLP1 expression. DLP1 overexpression lines phenocopied the Mpkai2a and Mpmax2 mutants, while dlp1 mutants phenocopied the Mpsmxl mutants. Mutations in the KL signaling genes largely suppressed these phenotypes, indicating that DLP1 acts upstream of the KL signaling pathway, although DLP1 also has KL pathway-independent functions. DLP1 exhibited enzymatic activity toward a potential substrate, suggesting the possibility that DLP1 works through KL inactivation. Investigation of DLP1 homologs in A. thaliana revealed that they do not play a major role in the KL pathway, suggesting different mechanisms for the KL signal regulation. Our findings provide new insights into the regulation of the KL signal in M. polymorpha and the evolution of the KL pathway in land plants.

Nitrogen-dependent binding of the transcription factor PBF1 contributes to the balance of protein and carbohydrate storage in maize endosperm

Fluctuations in nitrogen (N) availability influence protein and starch levels in maize (Zea mays) seeds, yet the underlying mechanism is not well understood. Here, we report that N limitation impacted the expression of many key genes in N and carbon (C) metabolism in the developing endosperm of maize. Notably, the promoter regions of those genes were enriched for P-box sequences, the binding motif of the transcription factor prolamin-box binding factor 1 (PBF1). Loss of PBF1 altered accumulation of starch and proteins in endosperm. Under different N conditions, PBF1 protein levels remained stable but PBF1 bound different sets of target genes, especially genes related to the biosynthesis and accumulation of N and C storage products. Upon N-starvation, the absence of PBF1 from the promoters of some zein genes coincided with their reduced expression, suggesting that PBF1 promotes zein accumulation in the endosperm. In addition, PBF1 repressed the expression of sugary1 (Su1) and starch branching enzyme 2b (Sbe2b) under normal N supply, suggesting that, under N-deficiency, PBF1 redirects the flow of C skeletons for zein toward the formation of C compounds. Overall, our study demonstrates that PBF1 modulates C and N metabolism during endosperm development in an N-dependent manner.

Identification and Validation of Genomic Regions Associated With Charcoal Rot Resistance in Tropical Maize by Genome-Wide Association and Linkage Mapping

Charcoal rot is a post-flowering stalk rot (PFSR) disease of maize caused by the fungal pathogen, Macrophomina phaseolina. It is a serious concern for smallholder maize cultivation, due to significant yield loss and plant lodging at harvest, and this disease is expected to surge with climate change effects like drought and high soil temperature. For identification and validation of genomic variants associated with charcoal rot resistance, a genome-wide association study (GWAS) was conducted on CIMMYT Asia association mapping panel comprising 396 tropical-adapted lines, especially to Asian environments. The panel was phenotyped for disease severity across two locations with high disease prevalence in India. A subset of 296,497 high-quality SNPs filtered from genotyping by sequencing was correcting for population structure and kinship matrices for single locus mixed linear model (MLM) of GWAS analysis. A total of 19 SNPs were identified to be associated with charcoal rot resistance with P-value ranging from 5.88 × 10^-06 to 4.80 × 10^-05. Haplotype regression analysis identified 21 significant haplotypes for the trait with Bonferroni corrected P ≤ 0.05. For validating the associated variants and identifying novel QTLs, QTL mapping was conducted using two F_2:3 populations. Two QTLs with overlapping physical intervals, qMSR6 and qFMSR6 on chromosome 6, identified from two different mapping populations and contributed by two different resistant parents, were co-located with the SNPs and haplotypes identified at 103.51 Mb on chromosome 6. Similarly, several SNPs/haplotypes identified on chromosomes 3, 6 and 8 were also found to be physically co-located within QTL intervals detected in one of the two mapping populations. The study also noted that several SNPs/haplotypes for resistance to charcoal rot were located within physical intervals of previously reported QTLs for Gibberella stalk rot resistance, which opens up a new possibility for common disease resistance mechanisms for multiple stalk rots.

Cis-regulation of the amino acid transporter genes ZmAAP2 and ZmLHT1 by ZmPHR1 transcription factors in maize ear under phosphate limitation

Phosphorus and nitrogen nutrition have profound and complicated innate connections; however, underlying molecular mechanisms are mostly elusive. PHR1 is a master phosphate signaling component, and whether it directly functions in phosphorus-nitrogen crosstalk remains a particularly interesting question. In maize, nitrogen limitation caused tip kernel abortion and ear shortening. By contrast, moderately low phosphate in the field reduced kernels across the ear, maintained ear elongation and significantly lowered concentrations of total free amino acids and soluble proteins 2 weeks after silking. Transcriptome profiling revealed significant enrichment and overall down-regulation of transport genes in ears under low phosphate. Importantly, 313 out of 847 differentially expressed genes harbored PHR1 binding sequences (P1BS) including those controlling amino acid/polyamine transport and metabolism. Specifically, both ZmAAP2 and ZmLHT1 are plasma membrane-localized broad-spectrum amino acid transporters, and ZmPHR1.1 and ZmPHR1.2 were able to bind to P1BS-containing ZmAAP2 and ZmLHT1 and down-regulate their expression in planta. Taken together, the results suggest that prevalence of P1BS elements enables ZmPHR1s to regulate a large number of low phosphate responsive genes. Further, consistent with reduced accumulation of free amino acids, ZmPHR1s down-regulate ZmAAP2 and ZmLHT1 expression as direct linkers of phosphorus and nitrogen nutrition independent of NIGT1 in maize ear under low phosphate.

The influence of polycyclic aromatic hydrocarbons in protein profile of Medicago sativa L

Medicago sativa L. (alfalfa) are studied as potential phytoremediation agents of priority pollutants like polycyclic aromatic hydrocarbons (PAH). However, elucidation of the biochemical mechanisms involved in phytoremediation is a topic to be explored with knowledge gaps. This study aims to identify and classify proteins expressed in the aerial parts of laboratory-cultivated alfalfa in the presence and absence of pyrene, anthracene, and phenanthrene. Soil samples were amended with 100 mg.kg^-1 of each PAH (total concentration of 300 ppm) and cultivated with alfalfa plants for 20 days. After this, aerial parts of cultivated plants from each condition were collected for qualitative proteomic analysis (ESI-Q/TOF). The results showed a significant increase (Student's t-test p < 0.05) of 41.7% in the concentration of proteins from plants grown in PAH-amended substrates, changes in the protein profile, with intense protein bands observed at 40-55, 34, 28, and 15 kDa when compared to the control. A total of 504 proteins were identified and classified into 12 functional categories, highlighting the identification of 11 phytoremediation-related proteins candidates in plants grown in the presence of PAH, with biological functions related to diverse metabolisms involved in the xenobiotics biodegradation (included PAH), glutathione and response to stress.

ZmCCD10a Encodes a Distinct Type of Carotenoid Cleavage Dioxygenase and Enhances Plant Tolerance to Low Phosphate

Carotenoid cleavage dioxygenases (CCDs) drive carotenoid catabolism to produce various apocarotenoids and immediate derivatives with particular developmental, ecological, and agricultural importance. How CCD genes evolved with species diversification and the resulting functional novelties in cereal crops have remained largely elusive. We constructed a unified four-clade phylogenetic tree of CCDs, revealing a previously unanchored basal clade CCD10 CCD10 underwent highly dynamic duplication or loss events, even in the grass family. Different from cleavage sites of CCD8 and ZAXINONE SYNTHASE (ZAS), maize (Zea mays) ZmCCD10a cleaved differentially structured carotenoids at 5, 6 (5', 6') and 9, 10 (9', 10') positions, generating C8 (6-methyl-5-hepten-2-one) and C13 (geranylacetone, α-ionone, and β-ionone) apocarotenoids in Escherichia coli Localized in plastids, ZmCCD10a cleaved neoxanthin, violaxanthin, antheraxathin, lutein, zeaxanthin, and β-carotene in planta, corroborating functional divergence of ZmCCD10a and ZAS. ZmCCD10a expression was dramatically stimulated in maize and teosinte (Z. mays ssp. parviglumis, Z. mays ssp. huehuetenangensis, Zea luxurians, and Zea diploperennis) roots by phosphate (Pi) limitation. ZmCCD10a silencing favored phosphorus retention in the root and reduced phosphorus and biomass accumulation in the shoot under low Pi. Overexpression of ZmCCD10a in Arabidopsis (Arabidopsis thaliana) enhanced plant tolerance to Pi limitation by preferential phosphorus allocation to the shoot. Thus, ZmCCD10a encodes a unique CCD facilitating plant tolerance to Pi limitation. Additionally, ZmCCD10a silencing and overexpression led to coherent alterations in expression of PHOSPHATE STARVATION RESPONSE REGULATOR 1 (PHR1) and Pi transporters, and cis-regulation of ZmCCD10a expression by ZmPHR1;1 and ZmPHR1;2 implies a probable ZmCCD10a-involved regulatory pathway that adjusts Pi allocation.

Warming and elevated CO2 alter the transcriptomic response of maize (Zea mays L.) at the silking stage

Exploring the transcriptome of crops in response to warming and elevated CO₂ (eCO₂) is important to gaining insights of botanical adaption and feedback to climate change. This study deployed Illumina sequencing technology to characterize transcriptomic profile of maize plants at the silking stage, which were grown under warming (2 °C higher than ambient temperature) and eCO₂ (550 ppm) conditions. The treatment of ambient temperature and ambient CO₂ concentration was considered as control (CK). Warming, eCO₂ and warming plus eCO₂ resulted in 2732, 1966 and 271 genes expressing differently (DEGs) compared to the CK, respectively. Among the DEGs, 48, 47 and 36 gene ontology (GO) terms were enriched in response to warming, eCO₂ and warming plus eCO₂ compared to the CK, respectively. The majority of genes were assigned to the biological process category and the cellular component category. Elevated CO₂ significantly inhibited gene expressions in terms of photosynthesis and carbohydrate biosynthesis pathways. Warming not only negatively affected expressions of these genes, but also secondary pathways of nitrogen (N) metabolism, including key enzymes of GST30, GST7, GST26, GST15, GLUL and glnA. These results indicated the negative biochemical regulation and physiological functions in maize in response to warming and eCO₂, highlighting the necessity to improve the genetic adaptability of plant to future climate change.

Role of brassinosteroids in rice spikelet differentiation and degeneration under soil-drying during panicle development

BACKGROUND

Brassinosteroids (BRs) are a new group of plant hormones and play important roles in plant growth and development. However, little information is available if BRs could regulate spikelet development in rice (Oryza sativa L.) especially under soil-drying conditions. This study investigated whether and how BRs mediate the effect of soil-drying on spikelet differentiation and degeneration in rice. A rice cultivar was field-grown and exposed to three soil moisture treatments during panicle development, that is, well-watered (WW), moderate soil-drying (MD) and severe soil-drying (SD).

RESULTS

Compared with the WW treatment, the MD treatment enhanced BRs biosynthesis in young panicles, increased spikelet differentiation and reduced spikelet degeneration. The SD treatment had the opposite effects. Changes in expression levels of key rice inflorescence development genes (OsAPO2 and OsTAW1), ascorbic acid (AsA) content, and activities of enzymes involved AsA synthesis and recycle, and amount of nonstructural carbohydrates (NSC) in young panicles were consistent with those in BRs levels, whereas hydrogen peroxide (H₂O₂) content showed opposite trend. Knockdown of the BRs synthesis gene OsD11 or application of a BRs biosynthesis inhibitor to young panicles markedly decreased OsAPO2 and OsTAW1 expression levels, BRs and AsA contents, activities of enzymes involved AsA synthesis and recycle, NSC amount in rice panicles and spikelet differentiation but increased the H₂O₂ content and spikelet degeneration compared to the control (the wide type or application of water). The opposite effects were observed when exogenous BRs were applied.

CONCLUSIONS

The results suggest that BRs mediate the effect of soil-drying on spikelet differentiation and degeneration, and elevated BRs levels in rice panicles promote spikelet development under MD by enhancing inflorescence meristem activity, AsA recycle and NSC partitioning to the growing panicles.

Brassinosteroids function in spikelet differentiation and degeneration in rice

Brassinosteroids (BRs) play crucial roles in many aspects of plant development. However, their function in spikelet differentiation and degeneration in rice (Oryza sativa L.) remains unclear. Here, we investigated the roles of these phytohormones in spikelet development in field-grown rice subjected to five different nitrogen (N) fertilization treatments during panicle differentiation. BR levels and expression of genes involved in BR biosynthesis and signal transduction were measured in spikelets. Pollen fertility and the number of differentiated spikelets were closely associated with 24-epicastasterone (24-epiCS) and 28-homobrassinolide (28-homoBL) levels in spikelets. Enhanced BR biosynthesis and signal transduction, in response to N treatment, enhanced spikelet differentiation, reduced spikelet degeneration, and increased grain yield. Increases in proton-pumping ATPase activity, ATP concentration, energy charge, and antioxidant system (AOS) levels were consistent with 24-epiCS and 28-homoBL concentrations. Exogenous application of 24-epiCS or 28-homoBL on young panicles induced a marked increase in endogenous 24-epiCS or 28-homoBL levels, energy charge, AOS levels, spikelet differentiation, and panicle weight. The opposite effects were observed following treatment with a BR biosynthesis inhibitor. Our findings indicate that, in rice, BRs mediate the effects of N fertilization on spikelet development and play a role in promoting spikelet development through increasing AOS levels and energy charge during panicle development.

Nitrogen Fertilizer Induced Alterations in The Root Proteome of Two Rice Cultivars

Nitrogen (N) is an essential nutrient for plants and a key limiting factor of crop production. However, excessive application of N fertilizers and the low nitrogen use efficiency (NUE) have brought in severe damage to the environment. Therefore, improving NUE is urgent and critical for the reductions of N fertilizer pollution and production cost. In the present study, we investigated the effects of N nutrition on the growth and yield of the two rice (Oryza sativa L.) cultivars, conventional rice Huanghuazhan and indica hybrid rice Quanliangyou 681, which were grown at three levels of N fertilizer (including 135, 180 and 225 kg/hm², labeled as N9, N12, N15, respectively). Then, a proteomic approach was employed in the roots of the two rice cultivars treated with N fertilizer at the level of N15. A total of 6728 proteins were identified, among which 6093 proteins were quantified, and 511 differentially expressed proteins were found in the two rice cultivars after N fertilizer treatment. These differentially expressed proteins were mainly involved in ammonium assimilation, amino acid metabolism, carbohydrate metabolism, lipid metabolism, signal transduction, energy production/regulation, material transport, and stress/defense response. Together, this study provides new insights into the regulatory mechanism of nitrogen fertilization in cereal crops.

Comparative Proteomic Analysis Unveils Critical Pathways Underlying the Role of Nitrogen Fertilizer Treatment in American Elderberry

American elderberry (Sambucus nigra subsp. canadensis) is a rapidly growing specialty crop in Missouri and eastern North America. Nitrogen (N) is a major nutrient involved in plant growth and development. However, proteome changes for different genotypes of elder in response to varying levels of N-treatment remain undefined. To reveal plant responses to N, comparative proteomic analyses were performed to determine consistent changes in three genotypes of elderberry leaves (Adams II, Bob Gordon and Wyldewood) grown under different N-fertilizer treatments. 165 proteins separated by two dimensional gel electrophoresis showed significant differences in abundance (p < 0.05 and greater than 2-fold). Principal component analysis of the abundance profiles of these proteins revealed Bob Gordon as a distinct genotype. The 165 proteins were identified by mass spectrometry and showed similar functional distributions in these genotypes underlying the N-treatment. Among the proteins identified, 23 are mainly involved in photosynthesis, protein metabolism and redox homeostasis. Their abundance profiles were not altered upon exposure to N or genotype. These results provide novel insights into plant responses to fertilizer treatment at the proteome level and could lead to a better understanding of molecular mechanisms of elderberry growth.

2D-DIGE comparative proteomic analysis of developing wheat grains under high-nitrogen fertilization revealed key differentially accumulated proteins that promote storage protein and starch biosyntheses

Nitrogen (N) serves as a macronutrient that is essential to plant growth and development, and significantly influences storage protein and starch biosyntheses and, ultimately, grain yield and quality. In this study, we performed the first comparative proteomic analysis of developing wheat grains under high-N conditions using 2D-DIGE and tandem mass spectrometry. High-N fertilizer application caused significant increases in ear number, ear grain number, and grain yield. 2D-DIGE identified 142 differentially accumulated proteins (DAPs) during grain development in the elite Chinese bread wheat cultivar Zhongmai 175, of which 132 (93%) were identified by MALDI-TOF/TOF-MS, representing 92 unique proteins. These proteins are involved mainly in energy, N and protein metabolism, carbon metabolism, and starch biosynthesis. Subcellular localization prediction and fluorescence confocal microscopic analysis showed that the DAPs identified were localized mainly in the cytosol and chloroplast. Principal component analysis (PCA) revealed a greater proteomic difference among grain developmental periods than between the high-N and control groups. Protein-protein interaction analysis highlighted a complex network centered around enzymes involved in energy, N and protein metabolism, and starch biosynthesis. Six key DAP genes showed expression patterns consistent with their protein accumulation trends during grain development. A putative metabolic pathway was proposed, with synergistic regulatory networks of grain storage protein and starch biosyntheses in response to high-N application.

Comparative shoot proteome analysis of two potato (Solanum tuberosum L.) genotypes contrasting in nitrogen deficiency responses in vitro

Aiming at a better understanding of the physiological and biochemical background of nitrogen use efficiency, alterations in the shoot proteome under N-deficiency were investigated in two contrasting potato genotypes grown in vitro with 60 and 7.5mM N, respectively. A gel based proteomic approach was applied to identify candidate proteins associated with genotype specific responses to N-deficiency. 21% of the detected proteins differed in abundance between the two genotypes. Between control and N-deficiency conditions 19.5% were differentially accumulated in the sensitive and 15% in the tolerant genotype. 93% of the highly N-deficiency responsive proteins were identified by MALDI TOF/TOF mass spectrometry. The major part was associated with photosynthesis, carbohydrate metabolism, stress response and regulation. Differential accumulation of enzymes involved in the Calvin cycle and glycolysis suggest activation of alternative carbohydrate pathways. In the tolerant genotype, increased abundance under N-deficiency was also found for enzymes involved in chlorophyll synthesis and stability of enzymes, which increase photosynthetic carbon fixation efficiency. Out of a total of 106 differentially abundant proteins, only eight were detected in both genotypes. Our findings suggest that mutually responsive proteins reflect universal stress responses while adaptation to N-deficiency in metabolic pathways is more genotype specific.

SIGNIFICANCE

Nitrogen losses from arable farm land considerably contribute to environmental pollution. In potato, this is a special problem due cultivation on light soils, irrigation and the shallow root system. Therefore, breeding of cultivars with improved nitrogen use efficiency and stable yields under reduced N fertilization is an important issue. Knowledge of genotype dependent adaptation to N-deficiency at the proteome level can help to understand regulation of N efficiency and development of N-efficient cultivars.

Aberrant Meiotic Modulation Partially Contributes to the Lower Germination Rate of Pollen Grains in Maize (Zea mays L.) Under Low Nitrogen Supply

Pollen germination is an essential step towards successful pollination during maize reproduction. How low niutrogen (N) affects pollen germination remains an interesting biological question to be addressed. We found that only low N resulted in a significantly lower germination rate of pollen grains after 4 weeks of low N, phosphorus or potassium treatment in maize production. Importantly, cytological analysis showed 7-fold more micronuclei in male meiocytes under the low N treatment than in the control, indicating that the lower germination rate of pollen grains was partially due to numerous chromosome loss events resulting from preceding meiosis. The appearance of 10 bivalents in the control and low N cells at diakinesis suggested that chromosome pairing and recombination in meiosis I was not affected by low N. Further gene expression analysis revealed dramatic down-regulation of Nuclear Division Cycle 80 (Ndc80) and Regulator of Chromosome Condensation 1 (Rcc1-1) expression and up-regulation of Cell Division Cycle 20 (Cdc20-1) expression, although no significant difference in the expression level of kinetochore foundation proteins Centromeric Histone H3 (Cenh3) and Centromere Protein C (Cenpc) and cohesion regulators Recombination 8 (Rec8) and Shugoshin (Sgo1) was observed. Aberrant modulation of three key meiotic regulators presumably resulted in a high likelihood of erroneous chromosome segregation, as testified by pronounced lagging chromosomes at anaphase I or cell cycle disruption at meiosis II. Thus, we proposed a cytogenetic mechanism whereby low N affects male meiosis and causes a higher chromosome loss frequency and eventually a lower germination rate of pollen grains in a staple crop plant.

Down-regulation of nitrogen/carbon metabolism coupled with coordinative hormone modulation contributes to developmental inhibition of the maize ear under nitrogen limitation

Developmental inhibition of the maize ear by nitrogen limitation is due to overall down-regulation of nitrogen/carbon metabolism, coordinative hormonal modulation, and probable early senescence. The kernel number is primarily determined from 2 weeks pre-silking to 3 weeks post-silking, largely depending on dynamic nitrogen (N) and carbohydrate metabolism and accumulation in the maize ear. Underlying physiological and molecular mechanisms of kernel abortion caused by N limitation needs to be further investigated. Using a widely grown maize hybrid ZD958, we found that the N deficient ear was shorter, with less biomass accumulation, lower N concentrations, and overall lower concentrations of N assimilates and soluble sugars at 1- or 2-week after silking. Such negative alterations were probably due to significant decreases in activities of nitrate reductase, glutamine synthetase, sucrose phosphate synthetase, and sucrose synthetase in the N deficient maize ear especially after silking. Compensatory up-regulation of corresponding gene expression, together with co-downregulation of gene expression and enzyme activities in certain circumstances, suggested regulatory complexity and mechanistic differentiation from gene expression to functioning at physiological and molecular levels in quickly developing maize ear in counteracting N deficiency. Importantly, auxin, gibberellin, cytokinin, and abscisic acid may act in a coordinative manner to negatively modulate ear development under N limitation, as indicated by their concentration variations and substantial up-regulation of IAA14, GA2-ox1, and CKX12. Lastly, early senescence may occur in the low-N ear driven by interplay of hormone functioning and senescence-related gene regulation.

Down-regulation of nitrogen/carbon metabolism coupled with coordinative hormone modulation contributes to developmental inhibition of the maize ear under nitrogen limitation

Developmental inhibition of the maize ear by nitrogen limitation is due to overall down-regulation of nitrogen/carbon metabolism, coordinative hormonal modulation, and probable early senescence. The kernel number is primarily determined from 2 weeks pre-silking to 3 weeks post-silking, largely depending on dynamic nitrogen (N) and carbohydrate metabolism and accumulation in the maize ear. Underlying physiological and molecular mechanisms of kernel abortion caused by N limitation needs to be further investigated. Using a widely grown maize hybrid ZD958, we found that the N deficient ear was shorter, with less biomass accumulation, lower N concentrations, and overall lower concentrations of N assimilates and soluble sugars at 1- or 2-week after silking. Such negative alterations were probably due to significant decreases in activities of nitrate reductase, glutamine synthetase, sucrose phosphate synthetase, and sucrose synthetase in the N deficient maize ear especially after silking. Compensatory up-regulation of corresponding gene expression, together with co-downregulation of gene expression and enzyme activities in certain circumstances, suggested regulatory complexity and mechanistic differentiation from gene expression to functioning at physiological and molecular levels in quickly developing maize ear in counteracting N deficiency. Importantly, auxin, gibberellin, cytokinin, and abscisic acid may act in a coordinative manner to negatively modulate ear development under N limitation, as indicated by their concentration variations and substantial up-regulation of IAA14, GA2-ox1, and CKX12. Lastly, early senescence may occur in the low-N ear driven by interplay of hormone functioning and senescence-related gene regulation.

ZmCCD7/ZpCCD7 encodes a carotenoid cleavage dioxygenase mediating shoot branching

ZmCCD7/ZpCCD7 encodes a carotenoid cleavage dioxygenase that may mediate strigolactone biosynthesis highly responsive to phosphorus deficiency and undergoes negative selection over domestication from Zea ssp. parviglumis to Zea mays. Carotenoid cleavage dioxygenase 7 (CCD7) functions to suppress shoot branching by controlling strigolactone biosynthesis. However, little is known about CCD7 and its functions in maize and its ancestor (Zea ssp. parviglumis) with numerous shoot branches. We found that ZmCCD7 and ZpCCD7 had the same coding sequence, indicating negative selection of the CCD7 gene over domestication from Zea ssp. parviglumis to Zea mays. CCD7 expression was highly responsive to phosphorus deficiency in both species, especially in the meristematic zone and the pericycle of the elongation zone of maize roots. Notably, the crown root had the strongest ZmCCD7 expression in the meristematic zone under phosphorus limitation. Transient expression of GFP tagged ZmCCD7/ZpCCD7 in maize protoplasts indicated their localization in the plastid. Further, ZmCCD7/ZpCCD7 efficiently catalyzed metabolism of six different linear and cyclic carotenoids in E. coli, and generated β-ionone by cleaving β-carotene at the 9,10 (9',10') position. Together with suppression of shoot branching in the max3 mutant by transformation of ZmCCD7/ZpCCD7, our work suggested that ZmCCD7/ZpCCD7 encodes a carotenoid cleavage dioxygenase mediating strigolactone biosynthesis in maize and its ancestor.

ZmCCD7/ZpCCD7 encodes a carotenoid cleavage dioxygenase mediating shoot branching

ZmCCD7/ZpCCD7 encodes a carotenoid cleavage dioxygenase that may mediate strigolactone biosynthesis highly responsive to phosphorus deficiency and undergoes negative selection over domestication from Zea ssp. parviglumis to Zea mays. Carotenoid cleavage dioxygenase 7 (CCD7) functions to suppress shoot branching by controlling strigolactone biosynthesis. However, little is known about CCD7 and its functions in maize and its ancestor (Zea ssp. parviglumis) with numerous shoot branches. We found that ZmCCD7 and ZpCCD7 had the same coding sequence, indicating negative selection of the CCD7 gene over domestication from Zea ssp. parviglumis to Zea mays. CCD7 expression was highly responsive to phosphorus deficiency in both species, especially in the meristematic zone and the pericycle of the elongation zone of maize roots. Notably, the crown root had the strongest ZmCCD7 expression in the meristematic zone under phosphorus limitation. Transient expression of GFP tagged ZmCCD7/ZpCCD7 in maize protoplasts indicated their localization in the plastid. Further, ZmCCD7/ZpCCD7 efficiently catalyzed metabolism of six different linear and cyclic carotenoids in E. coli, and generated β-ionone by cleaving β-carotene at the 9,10 (9',10') position. Together with suppression of shoot branching in the max3 mutant by transformation of ZmCCD7/ZpCCD7, our work suggested that ZmCCD7/ZpCCD7 encodes a carotenoid cleavage dioxygenase mediating strigolactone biosynthesis in maize and its ancestor.

Using RNA-seq to Profile Gene Expression of Spikelet Development in Response to Temperature and Nitrogen during Meiosis in Rice (Oryza sativa L.)

Rice reproductive development is sensitive to high temperature and soil nitrogen supply, both of which are predicted to be increased threats to rice crop yield. Rice spikelet development is a critical process that determines yield, yet little is known about the transcriptional regulation of rice spikelet development in response to the combination of heat stress and low nitrogen availability. Here, we profiled gene expression of rice spikelet development during meiosis under heat stress and different nitrogen levels using RNA-seq. We subjected plants to four treatments: 1) NN: normal nitrogen level (165 kg ha^-1) with normal temperature (30°C); 2) HH: high nitrogen level (264 kg ha^-1) with high temperature (37°C); 3) NH: normal nitrogen level and high temperature; and 4) HN: high nitrogen level and normal temperature. The de novo transcriptome assembly resulted in 52,250,482 clean reads aligned with 76,103 unigenes, which were then used to compare differentially expressed genes (DEGs) in the different treatments. Comparing gene expression in samples with the same nitrogen levels but different temperatures, we identified 70 temperature-responsive DEGs in normal nitrogen levels (NN vs NH) and 135 DEGs in high nitrogen levels (HN vs HH), with 27 overlapping DEGs. We identified 17 and seven nitrogen-responsive DEGs by comparing changes in nitrogen levels in lower temperature (NN vs HN) and higher temperature (NH vs HH), with one common DEG. The temperature-responsive genes were principally associated with cytochrome, heat shock protein, peroxidase, and ubiquitin, while the nitrogen-responsive genes were mainly involved in glutamine synthetase, amino acid transporter, pollen development, and plant hormone. Rice spikelet fertility was significantly reduced under high temperature, but less reduced under high-nitrogen treatment. In the high temperature treatments, we observed downregulation of genes involved in spikelet development, such as pollen tube growth, pollen maturation, especially sporopollenin biosynthetic process, and pollen exine formation. Moreover, we observed higher expression levels of the co-expressed DEGs in HN vs HH compared to NN vs NH. These included the six downregulated genes (one pollen maturation and five pollen exine formation genes), as well as the four upregulated DEGs in response to heat. This suggests that high-nitrogen treatment may enhance the gene expression levels to mitigate aspects of heat-stress. The spikelet genes identified in this study may play important roles in response to the combined effects of high temperature and high nitrogen, and may serve as candidates for crop improvement.

RNA-seq reveals differentially expressed genes of rice (Oryza sativa) spikelet in response to temperature interacting with nitrogen at meiosis stage

Background

Rice (Oryza sativa) is one of the most important cereal crops, providing food for more than half of the world’s population. However, grain yields are challenged by various abiotic stresses such as drought, fertilizer, heat, and their interaction. Rice at reproductive stage is much more sensitive to environmental temperatures, and little is known about molecular mechanisms of rice spikelet in response to high temperature interacting with nitrogen (N).

Results

Here we reported the transcriptional profiling analysis of rice spikelet at meiosis stage using RNA sequencing (RNA-seq) as an attempt to gain insights into molecular events associated with temperature and nitrogen. This study received four treatments: 1) NN: normal nitrogen level (165 kg ha⁻¹) with natural temperature (30 °C); 2) HH: high nitrogen level (330 kg ha⁻¹) with high temperature (37 °C); 3) NH: normal nitrogen level and high temperature; and 4) HN: high nitrogen level and natural temperature, respectively. The de novo assembly generated 52,553,536 clean reads aligned with 72,667 unigenes. About 10 M reads were identified from each treatment. In these differentially expressed genes (DEGs), we found 151 and 323 temperature-responsive DEGs in NN-vs-NH and HN-vs-HH, and 114 DEGs were co-expressed. Meanwhile, 203 and 144 nitrogen-responsive DEGs were focused in NN-vs-HN and NH-vs-HH, and 111 DEGs were co-expressed. The temperature-responsive genes were principally associated with calcium-dependent protein, cytochrome, flavonoid, heat shock protein, peroxidase, ubiquitin, and transcription factor while the nitrogen-responsive genes were mainly involved in glutamine synthetase, transcription factor, anthocyanin, amino acid transporter, leucine zipper protein, and hormone. It is noted that, rice spikelet fertility was significantly decreased under high temperature, but it was more reduced under higher nitrogen. Accordingly, numerous spikelet genes involved in pollen development, pollen tube growth, pollen germination, especially sporopollenin biosynthetic process, and pollen exine formation were mainly down-regulated under high temperature. Moreover, the expression levels of co-expressed DEGs including 5 sporopollenin biosynthetic process and 7 pollen exine formation genes of NN-vs-NH were lower than that of HN-vs-HH. Therefore, these spikelet genes may play important roles in response to high temperature with high nitrogen and may be good candidates for crop improvement.

Conclusions

This RNA-seq study will help elucidate the molecular mechanisms of rice spikelet defense response to high temperature interacting with high nitrogen level.

Electronic supplementary material

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Asymmetric transcriptomic signatures between the cob and florets in the maize ear under optimal- and low-nitrogen conditions at silking, and functional characterization of amino acid transporters ZmAAP4 and ZmVAAT3

Coordinated functioning of the cob and florets of the maize ear confers grain yield. The cob is critical for carbon partitioning and assimilated nitrogen (N) supply for grain development. However, molecular recognition of the cob and peripheral florets, characterization of genes mediating translocation of N assimilates, and responses of these two tissues to low N (LN) remain elusive. Transcriptional profiling of the ear of a maize hybrid at silking in the field revealed 1864 differentially expressed genes between the cob and florets, with 1314 genes up-regulated in the cob and 550 genes up-regulated in florets. The cob was characterized by striking enrichment of genes that are involved in carbon/N transport and metabolism, consistent with the physiological role of the cob in carbon/N storage and transfer during ear development. The florets were characterized by enrichment of hormone signalling components and development related genes. We next examined the response of the cob and florets to LN stress. LN caused differential expression of 588 genes in the cob and only 195 genes in the florets, indicating that the cob dominated the response of the ear to LN at the transcriptional level. LN caused comprehensive alterations such as carbon/N metabolism or partitioning, hormone signalling and protein phosphorylation in terms of gene expression in the cob and/or florets. Fourteen genes responsive specifically to LN provided potential molecular markers for N-efficient maize breeding. We further functionally characterized two newly identified broad-spectrum amino acid transporters, ZmAAP4 and ZmVAAT3, that showed distinct expression patterns in the cob and florets and potentially important roles in amino-N mobilization in the ear. While both proteins could transport various amino acids into yeast or Arabidopsis cells, ZmAAP4 appeared to have higher efficiencies than ZmVAAT3 in transporting seven out of 22 examined amino acids.

ZD958 is a low-nitrogen-efficient maize hybrid at the seedling stage among five maize and two teosinte lines

ZD958 was the most low-N-efficient line among five maize and two teosinte lines. Zea parviglumis and Zea diploperennis were insensitive to N limitation. Maize and teosinte genetically and evolutionarily diverged in gene regulation. GDH2, ASN2, and T4 were consistently down-regulated across seven lines. Maternal asymmetric inheritance and heterosis vigor made ZD958 low-N-efficient. Nitrogen (N) deficiency remains a serious limiting factor for maize production in many developing countries. It is particularly important to better understand how hybrid maize responds to N limitation. ZD958, a dominant high-yield hybrid in North China, was comparatively analyzed with four other maize and two teosinte lines at physiological and transcriptional levels. ZD958 was the most low-N-efficient line among five maize and two teosinte lines due to its largest biomass accumulation at a lowest N concentration under N limitation; while Zea parviglumis and Zea diploperennis had large root systems and were insensitive to N limitation. In anti-parallel with down-regulation of N metabolic genes in the ZD958 root, carbon allocation towards the root was enhanced for the significant increase in the root length. Variations in expression patterns of ten genes mediating N uptake, transport, and metabolism indicated large genetic and evolutionary divergence among seven lines under N limitation. Notably, GDH2, ASN2, and VAAT5 were consistently down-regulated under N limitation across these maize and teosinte lines, suggesting essential evolutionary conservation of gene regulation in response to N limitation and providing molecular markers for N nutritional diagnosis. Asymmetric inheritance, mostly from its maternal donor Z58, and heterosis vigor made ZD958 low-N-efficient at the seedling stage. The superior traits in crown roots in ZD958 may be derived from its paternal donor Chang7-2. Thus, Z58, Chang7-2, and two wild maize lines (Z. parviglumis and Z. diploperennis) provide valuable germplasms for N-efficient and large-root maize breeding.

Nitrate Starvation Induced Changes in Root System Architecture, Carbon:Nitrogen Metabolism, and miRNA Expression in Nitrogen-Responsive Wheat Genotypes

Improvement of nutrient use efficiency in cereal crops is highly essential not only to reduce the cost of cultivation but also to save the environmental pollution, reduce energy consumption for production of these chemical fertilizers, improve soil health, and ultimately help in mitigating climate change. In the present investigation, we have studied the morphological (with special emphasis on root system architecture) and biochemical responses (in terms of assay of the key enzymes involved in N assimilation) of two N-responsive wheat genotypes, at the seedling stage, under nitrate-optimum and nitrate-starved conditions grown in hydroponics. Expression profile of a few known wheat micro RNAs (miRNAs) was also studied in the root tissue. Total root size, primary root length, and first- and second-order lateral root numbers responded significantly under nitrate-starved condition. Morphological parameters in terms of root and shoot length and fresh and dry weight of roots and shoots have also been observed to be significant between N-optimum and N-starved condition for each genotypes. Nitrate reductase (NR), glutamine synthatase (GS), and glutamate dehydrogenase (GDH) activity significantly decreased under N-starved condition. Glutamine oxoglutarate amino transferase (GOGAT) and pyruvate kinase (PK) activity was found to be genotype dependent. Most of the selected miRNAs were expressed in root tissues, and some of them showed their differential N-responsive expression. Our studies indicate that one of the N-responsive genotype (NP-890) did not get affected significantly under nitrogen starvation at seedling stage.

Exploration of novel rhizospheric yeast isolate as fertilizing soil inoculant for improvement of maize cultivation

BACKGROUND

Chemical input in agriculture is a common practice but makes a serious impact to the environment. In this context, soil isolates having multiple plant growth-promoting (PGP) attributes have been studied. The isolates were tested for their PO4 and Zn solubilization, indole-3-acetic acid (IAA) production and N2 fixation ability. The selected isolate SSm-39 was characterized to molecular level. The isolate SSm-39 was applied to maize cultivation in various combinations with chemical fertilizers. Also, the chemical and microbial status of soil, its effect on maize growth and yield were investigated.

RESULTS

Isolate SSm-39 found most suitable for its PGP attributes and identified as Candida tropicalis. The inoculant (100%) with reduced dose of chemical fertilizer (T5) application notably increased the growth and yield performance of maize. It has improved grain quality by 85% as indicated by carbohydrate and protein content, in comparison to uninoculated control (T3). Soil nutrient status was found to increase twofold with T5 treatment compared with T3 treatment. Enhanced soil nutrient quality supported microbial growth and diversity, thus accelerating soil enzymatic activities.

CONCLUSION

The results validate the multiple PGP traits of C. tropicalis SSm-39, advocating reduction of chemical fertilizer for maize cultivation.

Nitrogen stress-induced alterations in the leaf proteome of two wheat varieties grown at different nitrogen levels

Inorganic nitrogen (N) is a key limiting factor of the agricultural productivity. Nitrogen utilization efficiency has significant impact on crop growth and yield as well as on the reduction in production cost. The excessive nitrogen application is accompanied with severe negative impact on environment. Thus to reduce the environmental contamination, improving NUE is need of an hour. In our study we have deployed comparative proteome analysis using 2-DE to investigate the effect of the nitrogen nutrition on differential expression pattern of leaf proteins in low-N sensitive and low-N tolerant wheat (Triticum aestivum L.) varieties. Results showed a comprehensive picture of the post-transcriptional response to different nitrogen regimes administered which would be expected to serve as a basic platform for further characterization of gene function and regulation. We detected proteins related to photosynthesis, glycolysis, nitrogen metabolism, sulphur metabolism and defence. Our results provide new insights towards the altered protein pattern in response to N stress. Through this study we suggest that genes functioning in many physiological events coordinate the response to availability of nitrogen and also for the improvement of NUE of crops.

Discovery and confirmation of genes/proteins associated with maize aflatoxin resistance

Maize (Zea mays L.) is one of the major crops susceptible to Aspergillus flavus infection and subsequent aflatoxin contamination. Many earlier studies indicated the roles of kernel proteins, especially constitutively expressed proteins, in maize resistance to A. flavus infection and aflatoxin production. In this review, we examined the past and current efforts in identifying maize genes and proteins from kernel, rachis, and silk tissues that may play an important role in resistance to A. flavus infection and aflatoxin contamination, as well as the efforts in determining the importance or involvement of them in maize resistance through biochemical, molecular and genetics studies. Through these studies, we gained a better understanding of host resistance mechanism: resistant lines appear to either express some stress-related and antifungal proteins at higher levels in endosperm, embryo, rachis and silk tissues before A. flavus infection or induce the expression of these proteins much faster compared to susceptible maize lines. In addition, we summarised several recent efforts in enhancing maize resistance to aflatoxin contamination using native genes from maize or heterologous and synthetic genes from other sources as well as from A. flavus. These efforts to either suppress A. flavus growth or aflatoxin production, have all shown some promising preliminary success. For example, maize plants transformed with an ?-amylase inhibitor protein from Lablab purpurea showed reduced aflatoxin levels by 56% in kernel screening assays. The antifungal potentials of transgenic maize plants expressing synthetic lytic peptides, such as cecropin-based D4E1 or tachyplesin-based AGM peptides with demonstrated anti-flavus activity (IC50 = 2.5 to 10 ?M), are yet to be assayed. Further investigation in these areas may provide a more cost-effective alternative to biocontrol in managing aflatoxin contamination in maize and other susceptible crops.

Manipulation of microRNA expression to improve nitrogen use efficiency

Nitrogen is the key limiting nutrient required for plant growth. The application of nitrogen-based fertilizers to crops has risen dramatically in recent years, resulting in significant yield increases. However, increased production has come at the cost of substantial negative environmental consequences. Higher crop production costs, increased consumption of food and fertilizer, and a growing global population have led to calls for a "second green revolution" using modern genetic manipulation techniques to improve the production, yield, and quality of crops. Considerable research is being directed toward the study and engineering of nitrogen use efficiency in crop plants. The end goal is to reduce the amount of nitrogen-based fertilizer used and thereby reduce production costs and environmental damage while increasing yields. In this review, we present an overview of recent advances in understanding the regulation of nitrogen metabolism by the action of microRNAs with a view toward engineering crops with increased nitrogen use efficiency.

Apoplastic infusion of sucrose into stem internodes during female flowering does not increase grain yield in maize plants grown under nitrogen-limiting conditions

Nitrogen (N) limitation reduces leaf growth and photosynthetic rates of maize (Zea mays), and constrains photosynthate translocation to developing ears. Additionally, the period from about 1 week before to 2 weeks after silking is critical for establishing the reproductive sink capacity necessary to attain maximum yield. To investigate the influence of carbohydrate availability in plants of differing N status, a greenhouse study was performed in which exogenous sucrose (Suc) was infused around the time of silking into maize stems grown under different N regimes. N deficiency significantly reduced leaf area, leaf longevity, leaf chlorophyll content and photosynthetic rate. High N-delayed leaf senescence, particularly of the six uppermost leaves, compared to the other two N treatments. While N application increased ear leaf soluble protein concentration, it did not influence glucose and suc concentrations. Interestingly, ear leaf starch concentration decreased with increasing N application. Infusion of exogenous suc tended to increase non-structural carbohydrate concentrations in the developing ears of all N treatments at silking and 6 days after silking. However, leaf photosynthetic rates were not affected by suc infusion, and suc infusion failed to increase grain yield in any N treatment. The lack of an effect of suc infusion on ear growth and the high ear leaf starch concentration of N-deficient maize, suggest that yield reduction under N deficiency may not be due to insufficient photosynthate availability to the developing ear during silking, and that yield reduction under N deficiency may be determined at an earlier growth stage.

Transcriptome Profiling Identifies Candidate Genes Associated with the Accumulation of Distinct Sulfur γ-Glutamyl Dipeptides in Phaseolus vulgaris and Vigna mungo Seeds

Common bean (Phaseolus vulgaris) and black gram (Vigna mungo) accumulate γ-Glutamyl-S-methylcysteine and γ-Glutamyl-methionine in seed, respectively. Transcripts were profiled by 454 pyrosequencing data at a similar developmental stage coinciding with the beginning of the accumulation of these metabolites. Expressed sequence tags were assembled into Unigenes, which were assigned to specific genes in the early release chromosomal assembly of the P. vulgaris genome. Genes involved in multiple sulfur metabolic processes were expressed in both species. Expression of Sultr3 members was predominant in P. vulgaris, whereas expression of Sultr5 members predominated in V. mungo. Expression of the cytosolic SERAT1;1 and -1;2 was approximately fourfold higher in P. vulgaris while expression of the plastidic SERAT2;1 was twofold higher in V. mungo. Among BSAS family members, BSAS4;1, encoding a cytosolic cysteine desulfhydrase, and BSAS1;1, encoding a cytosolic O-acetylserine sulphydrylase were most highly expressed in both species. This was followed by BSAS3;1 encoding a plastidic β-cyanoalanine synthase which was more highly expressed by 10-fold in P. vulgaris. The data identify BSAS3;1 as a candidate enzyme for the biosynthesis of S-methylcysteine through the use of methanethiol as substrate instead of cyanide. Expression of GLC1 would provide a complete sequence leading to the biosynthesis of γ-Glutamyl-S-methylcysteine in plastids. The detection of S-methylhomoglutathione in P. vulgaris suggested that homoglutathione synthetase may accept, to some extent, γ-Glutamyl-S-methylcysteine as substrate, which might lead to the formation of S-methylated phytochelatins. In conclusion, 454 sequencing was effective at revealing differences in the expression of sulfur metabolic genes, providing information on candidate genes for the biosynthesis of distinct sulfur amino acid γ-Glutamyl dipeptides between P. vulgaris and V. mungo.