Transcriptome profiling analysis for two Tibetan wild barley genotypes in responses to low nitrogen

Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L

Nitrate is the main source of inorganic nitrogen for plants, which also act as signaling molecule. Present study was aimed to understand nitrate regulatory mechanism in Brassica juncea cultivars, with contrasting nitrogen-use-efficiency (NUE) viz. Pusa Bold (PB, high-NUE) and Pusa Jai Kisan (PJK, low-NUE), employing RNA-seq approach. A total of 4031, 3874 and 3667 genes in PB and 2982, 2481 and 2843 genes in PJK were differentially expressed in response to early, low (0.25 mM KNO₃), medium (2 mM KNO₃) and high (4 mM KNO₃) nitrate treatments, respectively, as compared to control (0 mM KNO₃). Genes of N-uptake (NRT1.1, NRT1.8, and NRT2.1), assimilation (NR1, NR2, NiR, GS1.3, and Fd-GOGAT) and remobilization (GDH2, ASN2–3 and ALaT) were highly-upregulated in PB than in PJK in response to early nitrate treatments. We have also identified transcription factors and protein kinases that were rapidly induced in response to nitrate, suggesting their involvement in nitrate-mediated signaling. Co-expression network analysis revealed four nitrate specific modules in PB, enriched with GO terms like, “Phenylpropanoid pathway”, “Nitrogen compound metabolic process” and “Carbohydrate metabolism”. The network analysis also identified HUB transcription factors like mTERF, FHA, Orphan, bZip and FAR1, which may be the key regulators of nitrate-mediated response in B. juncea.

Molecular Mechanisms of Acclimatization to Phosphorus Starvation and Recovery Underlying Full-Length Transcriptome Profiling in Barley (Hordeum vulgare L.)

A lack of phosphorus (P) in plants can severely constrain growth and development. Barley, one of the earliest domesticated crops, is extensively planted in poor soil around the world. To date, the molecular mechanisms of enduring low phosphorus, at the transcriptional level, in barley are still unclear. In the present study, two different barley genotypes (GN121 and GN42)-with contrasting phosphorus efficiency-were used to reveal adaptations to low phosphorus stress, at three time points, at the morphological, physiological, biochemical, and transcriptome level. GN121 growth was less affected by phosphorus starvation and recovery than that of GN42. The biomass and inorganic phosphorus concentration of GN121 and GN42 declined under the low phosphorus-induced stress and increased after recovery with normal phosphorus. However, the range of these parameters was higher in GN42 than in GN121. Subsequently, a more complete genome annotation was obtained by correcting with the data sequenced on Illumina HiSeq X 10 and PacBio RSII SMRT platform. A total of 6,182 and 5,270 differentially expressed genes (DEGs) were identified in GN121 and GN42, respectively. The majority of these DEGs were involved in phosphorus metabolism such as phospholipid degradation, hydrolysis of phosphoric enzymes, sucrose synthesis, phosphorylation/dephosphorylation and post-transcriptional regulation; expression of these genes was significantly different between GN121 and GN42. Specifically, six and seven DEGs were annotated as phosphorus transporters in roots and leaves, respectively. Furthermore, a putative model was constructed relying on key metabolic pathways related to phosphorus to illustrate the higher phosphorus efficiency of GN121 compared to GN42 under low phosphorus conditions. Results from this study provide a multi-transcriptome database and candidate genes for further study on phosphorus use efficiency (PUE).

Nitrate Uptake Affects Cell Wall Synthesis and Modeling

Nowadays, the relationship(s) about N assimilation and cell wall remodeling in plants remains generally unclear. Enzymes involved in cell wall synthesis/modification, and nitrogen transporters play a critical role in plant growth, differentiation, and response to external stimuli. In this review, a co-expression analysis of nitrate and ammonium transporters of Arabidopsis thaliana was performed in order to explore the functional connection of these proteins with cell-wall related enzymes. This approach highlighted a strict relationship between inorganic nitrogen transporters and cell wall formation, identifying a number of co-expressed remodeling enzymes. The enzymes involved in pectin and xyloglucan synthesis resulted particularly co-regulated together with nitrate carriers, suggesting a connection between nitrate assimilation and cell wall growth regulation. Major Facilitator Carriers, and one chloride channel, are similarly co-expressed with pectin lyase, pectinacetylesterase, and cellulose synthase. Contrarily, ammonium transporters show little or no connection with those genes involved in cell wall synthesis. Different aspects related to plant development, embryogenesis, and abiotic stress response will be discussed, given the importance in plant growth of cell wall synthesis and nitrate uptake. Intriguingly, the improvement of abiotic stress tolerance in crops concerns both these processes indicating the importance in sensing the environmental constraints and mediating a response. These evaluations could help to identify candidate genes for breeding purposes.

Transcriptomic response of durum wheat to nitrogen starvation

Nitrogen (N) is a key macronutrient representing a limiting factor for plant growth and development and affects productivity in wheat. In this study, durum wheat response to N chronic starvation during grain filling was investigated through a transcriptomic approach in roots, leaves/stems, flag leaf and spikes of cv. Svevo. Nitrogen stress negatively influenced plant height, tillering, flag leaf area, spike and seed traits, and total N content. RNA-seq data revealed 4,626 differentially expressed genes (DEGs). Most transcriptomic changes were observed in roots, with 3,270 DEGs, while 963 were found in leaves/stems, 470 in flag leaf, and 355 in spike tissues. A total of 799 gene ontology (GO) terms were identified, 180 and 619 among the upregulated and downregulated genes, respectively. Among the most addressed GO categories, N compound metabolism, carbon metabolism, and photosynthesis were mostly represented. Interesting DEGs, such as N transporters, genes involved in N assimilation, along with transcription factors, protein kinases and other genes related to stress were highlighted. These results provide valuable information about the transcriptomic response to chronic N stress in durum wheat, which could be useful for future improvement of N use efficiency.

Analysis of the oligopeptide transporter gene family in Ganoderma lucidum: structure, phylogeny, and expression patterns

Oligopeptide transporters (OPTs) are believed to transport broad ranges of substrates across the plasma membrane from the extracellular environment into the cell and are thought to contribute to various biological processes. In the present study, 13 putative OPTs (Gl-OPT1 to Gl-OPT13) were identified through extensive search of Ganoderma lucidum genome database. Phylogenetic analysis with OPTs from other fungi and plants indicates that these genes can be further divided into five groups. Motif compositions of OPT members are highly conserved in each group, indicative of functional conservation. Expression profile analysis of the 13 Gl-OPT genes indicated that, with the exception of Gl-OPT7–Gl-OPT9, for which no transcripts were detected, all paralogues were differentially expressed, suggesting their potential involvement in stress response and functional development of fungi. Overall, the analyses in this study provide a starting point for elucidating the functions of OPT in G. lucidum, and for understanding the complexities of metabolic regulation.

Ionomic and physiological responses to low nitrogen stress in Tibetan wild and cultivated barley

In a previous study, we identified the low-nitrogen (LN) tolerant accessions from the Tibetan wild barley (Hordeum vulgare subsp. spontaneum). In this study, two wild barley genotypes (XZ149, LN-tolerant and XZ56, LN-sensitive) and a barley cultivar ZD9 (H. vulgare) were used to determine the LN tolerant mechanism underlying the wild barley in the ionomic and physiological aspects. XZ149 exhibited higher LN tolerance with highest relative dry weight and N accumulation among three barley genotypes under LN stress. When exposed to LN stress, XZ149 had more N transportation from roots to leaves, and remained relatively higher activities of nitrate reductase (NR, EC.1.7.1.1) and glutamine synthetase (GS, EC.6.3.1.2) in leaves than other two genotypes, ensuring its higher capacity of N assimilation and utilization. The ionome analysis showed that LN stress had a significant effect on tissue ionome and the effect was genotypic and tissue-specific difference. On the whole, XZ149 maintained more stable Mn and Cu contents in roots, and less reduction of root P, K and Ca contents than XZ56 and ZD9 when exposed to LN stress. It may be assumed that more N movement into shoots, greater N assimilating capacity and specific rearrangement of nutrient element levels in tissues under LN stress are attributed to LN tolerance in XZ149.

Comparative Phosphoproteomic Analysis under High-Nitrogen Fertilizer Reveals Central Phosphoproteins Promoting Wheat Grain Starch and Protein Synthesis

Nitrogen (N) is a macronutrient important for plant growth and development. It also strongly influences starch and protein synthesis, closely related to grain yield and quality. We performed the first comparative phosphoproteomic analysis of developing wheat grains in response to high-N fertilizer. Physiological and biochemical analyses showed that application of high-N fertilizer resulted in significant increases in leaf length and area, chlorophyll content, the activity of key enzymes in leaves such as nitrate reductase (NR), and in grains such as sucrose phosphate synthase (SPS), sucrose synthase (SuSy), and ADP glucose pyrophosphorylase (AGPase). This enhanced enzyme activity led to significant improvements in starch content, grain yield, and ultimately, bread making quality. Comparative phosphoproteomic analysis of developing grains under the application of high-N fertilizer performed 15 and 25 days post-anthesis identified 2470 phosphosites among 1372 phosphoproteins, of which 411 unique proteins displayed significant changes in phosphorylation level (>2-fold or <0.5-fold). These phosphoproteins are involved mainly in signaling transduction, starch synthesis, energy metabolism. Pro-Q diamond staining and Western blotting confirmed our phosphoproteomic results. We propose a putative pathway to elucidate the important roles of the central phosphoproteins regulating grain starch and protein synthesis. Our results provide new insights into the molecular mechanisms of protein phosphorylation modifications involved in grain development, yield and quality formation.

Metabolic analysis of two contrasting wild barley genotypes grown hydroponically reveals adaptive strategies in response to low nitrogen stress

Nitrogen (N) is an essential macronutrient for plants. The increasingly severe environmental problems caused by N fertilizer application urge alleviation of N fertilizer dependence in crop production. In previous studies, we identified the Tibetan wild barley accessions with high tolerance to low nitrogen (LN). In this study, metabolic analysis was done on two wild genotypes (XZ149, tolerant and XZ56, sensitive) to understand the mechanism of LN tolerance, using a hydroponic experiment. Leaf and root samples were taken at seven time points within 18 d after LN treatment, respectively. XZ149 was much less affected by low N stress than XZ56 in plant biomass. A total of 51 differentially accumulated metabolites were identified between LN and normal N treated plants. LN stress induced tissue-specific changes in carbon and nitrogen partitioning, and XZ149 had a pattern of energy-saving amino acids accumulation and carbon distribution in favor of root growth that contribute to its higher LN tolerance. Moreover, XZ149 is highly capable of producing energy and maintaining the redox homeostasis under LN stress. The current results revealed the mechanisms underlying the wild barley in high LN tolerance and provided the valuable references for developing barley cultivars with LN tolerance.