Nitrogen uptake and assimilation process in plants.

<p>The uptake of nitrate (NO₃^-) and ammonium (NH₄⁺) ions is mediated by nitrate (NRT) and ammonium transporters (AMT), respectively. The NO₃^- entered into the cell is reduced to nitrite ions (NO₂^-) by an enzyme nitrate reductase (NR). The nitrite ion then moves to plastid and reduced to ammonium ion by nitrite reductase (NiR) enzyme. The ammonium is then incorporated into amino acid by glutamine synthetase and glutamate synthase via GS/GOGAT cycle. The ammonium ion transported by ammonium transporters directly enters into GS/GOGAT cycle. The two additional enzymes glutamate dehydrogenase (GDH) and asparagine synthetase (ASN) also participates in ammonium assimilation. The GS, GDH and ASN are the key enzymes involved in synthesis of glutamine (Gln), Glutamate (Glu) and Asparagine (Asn).</p

The conserved domain architecture of various proteins involved in nitrate and ammonium uptake, nitrate reduction and ammonia assimilation in <i>B</i>. <i>juncea</i>.

<p>The conserved domain architecture of various proteins involved in nitrate and ammonium uptake, nitrate reduction and ammonia assimilation in <i>B</i>. <i>juncea</i>.</p

Bar diagrams showing relative expression of various genes encoding (A) nitrate and (B) ammonium transporters and enzymes involved in (C) nitrate and nitite reduction and (D,E) ammonium assimilation in <i>B</i>. <i>juncea</i> under abiotic stress conditions after 1h (grey bars) and 24h (white bars) as compared to untreated control plants.

<p>Relative expression ratios were determined using qRT-PCR. Asterisks on the top of the bars indicate statistically significant differences (* p-value<0.05 (significant), **p-value < .01(highly significant), ***p < .001 (very highly significant) between 1h and 24h stress treated samples.</p

Venn diagram showing genes commonly upregulated and downregulated after 1h and 24h of stress treatments.

<p>Venn diagram showing genes commonly upregulated and downregulated after 1h and 24h of stress treatments.</p

List of proteins along with their molecular weight (M. wt.), isoelectric point (PI), CDS and protein length, subcellular localization and <i>Arabidopsis thaliana</i> orthologs.

<p>List of proteins along with their molecular weight (M. wt.), isoelectric point (PI), CDS and protein length, subcellular localization and <i>Arabidopsis thaliana</i> orthologs.</p

Chilling-Mediated DNA Methylation Changes during Dormancy and Its Release Reveal the Importance of Epigenetic Regulation during Winter Dormancy in Apple (<i>Malus</i> x <i>domestica</i> Borkh.)

<div><p>Winter dormancy is a well known mechanism adopted by temperate plants, to mitigate the chilling temperature of winters. However, acquisition of sufficient chilling during winter dormancy ensures the normal phenological traits in subsequent growing period. Thus, low temperature appears to play crucial roles in growth and development of temperate plants. Apple, being an important temperate fruit crop, also requires sufficient chilling to release winter dormancy and normal phenological traits, which are often associated with yield and quality of fruits. DNA cytosine methylation is one of the important epigenetic modifications which remarkably affect the gene expression during various developmental and adaptive processes. In present study, methylation sensitive amplified polymorphism was employed to assess the changes in cytosine methylation during dormancy, active growth and fruit set in apple, under differential chilling conditions. Under high chill conditions, total methylation was decreased from 27.2% in dormant bud to 21.0% in fruit set stage, while no significant reduction was found under low chill conditions. Moreover, the demethylation was found to be decreased, while methylation increased from dormant bud to fruit set stage under low chill as compared to high chill conditions. In addition, RNA-Seq analysis showed high expression of DNA methyltransferases and histone methyltransferases during dormancy and fruit set, and low expression of DNA glcosylases during active growth under low chill conditions, which was in accordance with changes in methylation patterns. The RNA-Seq data of 47 genes associated with MSAP fragments involved in cellular metabolism, stress response, antioxidant system and transcriptional regulation showed correlation between methylation and their expression. Similarly, bisulfite sequencing and qRT-PCR analysis of selected genes also showed correlation between gene body methylation and gene expression. Moreover, significant association between chilling and methylation changes was observed, which suggested that chilling acquisition during dormancy in apple is likely to affect the epigenetic regulation through DNA methylation.</p></div

List of selected MSAP polymorphic fragments, their annotation, their location in apple genome and their corresponding contigs identified in RNA-Seq data.

<p>List of selected MSAP polymorphic fragments, their annotation, their location in apple genome and their corresponding contigs identified in RNA-Seq data.</p

Heat map representation of relative expression based on FPKM values of DNA methyltransferases, DNA glycosylases and histone methyltransferases in various developmental tissues.

<p>The relative FPKM values were used to generate the heat-map using MeV4. The color scale at the bottom represents the expression level, where red, green and black colors indicate upregulation, downregulation and unaltered expression, respectively. Contig number (starting with C_) and their annotation are given on the left and right side of the heat map, respectively.</p

The sample abbreviation and their collection intervals.

<p>The sample abbreviation and their collection intervals.</p

A representative gel image of MSAP assay showing polymorphic fragments in different samples.

<p>lane H: DNA digested with <i>Eco</i>RI–<i>Hpa</i>II; lane M: DNA digested with <i>Eco</i>RI–<i>Msp</i>I. The four developmental stages <i>viz</i>. Dormant bud (DB), Silver tip (ST), Green tip (GT) and Initial fruit set (FS) in apple, under low (L) chill and high (H) chill conditions, were used for MSAP analysis. The arrow marks show presence of polymorphic fragments.</p