Genome-Wide Identification of BTB Domain-Containing Gene Family in Grapevine (<i>Vitis vinifera</i> L.)

BTB (broad-complex, tram track and bric-a-brac) proteins have broad functions in different growth processes and biotic and abiotic stresses. However, the biological role of these proteins has not yet been explored in grapevine, which draws our attention towards the BTB gene family. Herein, we identified 69 BTB genes (VvBTB) in the Vitis vinifera genome and performed comprehensive in silico analysis. Phylogenetic analysis classified VvBTB proteins into five groups, and further domain analysis revealed the presence of other additional functional domains. The majority of BTB proteins were localized in the nucleus. We also performed differential expression analysis by harnessing RNA- seq data of 10 developmental stages and different biotic and abiotic stresses. Our findings revealed the plausible roles of the BTB gene family in developmental stages; Fifty VvBTB were differentially expressed at different developmental stages. In addition, 47 and 16 VvBTB were responsive towards abiotic and biotic stresses, respectively. Interestingly, 13 VvBTB genes exhibited differential expression in at least one of the developmental stages and biotic and abiotic stresses. Further, miRNA target prediction of 13 VvBTB genes revealed that vvi-miR482 targets VvBTB56, and multiple miRNAs, such as vvi-miR172, vvi-miR169 and vvi-miR399, target VvBTB24, which provides an insight into the essential role of the BTB family in the grapevine. Our study provides the first comprehensive analysis and essential information that can potentially be used for further functional investigation of BTB genes in this economically important fruit crop

Carbon: Nitrogen Interaction Regulates Expression of Genes Involved in N-Uptake and Assimilation in <i>Brassica juncea</i> L.

<div><p>In plants, several cellular and metabolic pathways interact with each other to regulate processes that are vital for their growth and development. Carbon (C) and Nitrogen (N) are two main nutrients for plants and coordination of C and N pathways is an important factor for maintaining plant growth and development. In the present work, influence of nitrogen and sucrose (C source) on growth parameters and expression of genes involved in nitrogen transport and assimilatory pathways was studied in <i>B</i>. <i>juncea</i> seedlings. For this, <i>B</i>. <i>juncea</i> seedlings were treated with four combinations of C and N source <i>viz</i>., N source alone (-Suc+N), C source alone (+Suc-N), with N and C source (+Suc+N) or without N and C source (-Suc-N). Cotyledon size and shoot length were found to be increased in seedlings, when nitrogen alone was present in the medium. Distinct expression pattern of genes in both, root and shoot tissues was observed in response to exogenously supplied N and C. The presence or depletion of nitrogen alone in the medium leads to severe up- or down-regulation of key genes involved in N-uptake and transport (<i>BjNRT1</i>.<i>1</i>, <i>BjNRT1</i>.<i>8</i>) in root tissue and genes involved in nitrate reduction (<i>BjNR1</i> and <i>BjNR2</i>) in shoot tissue. Moreover, expression of several genes, like <i>BjAMT1</i>.<i>2</i>, <i>BjAMT2</i> and <i>BjPK</i> in root and two genes <i>BjAMT2</i> and <i>BjGS1</i>.<i>1</i> in shoot were found to be regulated only when C source was present in the medium. Majority of genes were found to respond in root and shoot tissues, when both C and N source were present in the medium, thus reflecting their importance as a signal in regulating expression of genes involved in N-uptake and assimilation. The present work provides insight into the regulation of genes of N-uptake and assimilatory pathway in <i>B</i>. <i>juncea</i> by interaction of both carbon and nitrogen.</p></div

Interaction of Carbon and Nitrogen pathways.

<p>The carbon metabolic pathway provides energy (ATP) and reducing potential NAD(P)H to nitrogen assimilation process. Moreover, the carbon skeleton part in amino acids also comes from 2-OG (2-oxoglutarate) of TCA (Tricarboxylic acid cycle) cycle. Nitrate transporter (NRT), Ammonia transporter (AMT), Nitrate Reductase (NR), Nitrite Reductase (NiR), Glutamine Synthetase isoforms (GS1, GS2), Glutamate Synthase (GOGAT), Glutamate (Glu), Glutamine (Gln), 2-OG (2-Oxoglutarate), Phosphoenol pyruvate (PEP), Pyruvate kinase (PK), Oxaloacetic acid (OAA).</p

Venn diagram showing number of genes up-regulated or downregulated in root and shoot tissues in presence of Sucrose (Suc) alone in the medium (A) and in presence of both Nitrogen (N) and (Suc) in the medium (B).

<p>Genes with a relative fold change ≥2 and ≤0.5 with respect to control conditions were considered as up-regulated and down-regulated, respectively.</p

Effect of Carbon: Nitrogen availabilities on (A) root fresh weight (B) shoot fresh weight (C) root dry weight (D) shoot dry weight (E) root length (F) shoot length (G) chlorophyll content and (H) anthocyanin content in <i>B</i>. <i>juncea</i> seedlings.

<p>The vertical bars represent the mean ±SD of three independent experiments (n = 3) with nine seedlings under each treatment. Different letters on the top of the bars indicate significant difference at a level of P<0.05 by ANOVA using Duncan’s Multiple Range Test (DMRT).</p

Heat maps showing relative expression of genes involved in nitrogen uptake, assimilation and gene of organic acid metabolism in root and shoot tissue of <i>B</i>. <i>juncea</i> in presence of N alone (-Suc+N) w.r.t -Suc-N condition (A) and in absence of N source alone (+Suc-N) w.r.t +Suc+ N condition (B).

<p>The vertical bars indicate relative expression ratio where red, black and green represent up-regulation, no change and down-regulation in transcript levels, respectively.</p

Relative expression values (Fold change with p-value) of 25 genes under different conditions as determined by qRT-PCR.

<p>The genes with relative fold change ≥2 and P-value <0.05 were considered as significantly upregulated and genes with relative fold change ≤0.5 and P-value <0.05 were considered as significantly downregulated.</p

Heat maps showing relative expression of genes involved in nitrogen uptake, assimilation and gene of organic acid metabolism in root and shoot tissues of <i>B</i>. <i>juncea</i> in presence of carbon source alone (+Suc-N) w.r.t -Suc-N condition (A) and in presence of both carbon and sucrose source (+Suc+N) w.r.t -Suc-N condition (B).

<p>The vertical bars indicate relative expression ratio where red, black and green represent upregulation, no change and downregulation in transcript levels, respectively.</p

Not Available

Not AvailableNitrate 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.Not Availabl