Genome-wide analyses of the mung bean NAC gene family reveals orthologs, co-expression networking and expression profiling under abiotic and biotic stresses.

BACKGROUND: Mung bean is a short-duration and essential food crop owing to its cash prominence in Asia. Mung bean seeds are rich in protein, fiber, antioxidants, and phytonutrients. The NAC transcription factors (TFs) family is a large plant-specific family, participating in tissue development regulation and abiotic and biotic stresses. RESULTS: In this study, we perform genome-wide comparisons of VrNAC with their homologs from Arabidopsis. We identified 81 NAC transcription factors (TFs) in mung bean genome and named as per their chromosome location. A phylogenetic analysis revealed that VrNACs are broadly distributed in nine groups. Moreover, we identified 20 conserved motifs across the VrNACs highlighting their roles in different biological process. Based on the gene structure of the putative VrNAC and segmental duplication events might be playing a vital role in the expansion of mung bean genome. A comparative phylogenetic analysis of mung bean NAC together with homologs from Arabidopsis allowed us to classify NAC genes into 13 groups, each containing several orthologs and paralogs. Gene ontology (GO) analysis categorized the VrNACs into biological process, cellular components and molecular functions, explaining the functions in different plant physiology processes. A gene co-expression network analysis identified 173 genes involved in the transcriptional network of putative VrNAC genes. We also investigated how miRNAs potentially target VrNACs and shape their interactions with proteins. VrNAC1.4 (Vradi01g03390.1) was targeted by the Vra-miR165 family, including 9 miRNAs. Vra-miR165 contributes to leaf development and drought tolerance. We also performed qRT-PCR on 22 randomly selected VrNAC genes to assess their expression patterns in the NM-98 genotype, widely known for being tolerant to drought and bacterial leaf spot disease. CONCLUSIONS: This genome-wide investigation of VrNACs provides a unique resource for further detailed investigations aimed at predicting orthologs functions and what role the play under abiotic and biotic stress, with the ultimate aim to improve mung bean production under diverse environmental conditions.

RNA-Seq profiling reveals the plant hormones and molecular mechanisms stimulating the early ripening in apple.

Fruit development and ripening are essential components of human and animal diets. Fruit ripening is also a vital plant trait for plant shelf life at the commercial level. In the present study, two apple cultivars, Hanfu wild (HC) and Hanfu mutant (HM), were employed for RNA-Sequencing (RNA-Seq) to explore the genes involved in fruit ripening. We retrieved 2642 genes, differentially expressed in HC and HM apple cultivars. Gene ontology (GO) analysis revealed the 569 categories, significantly enriched in biological process, cellular component, and molecular function. KEGG analysis exhibited the plant hormone transduction and flavonoid-anthocyanin biosynthesis pathways, might be involved in the fruit ripening and anthocyanin biosynthesis mechanism. A cluster of 13 and 26 DEGs was retrieved, representing the plant hormones and transcription factors, respectively, that may be important for early ripening in HM genotype. This transcriptome study would be useful for researchers to functionally characterize the DEGs responsible for early ripening.

Comparative Transcriptome Profiling of Rice Near-Isogenic Line Carrying Xa23 under Infection of Xanthomonas oryzae pv. oryzae.

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is an overwhelming disease in rice-growing regions worldwide. Our previous studies revealed that the executor R gene Xa23 confers broad-spectrum disease resistance to all naturally occurring biotypes of Xoo. In this study, comparative transcriptomic profiling of two near-isogenic lines (NILs), CBB23 (harboring Xa23) and JG30 (without Xa23), before and after infection of the Xoo strain, PXO99A, was done by RNA sequencing, to identify genes associated with the resistance. After high throughput sequencing, 1645 differentially expressed genes (DEGs) were identified between CBB23 and JG30 at different time points. Gene Ontlogy (GO) analysis categorized the DEGs into biological process, molecular function, and cellular component. KEGG analysis categorized the DEGs into different pathways, and phenylpropanoid biosynthesis was the most prominent pathway, followed by biosynthesis of plant hormones, flavonoid biosynthesis, and glycolysis/gluconeogenesis. Further analysis led to the identification of differentially expressed transcription factors (TFs) and different kinase responsive genes in CBB23, than that in JG30. Besides TFs and kinase responsive genes, DEGs related to ethylene, jasmonic acid, and secondary metabolites were also identified in both genotypes after PXO99A infection. The data of DEGs are a precious resource for further clarifying the network of Xa23-mediated resistance.

Genome-Wide Expression and Physiological Profiling of Pearl Millet Genotype Reveal the Biological Pathways and Various Gene Clusters Underlying Salt Resistance.

Pearl millet (Pennisetum glaucum L.) is a vital staple food and an important cereal crop used as food, feed, and forage. It can withstand heat and drought due to the presence of some unique genes; however, the mechanism of salt stress has been missing in pearl millet until now. Therefore, we conducted a comparative transcriptome profiling to reveal the differentially expressed transcripts (DETs) associated with salt stress in pearl millet at different time points, such as 1, 3, and 7 h, of salt treatment. The physiological results suggested that salt stress significantly increased proline, malondialdehyde (MDA) content, and hydrogen peroxide (H2O2) in pearl millet at 1, 3, and 7 h of salt treatment. In addition, pearl millet plants regulated the activities of superoxide dismutase, catalase, and peroxidase to lessen the impact of salinity. The transcriptomic results depicted that salt stress upregulated and downregulated the expression of various transcripts involved in different metabolic functions. At 1 and 7 h of salt treatment, most of the transcripts were highly upregulated as compared to the 3 h treatment. Moreover, among commonly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, the mitogen-activated protein kinase (MAPK) signaling pathway and peroxisome pathway were significantly enriched. The DETs related to hormone signaling (auxins, ethylene, gibberellin, and abscisic acid), kinases, protein modifications, and degradation were also identified, depicting the possible role of hormones and kinases to enhance plant tolerance against salt stress. Furthermore, the transcription factors, such as ethylene-responsive element binding factors (ERF), basic helix-loop-helix (bHLH), HMG box-containing protein (HBP), MADS, myeloblastosis (MYB), and WRKY, were predicted to significantly regulate different transcripts involved in salt stress responses at three different time points. Overall, this study will provide new insights to better understand the salt stress regulation mechanisms in pearl millet to improve its resistance against salinity and to identify new transcripts that control these mechanisms in other cereals.

Nanoparticle's uptake and translocation mechanisms in plants via seed priming, foliar treatment, and root exposure: a review.

Nanotechnology is one of the promising techniques and shares wide ranges of applications almost in every field of life. Nanomaterials are getting continuous attractions due to specific physical and chemical properties and being applied as multifunctional material. The use of nanomaterials/nanoparticles in agriculture sector for crop improvement and protection against various environmental threats have attained greater significance. Size and nature of nanoparticles, mode of application, environmental conditions, rhizospheric and phyllospheric environment, and plant species are major factors that influence the action of nanoparticles. The mode or method of nanoparticle applications to plants is attaining greater attentions. Recently, different methods for nanoparticle applications (seed priming, foliar, and root application) are being used to improve crop growth. It is of quite worth that which method is suitable for nanoparticle application, and how nanoparticles can possibly translocate to various plant tissues from root to shoot or vice versa. These information's are poorly understood and need more investigations to explore the comprehensive mechanism by which nanoparticles make their possible entry through different plant organs and how they transport to regulate various physiological and molecular functions in plant cells. Therefore, this study comprehensively provides the knowledge of nanoparticles uptake via seed priming, foliar exposure, and root application, and their possible translocation mechanism within plants influenced by various factors that has not clearly presented. This study will provide new insights to find out an actual uptake and translocation mechanism of nanoparticles that may help researchers to develop nanoparticle-based new strategies for plants to cope with various environmental challenges. This study also focuses on different soil factors or above ground factors that are involved in nanoparticles uptake and translocation and ultimately their functioning in plants.

Silver nanoparticles improved the plant growth and reduced the sodium and chlorine accumulation in pearl millet: a life cycle study.

Salt stress in agricultural soils is a global issue and little information is available about the efficiency of silver nanoparticles (AgNPs) in plants under salt stress. The aim of current study was to assess the efficacy of AgNPs in improving plant growth and reducing the salt-induced damages in pearl millet. The exposure of pearl millet plants grown in pots containing soil to different doses of salinity (0, 120, 150 mM) and AgNPs (0, 10, 20 and 30 mM) significantly influenced the morphology, physiology and yield-related attributes. Salt stress remarkably increased the concentration of sodium (Na) and chloride (Cl) in different organs of pearl millet plants. This led to increase the enhancement of hydrogen peroxide (H2O2) and malondialdehyde (MDA) content and caused severe oxidative damage by augmenting the activities of antioxidant enzymes. The obvious decrease in plant growth, height, dry biomass of root and shoot, chlorophylls and carotenoid contents was observed in salt-stressed plants which ultimately reduced the yield of plants. The AgNPs remarkably improved the plant growth by reducing oxidative stress and Na and Cl uptake by salt-stressed plants. The AgNPs were also found to maintain the ionic balance of cell (Na+, K+ and Na+/K+ ratio). The AgNPs improved the superoxide dismutase, catalase activities and decreased the peroxidase activity while reduced the H2O2 and MDA contents in plants under salt stress. Overall, AgNPs increased the plant height, yield, and photosynthesis of salt-stressed plants in a dose-additive manner.

Bacillus siamensis Reduces Cadmium Accumulation and Improves Growth and Antioxidant Defense System in Two Wheat (Triticum aestivum L.) Varieties.

Bioavailability of cadmium (Cd) metal in the soils due to the scarcity of good quality water and industrial waste could be the major limiting factor for the growth and yield of crops. Therefore, there is a need for a prompt solution to the Cd toxicity, to fulfill increasing food demand resulting from growing world population. Today, a variable range of plant growth promoting rhizobacteria (PGPR) is being used at a large scale in agriculture, to reduce the risk of abiotic stresses on plants and increase crop productivity. The objective of this study was to evaluate the efficacy of Bacillus siamensis in relieving the Cd induced damage in two wheat varieties (i.e., NARC-2009 and NARC-2011) grown in Cd spiked soil at different concentrations (0, 20, 30, 50 mg/kg). The plants under Cd stress accumulated more Cd in the roots and shoots, resulting in severe oxidative stress, evident by an increase in malondialdehyde (MDA) content. Moreover, a decrease in cell osmotic status, and alteration in antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) were also observed in wheat plants under Cd stress. As a result, the Cd exposed plants showed a reduction in growth, tissue biomass, photosynthetic pigments, membrane stability, total soluble sugars, and amino acids, in comparison to control plants. The extent of damage was observed to be higher with an increase in Cd concentration. However, the inoculation of wheat with B. siamensis improved plant growth, reduced oxidative stress, and enhanced the activities of antioxidant enzymes in both wheat varieties. B. siamensis amendment brought a considerable improvement in every parameter determined with respect to Cd stress. The response of both wheat varieties on exposure to B. siamensis was positively enhanced, whereas NARC-2009 accumulated less Cd compared to NARC-2011, which indicated a higher tolerance to Cd stress mediated by B. siamensis inoculation. Overall, the B. siamensis reduced the Cd toxicity in wheat plants through the augmentation of the antioxidant defense system and sugars production.

Amelioration of salt induced toxicity in pearl millet by seed priming with silver nanoparticles (AgNPs): The oxidative damage, antioxidant enzymes and ions uptake are major determinants of salt tolerant capacity.

Abiotic stresses in plants reduce crop growth and productivity. Nanoparticles (NPs) are effectively involved in the physiochemical processes of crop plants, especially under the abiotic stresses; whereas, less information is available regarding the role of AgNPs in salt-stressed plants. Therefore, in the current study, we investigated the effects of seed priming with commercially available silver nanoparticles (AgNPs) (size range between 50 and 100 nm) on plant morphology, physiology, and antioxidant defence system of pearl millet (Pennisetum glaucum L.) under different concentrations of salt stress (0, 120 and 150 mM NaCl). The seed priming with AgNPs at different levels (0, 10, 20 and 30 mM) mitigated the adverse impacts of salt stress and improved plant growth and defence system. The results demonstrated that salt-stressed plants had restricted growth and a noticeable decline in fresh and dry weight. Salt stress enhanced the oxidative damage by excessive production of hydrogen peroxide (H2O2), malondialdehyde (MDA) contents in pearl millet leaves. However, seed priming with AgNPs significantly improved the plant height growth related attributes, relative water content, proline contents and ultimately fresh and dry weight at 20 mM AgNPs alone or with salt stress. The AgNPs reduced the oxidative damage by improving antioxidant enzyme activities in the pearl millet leaves under salt stress. Furthermore, sodium (Na+) and Na+/K+ ratio was decreased and potassium (K+) increased by NPs, and the interactive effects between salt and AgNPs significantly impacted the total phenolic and flavonoid content in pearl millet. It was concluded that seed priming with AgNPs could enhance salinity tolerance in crop plants by enhancing physiological and biochemical responses. This might boost global crop production in salt-degraded lands.

Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae.

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating disease in most of the rice growing regions worldwide. Among the 42 BB resistance (R) genes, Xa23 is an executor R gene, conferring broad-spectrum disease resistance to all naturally occurring biotypes of Xoo. In this study, CBB23, a rice line carrying Xa23 gene, was inoculated with wild PXO99A and its mutant, P99M2, to retrieve the differentially expressed genes (DEGs). RNA-Seq analysis retrieved 1,235 DEGs (p-value ≤ 0.05) at 12, 24, 36, and 48 hours of post inoculation (hpi). Gene ontology (GO) analysis classified the DEGs functionally into biological process, cellular component and molecular function. KEGG pathway analysis categorized the DEGs into 11 different pathways, and the ribosome is a prominent pathway followed by biosynthesis of phenylpropanoids. Gene co-expression network analysis identified the clusters of transcription factors (TFs) which may be involved in PXO99A resistance. Additionally, we retrieved 67 differentially expressed TFs and 26 peroxidase responsive genes which may be involved in disease resistance mechanism. DEGs involved in the host-pathogen interaction, e.g., signaling mechanism, cell wall and plant hormones were identified. This data would be a valuable resource for researchers to identify the candidate genes associated with Xoo resistance.

RNA-Seq analysis of gene expression changes triggered by Xanthomonas oryzae pv. oryzae in a susceptible rice genotype.

BACKGROUND: Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease in most of the rice growing regions worldwide. Xoo injects the transcriptional activator-like (TAL) effector protein into the host cell to induce the susceptibility (S) gene(s) for spreading the disease. In the current study, a susceptible rice genotype, JG30, was inoculated with wild Xoo strain PXO99A and its mutant PH without any TAL effector, to retrieve the differentially expressed genes (DEGs) having a role in susceptibility. RESULTS: RNA-Seq data analysis showed that 1143 genes were significantly differentially expressed (p-value ≤0.05) at 12, 24, 36 and 48 h post inoculation (hpi). Expression patterns, evaluated by quantitative real-time PCR (qRT-PCR), of randomly selected eight genes were similar to the RNA-Seq data. KEGG pathway classified the DEGs into photosynthesis and biosynthesis of phenylpropanoid pathway. Gene ontology (GO) analysis categorized the DEGs into the biological pathway, cellular component, and molecular function. We identified 43 differentially expressed transcription factors (TFs) belonging to different families. Also, clusters of the DEGs representing kinase and peroxidase responsive genes were retrieved. MapMan pathway analysis representing the expression pattern of genes expressed highly in biotic stress and metabolic pathways after PXO99A infection relative to PH. CONCLUSIONS: DEGs were identified in susceptible rice genotype inoculated with PXO99A relative to mutant strain PH. The identified 1143 DEGs were predicted to be included in the different biological processes, signaling mechanism and metabolic pathways. The Jasmonic acid (JA) responsive genes were identified to be downregulated in PXO99A infected leaves. This study would be useful for the researchers to reveal the potential functions of genes involved in the rice susceptibility to PXO99A infection.