MicroRNAs expression profiles in early responses to different levels of water deficit in .

Unlabelled: Water deficit is a major constraint for crops of economic importance in almost all agricultural regions. However, plants have an active defense system to adapt to these adverse conditions, acting in the reprogramming of gene expression responsible for encoding microRNAs (miRNAs). These miRNAs promote the regulation to the target gene expression by the post-transcriptional (PTGS) and transcriptional gene silencing (TGS), modulating several pathways including defense response to water deficit.

Efficient genome editing and gene knockout in with CRISPR/Cas9 directed gene editing by the non-homologous end-joining pathway.

The CRISPR/Cas9 system has been used for genome editing in several organisms, including higher plants. This system induces site-specific mutations in the genome based on the nucleotide sequence of engineered guide RNAs. The complex genomes of C4 grasses makes genome editing a challenge in key grass crops like maize (), sorghum (), spp.

Enhanced aluminum tolerance in sugarcane: evaluation of SbMATE overexpression and genome-wide identification of ALMTs in Saccharum spp.

Background: A major limiting factor for plant growth is the aluminum (Al) toxicity in acidic soils, especially in tropical regions. The exclusion of Al from the root apex through root exudation of organic acids such as malate and citrate is one of the most ubiquitous tolerance mechanisms in the plant kingdom. Two families of anion channels that confer Al tolerance are well described in the literature, ALMT and MATE family.

Suppression of a BAHD acyltransferase decreases p-coumaroyl on arabinoxylan and improves biomass digestibility in the model grass Setaria viridis.

Grass cell walls have hydroxycinnamic acids attached to arabinosyl residues of arabinoxylan (AX), and certain BAHD acyltransferases are involved in their addition. In this study, we characterized one of these BAHD genes in the cell wall of the model grass Setaria viridis. RNAi silenced lines of S.

Correction to: Silencing of a BAHD acyltransferase in sugarcane increases biomass digestibility.

[This corrects the article DOI: 10.1186/s13068-019-1450-7.].

Silencing of a BAHD acyltransferase in sugarcane increases biomass digestibility.

Background: Sugarcane ( spp.) covers vast areas of land (around 25 million ha worldwide), and its processing is already linked into infrastructure for producing bioethanol in many countries. This makes it an ideal candidate for improving composition of its residues (mostly cell walls), making them more suitable for cellulosic ethanol production.

Using Thermography to Confirm Genotypic Variation for Drought Response in Maize.

The feasibility of thermography as a technique for plant screening aiming at drought-tolerance has been proven by its relationship with gas exchange, biomass, and yield. In this study, unlike most of the previous, thermography was applied for phenotyping contrasting maize genotypes whose classification for drought tolerance had already been established in the field. Our objective was to determine whether thermography-based classification would discriminate the maize genotypes in a similar way as the field selection in which just grain yield was taken into account as a criterion.

MicroRNAs and new biotechnological tools for its modulation and improving stress tolerance in plants.

MicroRNAs (miRNAs) modulate the abundance and spatial-temporal accumulation of target mRNAs and indirectly regulate several plant processes. Transcriptional regulation of the genes encoding miRNAs (MIR genes) can be activated by numerous transcription factors, which themselves are regulated by other miRNAs. Fine-tuning of MIR genes or miRNAs is a powerful biotechnological strategy to improve tolerance to abiotic or biotic stresses in crops of economic importance.

Identification and characterization of core abscisic acid (ABA) signaling components and their gene expression profile in response to abiotic stresses in Setaria viridis.

Abscisic acid (ABA) is an essential phytohormone that regulates growth, development and adaptation of plants to environmental stresses. In Arabidopsis and other higher plants, ABA signal transduction involves three core components namely PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs) and class III SNF-1-related protein kinase 2 (SnRK2s). In the present study, we reported the identification and characterization of the core ABA signaling components in Setaria viridis, an emerging model plant for cereals and feedstock crops presenting C4 metabolism, leading to the identification of eight PYL (SvPYL1 to 8), twelve PP2C (SvPP2C1 to 12) and eleven SnRK2 (SvSnRK2.

Setaria viridis as a Model Plant for Functional Genomic Studies in C4 Crops.

Setaria viridis is an emerging model for C4 species, and it is an important model to validate some genes for further C4 crop transformation, such as sugarcane, maize, and wheat. Here, we describe two protocols for stable transformation of S. viridis mediated by Agrobacterium tumefaciens with three different reporter genes and two selectable markers.

Correction: Genome-wide identification, characterization and expression profile analysis of expansins gene family in sugarcane (Saccharum spp.).

[This corrects the article DOI: 10.1371/journal.pone.

Genome-wide identification, characterization and expression profile analysis of expansins gene family in sugarcane (Saccharum spp.).

Expansins refer to a family of closely related non-enzymatic proteins found in the plant cell wall that are involved in the cell wall loosening. In addition, expansins appear to be involved in different physiological and environmental responses in plants such as leaf and stem initiation and growth, stomata opening and closing, reproduction, ripening and stress tolerance. Sugarcane (Saccharum spp.

Suppression of a single BAHD gene in Setaria viridis causes large, stable decreases in cell wall feruloylation and increases biomass digestibility.

Feruloylation of arabinoxylan (AX) in grass cell walls is a key determinant of recalcitrance to enzyme attack, making it a target for improvement of grass crops, and of interest in grass evolution. Definitive evidence on the genes responsible is lacking so we studied a candidate gene that we identified within the BAHD acyl-CoA transferase family. We used RNA interference (RNAi) silencing of orthologs in the model grasses Setaria viridis (SvBAHD01) and Brachypodium distachyon (BdBAHD01) and determined effects on AX feruloylation.

Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization.

Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding.

Improved Genetic Transformation of Sugarcane (Saccharum spp.) Embryogenic Callus Mediated by Agrobacterium tumefaciens.

Sugarcane (Saccharum spp.) is a monocotyledonous semi-perennial C4 grass of the Poaceae family. Its capacity to accumulate high content of sucrose and biomass makes it one of the most important crops for sugar and biofuel production.

A procedure for maize genotypes discrimination to drought by chlorophyll fluorescence imaging rapid light curves.

Background: Photosynthesis can be roughly separated into biochemical and photochemical processes. Both are affected by drought and can be assessed by non-invasive standard methods. Gas exchange, which mainly assesses the first process, has well-defined protocols.

Functional Characterization of a Putative in Transgenic Arabidopsis and Its Role during Flowering Control.

Flowering is an important trait in major crops like soybean due to its direct relation to grain production. The circadian clock mediates the perception of seasonal changes in day length and temperature to modulate flowering time. The circadian clock gene () was identified in and is believed to play a key role in the integration of photoperiod, circadian regulation, and flowering.

Characterization of Soybean Genetically Modified for Drought Tolerance in Field Conditions.

Drought is one of the most stressful environmental factor causing yield and economic losses in many soybean-producing regions. In the last decades, transcription factors (TFs) are being used to develop genetically modified plants more tolerant to abiotic stresses. Dehydration responsive element binding (DREB) and ABA-responsive element-binding (AREB) TFs were introduced in soybean showing improved drought tolerance, under controlled conditions.

Characterization of sugarcane (Saccharum spp.) leaf senescence: implications for biofuel production.

Background: Second-generation ethanol (2G-bioethanol) uses lignocellulosic feedstocks for ethanol production. Sugarcane is one among the most suitable crops for biofuel production. Its juice is extracted for sugar production, while sugarcane bagasse, straw, and senescing leaves are considered industrial waste.

Selection of reliable reference genes for RT-qPCR analysis during developmental stages and abiotic stress in Setaria viridis.

Real-time PCR (RT-qPCR) expression analysis is a powerful analytical technique, but reliable results depend on the use of stable reference genes for proper normalization. This study proposed to test the expression stability of 13 candidate reference genes in Setaria viridis, a monocot species recently proposed as a new C4 model plant. Gene expression stability of these genes was assayed across different tissues and developmental stages of Setaria and under drought or aluminum stress.

Daytime soybean transcriptome fluctuations during water deficit stress.

Background: Since drought can seriously affect plant growth and development and little is known about how the oscillations of gene expression during the drought stress-acclimation response in soybean is affected, we applied Illumina technology to sequence 36 cDNA libraries synthesized from control and drought-stressed soybean plants to verify the dynamic changes in gene expression during a 24-h time course. Cycling variables were measured from the expression data to determine the putative circadian rhythm regulation of gene expression.

Results: We identified 4866 genes differentially expressed in soybean plants in response to water deficit.

floral-dip: A simple and rapid -mediated transformation method.

was recently described as a new monocotyledonous model species for C4 photosynthesis research and genetic transformation. It has biological attributes (rapid life cycle, small genome, diploid, short stature and simple growth requirements) that make it suitable for use as a model plant. We report an alternative method of transformation using floral dip to circumvent the necessity of tissue culture phase for transgenic plant regeneration.

A simple and highly efficient -mediated transformation protocol for .

The production and use of sugarcane in Brazil is very important for bioenergy production and is recognized as one of the most efficient in the world. In our laboratory, is being tested as a model plant for sugarcane. has biological attributes (rapid life cycle, small genome, diploid, short stature and simple growth requirements) that make it suitable for use as a model system.

Ferulic acid: a key component in grass lignocellulose recalcitrance to hydrolysis.

In the near future, grasses must provide most of the biomass for the production of renewable fuels. However, grass cell walls are characterized by a large quantity of hydroxycinnamic acids such as ferulic and p-coumaric acids, which are thought to reduce the biomass saccharification. Ferulic acid (FA) binds to lignin, polysaccharides and structural proteins of grass cell walls cross-linking these components.