Functional characterization of a putative Glycine max ELF4 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 EARLY FLOWERING 4 (ELF4) was identified in Arabidopsis thaliana and is believed to play a key role in the integration of photoperiod, circadian regulation, and flowering. The molecular circuitry that comprises the circadian clock and flowering control in soybeans is just beginning to be understood. To date, insufficient information regarding the soybean negative flowering regulators exist, and the biological function of the soybean ELF4 (GmELF4) remains unknown. Here, we investigate the ELF4 family members in soybean and functionally characterize a GmELF4 homologous gene. The constitutive overexpression of GmELF4 delayed flowering in Arabidopsis, showing the ELF4 functional conservation among plants as part of the flowering control machinery. We also show that GmELF4 alters the expression of Arabidopsis key flowering time genes (AtCO and AtFT), and this down-regulation is the likely cause of flowering delay phenotypes. Furthermore, we identified the GmELF4 network genes to infer the participation of GmELF4 in soybeans. The data generated in this study provide original insights for comprehending the role of the soybean circadian clock ELF4 gene as a negative flowering controller

Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit

Soybean has a wide range of applications in the industry and, due to its crop potential, its improvement is widely desirable. During drought conditions, soybean crops suffer significant losses in productivity. Therefore, understanding the responses of the soybean under this stress is an effective way of targeting crop improvement techniques. In this study, we employed the Suppressive Subtractive Hybridization (SSH) technique to investigate differentially expressed genes under water deficit conditions. Embrapa 48 and BR 16 soybean lines, known as drought-tolerant and -sensitive, respectively, were grown hydroponically and subjected to different short-term periods of stress by withholding the nutrient solution. Using this approach, we have identified genes expressed during the early response to water deficit in roots and leaves. These genes were compared among the lines to assess probable differences in the plant transcriptomes. In general, similar biochemical processes were predominant in both cultivars; however, there were more considerable differences between roots and leaves of Embrapa 48. Moreover, we present here a fast, clean and straightforward method to obtain drought-stressed root tissues and a large enriched collection of transcripts expressed by soybean plants under water deficit that can be useful for further studies towards the understanding of plant responses to stress.304314Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Lettuce Production under Reduced Levels of N-fertilizer in the Presence of Plant Growth-promoting Bacillus spp. Bacteria

Lettuce consumption has increased worldwide due to the recognition of its nutritional value and to the consumers’ search for healthier foods. Increased consumption must be coupled with more efficient production, demanding more nutrients. However, the utilization of chemical inputs in horticulture is decreasing, and biological approaches, such as the inoculation with plant growth-promoting bacteria (PGPB), are becoming more popular. Species of Bacillus have long been known promote the growth of plants, including lettuce, in agricultural soils, but little is known about their potential under Brazilian conditions. We have tested the ability of B. subtilis, B. pumilus, and B. amyloliquefaciens, carried in single or combined pre-commercial inoculants, to act as PGPB for field-grown lettuce plants of cultivar Elisa. In our experiments, the PGPB were challenged to promote plant growth when the recommended dose of nitrogen (N) fertilizer was reduced by 50%. Our results demonstrated that all species, either alone or combined, were able to improve plant vigor, the number of leaves, and the average diameter and weight of the lettuce heads, under the test conditions. Average gains in plant vigor and head weight due to all species were of the order of 50% relative to the control (no N fertilizer) treatment and, in most cases, gains due to the presence of the bacteria were superior to those promoted by the full (100%) N fertilization. This is the first report of positive utilization of pre-commercial products containing Bacillus for lettuce growth in Brazil

Identification of primary and secondary metabolites and transcriptome profile of soybean tissues during different stages of hypoxia

NMR and chromatography methods combined with mass spectrometry are the most important analytical techniques employed for plant metabolomics screening. Metabolomic analysis integrated to transcriptome screening add an important extra dimension to the information flow from DNA to RNA to protein. The most useful NMR experiment in metabolomics analysis is the proton spectra due the high receptivity of 1H and important structural information, through proton–proton scalar coupling. Routinely, databases have been used in identification of primary metabolites, however, there is currently no comparable data for identification of secondary metabolites, mainly, due to signal overlap in normal 1H NMR spectra and natural variation of plant. Related to spectra overlap, alternatively, better resolution can be find using 1H pure shift and 2D NMR pulse sequence in complex samples due to spreading the resonances in a second dimension. Thus, in data brief we provide a catalogue of metabolites and expression levels of genes identified in soy leaves and roots under flooding stress

Identification of novel soybean microRNAs involved in abiotic and biotic stresses

Background: Small RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and posttranscriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs) act in several plant pathways associated with tissue proliferation, differentiation, and development and in response to abiotic and biotic stresses. In order to identify new miRNAs in soybean and to verify those that are possibly water deficit and rust-stress regulated, eight libraries of small RNAs were constructed and submitted to Solexa sequencing. Results: The libraries were developed from drought-sensitive and tolerant seedlings and rust-susceptible and resistant soybeans with or without stressors. Sequencing the library and subsequent analyses detected 256 miRNAs. From this total, we identified 24 families of novel miRNAs that had not been reported before, six families of conserved miRNAs that exist in other plants species, and 22 families previously reported in soybean. We also observed the presence of several isomiRNAs during our analyses. To validate novel miRNAs, we performed RT-qPCR across the eight different libraries. Among the 11 miRNAs analyzed, all showed different expression profiles during biotic and abiotic stresses to soybean. The majority of miRNAs were up-regulated during water deficit stress in the sensitive plants. However, for the tolerant genotype, most of the miRNAs were down regulated. The pattern of miRNAs expression was also different for the distinct genotypes submitted to the pathogen stress. Most miRNAs were down regulated during the fungus infection in the susceptible genotype; however, in the resistant genotype, most miRNAs did not vary during rust attack. A prediction of the putative targets was carried out for conserved and novel miRNAs families. Conclusions: Validation of our results with quantitative RT-qPCR revealed that Solexa sequencing is a powerful tool miRNA discovery. The identification of differentially expressed plant miRNAs provides molecular evidence for the possible involvement of miRNAs in the process of water deficit- and rust-stress responses

Expression Patterns of GmAP2/EREB-Like Transcription Factors Involved in Soybean Responses to Water Deficit

<div><p>Soybean farming has faced several losses in productivity due to drought events in the last few decades. However, plants have molecular mechanisms to prevent and protect against water deficit injuries, and transcription factors play an important role in triggering different defense mechanisms. Understanding the expression patterns of transcription factors in response to water deficit and to environmental diurnal changes is very important for unveiling water deficit stress tolerance mechanisms. Here, we analyzed the expression patterns of ten APETALA2/Ethylene Responsive Element Binding-like (AP2/EREB-like) transcription factors in two soybean genotypes (BR16: drought-sensitive; and Embrapa 48: drought-tolerant). According to phylogenetic and domain analyses, these genes can be included in the DREB and ERF subfamilies. We also analyzed a <i>GmDRIP</i>-like gene that encodes a DREB negative regulator. We detected the up-regulation of 9 <i>GmAP2/EREB</i>-like genes and identified transcriptional differences that were dependent on the levels of the stress applied and the tissue type analyzed (the expression of the <i>GmDREB1F</i>-like gene, for example, was four times higher in roots than in leaves). The <i>GmDRIP-like</i> gene was not induced by water deficit in BR16 during the longest periods of stress, but was significantly induced in Embrapa 48; this suggests a possible genetic/molecular difference between the responses of these cultivars to water deficit stress. Additionally, RNAseq gene expression analysis over a 24-h time course indicates that the expression patterns of several <i>GmDREB</i>-like genes are subject to oscillation over the course of the day, indicating a possible circadian regulation.</p></div

Transcriptome-Wide Identification of Reference Genes for Expression Analysis of Soybean Responses to Drought Stress along the Day.

The soybean transcriptome displays strong variation along the day in optimal growth conditions and also in response to adverse circumstances, like drought stress. However, no study conducted to date has presented suitable reference genes, with stable expression along the day, for relative gene expression quantification in combined studies on drought stress and diurnal oscillations. Recently, water deficit responses have been associated with circadian clock oscillations at the transcription level, revealing the existence of hitherto unknown processes and increasing the demand for studies on plant responses to drought stress and its oscillation during the day. We performed data mining from a transcriptome-wide background using microarrays and RNA-seq databases to select an unpublished set of candidate reference genes, specifically chosen for the normalization of gene expression in studies on soybean under both drought stress and diurnal oscillations. Experimental validation and stability analysis in soybean plants submitted to drought stress and sampled during a 24 h timecourse showed that four of these newer reference genes (FYVE, NUDIX, Golgin-84 and CYST) indeed exhibited greater expression stability than the conventionally used housekeeping genes (ELF1-β and β-actin) under these conditions. We also demonstrated the effect of using reference candidate genes with different stability values to normalize the relative expression data from a drought-inducible soybean gene (DREB5) evaluated in different periods of the day

Selected DRIP and ERF superfamily target genes.

<p>The BLAST description and Gene Ontology are presented for each gene, and the sequences with greater similarity were used (GenBank access #). The BLAST results are from Aug. 2012 and the GO terms for Biological Process and Molecular Function are listed in the Gene Ontology annotation.</p><p>The BLAST description and Gene Ontology are presented for each gene; the sequences with greater similarity were used (GenBank accession #). The BLAST results are from Aug. 2012, and the GO terms for Biological Processes and Molecular Function are listed in the Gene Ontology annotation.</p