Transcriptional profiling of Zea mays genotypes with different drought tolerances – new perspectives for gene expression markers selection

Drought is considered to be one of the greatest limiting factors in agriculture. Therefore, the ability of plants to adapt to drought conditions is crucial to sustain worldwide crop production. The aim of this work was to identify gene expression markers for drought tolerance in Zea mays with the potential to assist breeding. Selected maize genotypes were characterized with respect to drought tolerance by measurements of the relative water content after drought stress conditions. Tolerant genotypes were screened for up-regulated genes in drought conditions detected by previous microarray hybridizations. Five cDNAs coding for drought inducible genes in maize were identified and further characterized by semi-quantitative reverse transcription polymerase chain reactions. The expression levels of two of them (MZ00023411 and MZ00037881) allow a significant discrimination between toler¬ant and susceptible genotypes. In tolerant genotypes (MK01, MK01xRF7, 002x250) the expression level of these genes was at least twice higher as compared to susceptible genotypes (XL12, 005, 005x301) throughout all condi¬tions tested. Almost for all tolerant genotypes were registered significant differences (P≤0.05), versus susceptible ones, in expression of these genes. Specific primers for these two genes allow discrimination of drought tolerant and susceptible maize genotypes even after 2h of dehydration stress based on expression level and are suitable as potential gene expression markers, associated with drought tolerance

Forest age and plant species composition determine the soil fungal community composition in a Chinese subtropical forest

Non peer reviewedPublisher PD

DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.

Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion

Dissecting grain yield pathways and their interactions with grain dry matter content by a two-step correlation approach with maize seedling transcriptome

<p>Abstract</p> <p>Background</p> <p>The importance of maize for human and animal nutrition, but also as a source for bio-energy is rapidly increasing. Maize yield is a quantitative trait controlled by many genes with small effects, spread throughout the genome. The precise location of the genes and the identity of the gene networks underlying maize grain yield is unknown. The objective of our study was to contribute to the knowledge of these genes and gene networks by transcription profiling with microarrays.</p> <p>Results</p> <p>We assessed the grain yield and grain dry matter content (an indicator for early maturity) of 98 maize hybrids in multi-environment field trials. The gene expression in seedlings of the parental inbred lines, which have four different genetic backgrounds, was assessed with genome-scale oligonucleotide arrays. We identified genes associated with grain yield and grain dry matter content using a newly developed two-step correlation approach and found overlapping gene networks for both traits. The underlying metabolic pathways and biological processes were elucidated. Genes involved in sucrose degradation and glycolysis, as well as genes involved in cell expansion and endocycle were found to be associated with grain yield.</p> <p>Conclusions</p> <p>Our results indicate that the capability of providing energy and substrates, as well as expanding the cell at the seedling stage, highly influences the grain yield of hybrids. Knowledge of these genes underlying grain yield in maize can contribute to the development of new high yielding varieties.</p

Re-annotation of the maize oligonucleotide array

The microarray technology has become an established approach for large-scale gene expression analysis with mature protocols for sample, microarray, and data processing. The maize oligonucleotide array (maizearray) is one of the few microarray platforms designed for genome-wide gene expression analysis in Zea mays L. Many datasets addressing various genetic, physiological and developmental topics generated with this platform are available. The original 57,452 microarray probes were compiled based on expressed sequence tags (ESTs). Meanwhile the maize genome sequence became available providing the possibility for an improved annotation of the microarray probe set. In this study we determined the genome positions of all maize array probes to obtain current gene annotations and generated current Gene Ontology (GO) annotations. These new data allow tracing redundancy of the probe set and interfering cross-hybridizations, and doubled the number of genes with functional GO data. Our re-annotation will largely improve the functional analysis of available and future datasets generated on this microarray platform

Characterization of paired Cas9 nickases induced mutations in maize mesophyll protoplasts

Targeted genome modifications are important for both fundamental and applied research. The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats / CRISPR-associated protein 9) technology has been successfully used in various plant species with high efficiency. Approaches with paired Cas9 nickase enhance the specificity of the CRISPR/Cas9 system by using guide RNA pairs to create two staggered single strand breaks on complementary DNA strands. Here we used maize mesophyll protoplasts as a transient test system and demon- strated the mutagenic potential of Cas9 nickases. Although we found activity for all the three different guide RNA pairs tested, their efficiency varied considerably. Characterization of the modification events revealed a high ratio of large deletions as well as insertions of donor DNA fragments. By the use of the maternally expressed in embryo 1 gene (mee1) as model target sequence, we could demonstrate that transcriptionally inactive and methylated genomic loci are practical targets of Cas9 nickase. The high specificity of Cas9 nickase approaches might provide advantage for genome modifications of certain loci in the complex and highly repetitive maize genome

Designing forest biodiversity experiments : general considerations illustrated by a new large experiment in subtropical China

Funded by German Research Foundation. Grant Number: DFG FOR 891/1 and 2 National Natural Science Foundation of China. Grant Numbers: NSFC 30710103907, 30930005, 31170457 , 31210103910 Swiss National Science Foundation (SNSF) Sino-German Centre for Research Promotion in BeijingPeer reviewedPublisher PD

Forest Age and Plant Species Composition Determine the Soil Fungal Community Composition in a Chinese Subtropical Forest

Fungal diversity and community composition are mainly related to soil and vegetation factors. However, the relative contribution of the different drivers remains largely unexplored, especially in subtropical forest ecosystems. We studied the fungal diversity and community composition of soils sampled from 12 comparative study plots representing three forest age classes (Young: 10-40 yrs; Medium: 40-80 yrs; Old: ⋝ 80 yrs) in Gutianshan National Nature Reserve in South-eastern China. Soil fungal communities were assessed employing ITS rDNA pyrotag sequencing. Members of Basidiomycota and Ascomycota dominated the fungal community, with 22 putative ectomycorrhizal fungal families, where Russulaceae and Thelephoraceae were the most abundant taxa. Analysis of similarity showed that the fungal community composition significantly differed among the three forest age classes. Forest age class, elevation of the study plots, and soil organic carbon (SOC) were the most important factors shaping the fungal community composition. We found a significant correlation between plant and fungal communities at different taxonomic and functional group levels, including a strong relationship between ectomycorrhizal fungal and non-ectomycorrhizal plant communities. Our results suggest that in subtropical forests, plant species community composition is the main driver of the soil fungal diversity and community composition

Spectrophotometric analysis of the Ryugu rock seen by MASCOT: Searching for a carbonaceous chondrite analog

We analyze images of a rock on Ryugu acquired in situ by MASCam, camera of the MASCOT lander, with the aim of identifying possible carbonaceous chondrite (CC) analogs. The rock's reflectance ($r_{\rm F} = 0.034 \pm 0.003$ at phase angle $4.5^\circ \pm 0.1^\circ$) is consistent with Ryugu's average reflectance, suggesting that the rock is typical for this asteroid. A spectrophotometric analysis of the rock's inclusions provides clues to CC group membership. Inclusions are generally brighter than the matrix. The dominant variation in their color is a change of the visible spectral slope, with many inclusions being either red or blue. Spectral variation in the red channel hints at the presence of the 0.7~$\mu$m absorption band linked to hydrated phyllosilicates. The inclusions are unusually large for a CC; we find that their size distribution may best match that of the Renazzo (CR2) and Leoville (CV3) meteorites. The Ryugu rock does not easily fit into any of the CC groups, consistent with the idea that typical Ryugu-type meteorites are too fragile to survive atmospheric entry