Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa

Developmental and genomic architecture of plant embryogenesis: from model plant to crops

Embryonic development represents an important reproductive phase of sexually reproducing plant species. The fusion of egg and sperm produces the plant zygote, a totipotent cell that, through cell division and cell identity specification in early embryogenesis, establishes the major cell lineages and tissues of the adult plant. The subsequent morphogenesis phase produces the full-sized embryo, while the late embryogenesis maturation process prepares the seed for dormancy and subsequent germination, ensuring continuation of the plant life cycle. In this review on embryogenesis, we compare the model eudicot Arabidopsis thaliana with monocot crops, focusing on genome activation, paternal and maternal regulation of early zygote development, and key organizers of patterning, such as auxin and WOX transcription factors. While the early stages of embryo development are apparently conserved among plant species, embryo maturation programs have diversified between eudicots and monocots. This diversification in crop species reflects the likely effects of domestication on seed quality traits that are determined during embryo maturation, and also assures seed germination in different environmental conditions. This review describes the most important features of embryonic development in plants, and the scope and applications of genomics in plant embryo studies.

Linkage-linkage disequilibrium dissection of the epigenetic quantitative trait loci (epiQTLs) underlying growth and wood properties in Populus

Increasing evidence indicates that DNA methylation is heritable and serves as an essential marker contributing to phenotypic variation. Linkage-linkage disequilibrium mapping was used to decipher the epigenetic architecture underlying nine growth and wood property traits in a linkage population (550 F₁ progeny) and a natural population (435 unrelated individuals) of Populus using methylation-sensitive amplification polymorphism (MSAP)-based analysis. The interactions between genetic and epigenetic variants in the causative genes was further unveiled using expression quantitative trait methylation (eQTM) and nucleotide (eQTN) mapping strategies. A total of 163 epigenetic quantitative trait loci (epiQTLs; LOD ≥ 3.0), explaining 1.7-44.5% of phenotypic variations, were mapped to a high-resolution epigenetic map with 19 linkage groups, which was supported by the significant MSAP associations (P < 0.001) in the two populations. There were 23 causal genes involved in growth regulation and wood formation, whose markers were located in epiQTLs and associated with the same traits in both populations. Further eQTN and eQTM mapping showed that causal genetic and epigenetic variants within the 23 candidate genes may interact more in trans in gene expression and phenotype. The present study provides strategies for investigating epigenetic architecture and the interaction between genetic and epigenetic variants modulating complex traits in forest trees.

An RNA-binding protein MUG13.4 interacts with AtAGO2 to modulate salinity tolerance in Arabidopsis

Salt stress is a major constraint to plant growth and development, and plants have developed sophisticated mechanisms to cope with it. AtAGO2, an argonaute protein, is known to play an important role in plant adaptation to salt stress; however, the molecular mechanism of this phenomenon remains essentially unexplored. Here, we performed the yeast two-hybrid assay and found an R3H-domain containing protein, designated as MUG13.4, interacting with AtAGO2. Further bimolecular fluorescence complement (BiFC), glutathione-S-transferase (GST) pull-down, and co-immunoprecipitation (Co-IP) assays confirmed that MUG13.4 interacted with AtAGO2, and MUG13.4 could affect the slicing activity of AtAGO2 associated with miR173. MUG13.4 and AtAGO2 were both predominantly expressed in seeds and roots. Phenotypic analyses of the single and double mutants under salt stress confirmed involvement of MUG13.4-AtAGO2 complex as a component of the salt tolerance mechanism. The mug13.4×ago2-1 double mutant displayed retarded growth and hypersensitivity to salt stress that was more pronounced than in mug13.4 or atago2-1 single mutants. TAS1c-tasiRNA generating system in Nicotiana benthamiana revealed that MUG13.4 could influence the slicing activity of AtAGO2. We also found that MUG13.4 increasingly changed the phenotype of slicer-defected mutants of AtAGO2 in response to salt stress. These findings suggested that the function of AtAGO2 upon salt stress was dependent on MUG13.4. Further investigation suggested that AtAGO2 improved Arabidopsis tolerance to salt stress by affecting operation of the SOS signaling cascade at the transcript level. Taken together, these findings reveal a novel function of MUG13.4 in adjusting Arabidopsis adaptation to salt stress.

A role for ecophysiology in the 'omics' era

Plant Ecophysiology is the study on how Plant Physiology is modulated by the environment. This discipline could have benefited greatly from the development of the different 'omic' technologies (from genomics to metabolomics). Instead, the overall impression is that ecophysiology and 'omics' have developed mostly independent each other. Here we provide a literature analysis over the past 20 years which fully confirms this view. Then, we review a few examples of studies in which ecophysiology and 'omics' studies have combined to different extents to illustrate the potential benefits from their mutualistic interaction. In addition, we debate on the possibilities of working with plants other than Arabidopsis, which is illustrated with some examples of fascinating plants from extreme environments of the world, what we call the 'sherplants'. Finally, we raise a call to both communities (ecophysiology and 'omics') to integrate these disciplines to enter an 'ecophysiolomics era' to maximize our understanding about plant mechanisms from a multidisciplinary approach.