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Regulatory non-coding RNAs are emerging as key players in host-pathogen interactions. Small RNAs such as microRNAs are implicated in regulating plant transcripts involved in immunity and defence. Surprisingly, RNAs with silencing properties can be translocated from plant hosts to various invading pathogens and pests. Small RNAs are now confirmed virulence factors, with the first report of fungal RNAs that travel to host cells and hijack post-transcriptional regulatory machinery to suppress host defence. Here, we argue that trans-organism movement of RNAs represents a common mechanism of control in diverse interactions between plants and other eukaryotes. We suggest that extracellular vesicles are the key to such RNA movement events. Plant pathosystems serve as excellent experimental models to dissect RNA 'information warfare' and other RNA-mediated interactions., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Plant pathology has a long-standing tradition of classifying microbes as pathogens, endophytes or saprophytes. Lifestyles of pathogens are categorized as biotrophic, necrotrophic or hemibiotrophic. Botrytis species are considered by many to be archetypal examples of necrotrophic fungi, with B. cinerea being the most extensively studied species because of its broad host range and economic impact. In this review, we discuss recent work which illustrates that B. cinerea is capable of colonizing plants internally, presumably as an endophyte, without causing any disease or stress symptoms. The extent of the facultative endophytic behaviour of B. cinerea and its relevance in the ecology and disease epidemiology may be vastly underestimated. Moreover, we discuss the recent discovery of a novel Botrytis species, B. deweyae, which normally grows as an endophyte in ornamental daylilies (Hemerocallis), but displays facultative pathogenic behaviour, and is increasingly causing economic damage. We propose that the emergence of endophytes 'gone rogue' as novel diseases may be related to increased inbreeding of hybrid lines and reduced genetic diversity. These observations lead us to argue that the sometimes inflexible classification of pathogenic microbes by their lifestyles requires serious reconsideration. There is much more variety to the interactions of Botrytis with its hosts than the eye (or the plant pathologist) can see, and this may be true for other microbes interacting with plants., (© 2014 BSPP AND JOHN WILEY & SONS LTD.)

Foliar tissue samples of cultivated daylilies (Hemerocallis hybrids) showing the symptoms of a newly emergent foliar disease known as 'spring sickness' were investigated for associated fungi. The cause(s) of this disease remain obscure. We isolated repeatedly a fungal species which proved to be member of the genus Botrytis, based on immunological tests. DNA sequence analysis of these isolates, using several different phyogenetically informative genes, indicated that they represent a new Botrytis species, most closely related to B. elliptica (lily blight, fire blight) which is a major pathogen of cultivated Lilium. The distinction of the isolates was confirmed by morphological analysis of asexual sporulating cultures. Pathogenicity tests on Hemerocallis tissues in vitro demonstrated that this new species was able to induce lesions and rapid tissue necrosis. Based on this data, we infer that this new species, described here as B. deweyae, is likely to be an important contributor to the development of 'spring sickness' symptoms. Pathogenesis may be promoted by developmental and environmental factors that favour assault by this necrotrophic pathogen. The emergence of this disease is suggested to have been triggered by breeding-related changes in cultivated hybrids, particularly the erosion of genetic diversity. Our investigation confirms that emergent plant diseases are important and deserve close monitoring, especially in intensively in-bred plants.

Background: The identification of QTL involved in heterosis formation is one approach to unravel the not yet fully understood genetic basis of heterosis - the improved agronomic performance of hybrid F1 plants compared to their inbred parents. The identification of candidate genes underlying a QTL is important both for developing markers and determining the molecular genetic basis of a trait, but remains difficult owing to the large number of genes often contained within individual QTL. To address this problem in heterosis analysis, we applied a meta-analysis strategy for grain yield (GY) of Zea mays L. as example, incorporating QTL-, hybrid field-, and parental gene expression data., Results: For the identification of genes underlying known heterotic QTL, we made use of tight associations between gene expression pattern and the trait of interest, identified by correlation analyses. Using this approach genes strongly associated with heterosis for GY were discovered to be clustered in pericentromeric regions of the complex maize genome. This suggests that expression differences of sequences in recombination-suppressed regions are important in the establishment of heterosis for GY in F1 hybrids and also in the conservation of heterosis for GY across genotypes. Importantly functional analysis of heterosis-associated genes from these genomic regions revealed over-representation of a number of functional classes, identifying key processes contributing to heterosis for GY. Based on the finding that the majority of the analyzed heterosis-associated genes were addtitively expressed, we propose a model referring to the influence of cis-regulatory variation on heterosis for GY by the compensation of fixed detrimental expression levels in parents., Conclusions: The study highlights the utility of a meta-analysis approach that integrates phenotypic and multi-level molecular data to unravel complex traits in plants. It provides prospects for the identification of genes relevant for QTL, and also suggests a model for the potential role of additive expression in the formation and conservation of heterosis for GY via dominant, multigenic quantitative trait loci. Our findings contribute to a deeper understanding of the multifactorial phenomenon of heterosis, and thus to the breeding of new high yielding varieties.

In addition to its importance in studies of plant reproduction and fertility, pollen is as widely employed as a model system of cell growth and development. This work demands robust, reproducible methods to induce pollen germination and morphologically normal growth of pollen tubes in vitro. Despite numerous advantages of Arabidopsis thaliana as a model plant, such experiments on pollen germination and pollen tube growth have often proved challenging. Our new method employs a physical cellulosic membrane, overlying an agarose substrate. By modulating the substrate composition, we provide important insights into the mechanisms promoting pollen growth both in vitro and in vivo. This effective new technical approach to A. thaliana pollen germination and tube growth results in swift, consistent and unprecedented levels of germination to over 90%. It can also promote rapid growth of long, morphologically normal pollen tubes. This technical development demonstrates that exogenous spermidine and a cellulosic substrate are key factors in stimulating germination. It has potential to greatly assist the study of reproduction in A. thaliana and its closest relatives, not only for the study of germination levels and pollen tube growth dynamics by microscopy, but also for biochemical and molecular analysis of germinating pollen., (© 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.)

Genetic model organisms have revolutionized science, and today, with the rapid advances in technology, there is significant potential to launch many more plant species towards model status. However, these new model organisms will have to be carefully selected. Here, we argue that Hemerocallis (daylily) satisfies multiple criteria for selection and deserves serious consideration as a subject of intensive biological investigation. Several attributes of the genus are of great biological interest. These include the strict control of flower opening and, within a short period, the precisely regulated floral death by a programmed cell death system. The self-incompatibility system in Hemerocallis is also noteworthy and deserves more attention. Importantly, the genus is widely cultivated for food, medicinal value and ornamental interest. Hemerocallis has considerable potential as a 'nutraceutical' food plant and the source of new compounds with biomedical activity. The genus has also been embraced by ornamental plant breeders and the extraordinary morphological diversity of hybrid cultivars, produced within a relatively short time by amateur enthusiasts, is an exceptional resource for botanical and genetic studies. We explore these points in detail, explaining the reasons why this genus has considerable value-both academic and socio-economic-and deserves new resources devoted to its exploration as a model. Its impact as a future model will be enhanced by its amenability to cultivation in laboratory and field conditions. In addition, established methods for various tissue and cell culture systems as well as transformation will permit maximum exploitation of this genus by science.

Somaclonal variation is an important phenomenon that can be observed at high levels in plant tissue culture. Although known to science since plant cell culture techniques were first developed, its origins remain mysterious. Here, we propose that misregulation of microRNAs and small RNA pathways can make a significant contribution to the phenomenon. For many reasons, microRNAs and related small RNAs appear ideal candidates. Their mode of action gives them disproportionate influence over the transcriptome, proteome and epigenome. They regulate important developmental and physiological events such as meristem formation, phase changes and hormone responses. However, the genomic locations of microRNA genes and their unique biogenesis might make them unusually susceptible to aberrant regulation in vitro., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Small non-coding RNAs are key post-transcriptional and transcriptional regulators of plant gene expression in angiosperm sporophytes. In recent years, gametophytic small RNAs have also been investigated, predominantly in Arabidopsis male gametophytes, revealing features in common with the sporophyte as well as some surprising differences. Transcriptomic and deep-sequencing studies confirm that multiple small RNA pathways operate in male gametophytes, with over 100 miRNAs detected throughout development. Trans-acting siRNA pathways that are associated with novel phased transcripts in pollen, and the nat-siRNA pathway have important roles in pollen maturation and gamete function. Moreover, a role for siRNA-triggered silencing of transposable elements in male and female germ cells has been established, a feature in common with the role of piRNAs in animal germlines. Current evidence supports an integral role for small RNAs in angiosperm gametophyte development and it can be anticipated that novel small RNAs with significant roles in germline development and genome integrity await discovery.

The various classes of small non-coding RNAs are a fundamentally important component of the transcriptome. These molecules have roles in many essential processes such as regulation of gene expression at the transcriptional and post-transcriptional levels, guidance of DNA methylation and defence against selfish replicators such as transposons. Their diversity and functions in the sporophytic generation of angiosperms is well explored compared with the gametophytic generation, where little is known about them. Recent progress in understanding their abundance, diversity and function in the gametophyte is reviewed.

Scope: In the second part of a two-part review, the ubiquity and universality of epigenetic systems is emphasized, and attention is drawn to the key roles they play, ranging from transducing environmental signals to altering gene expression, genomic architecture and defence., Key Issues: The importance of transience versus heritability in epigenetic marks is examined, as are the potential for stable epigenetic marks to contribute to plant evolution, and the mechanisms generating novel epigenetic variation, such as stress and interspecific hybridization., Future Prospects: It is suggested that the ramifications of epigenetics in plant biology are immense, yet unappreciated. In contrast to the ease with which the DNA sequence can be studied, studying the complex patterns inherent in epigenetics poses many problems. Greater knowledge of patterns of epigenetic variation may be informative in taxonomy and systematics, as well as population biology and conservation.

Background: Epigenetics has rapidly evolved in the past decade to form an exciting new branch of biology. In modern terms, 'epigenetics' studies molecular pathways regulating how the genes are packaged in the chromosome and expressed, with effects that are heritable between cell divisions and even across generations., Context: Epigenetic mechanisms often conflict with Mendelian models of genetics, and many components of the epigenetic systems in plants appeared anomalous. However, it is now clear that these systems govern how the entire genome operates and evolves., Scope: In the first part of a two-part review, how epigenetic systems in plants were elucidated is addressed. Also there is a discussion on how the different components of the epigenetic system--regulating DNA methylation, histones and their post-translational modification, and pathways recognizing aberrant transcripts--may work together.

An RNA-based communication network appears to play a crucial role in regulating gene expression and in repressing viral and transposon sequences in plant genomes. In this article, we consider the evidence that gene expression might also be controlled epigenetically at a level other than non-coding RNA species-chromosome pairing. This epigenetic communication between sequences might be based--as it is in other organisms--on the physical pairing between homologues and the transfer of information between corresponding epigenetic landscapes. We suggest that paramutation might represent just one--albeit extreme and obvious--facet of a pairing-based gene expression regulation system in plants. Further exciting evidence for pairing occurring between homologues in plants is now mounting. An appreciation that pairing interactions might be important throughout plant development could assist in understanding phenomena such as endosperm imprinting, hybrid phenotypes and inbreeding depression.