Plant growth and development are controlled by a delicate balance of hormonal cues. Growth-promoting hormones and growth-inhibiting counterparts often antagonize each other in their action, but the molecular mechanisms underlying these events remain largely unknown. Here, we report a cross-talk mechanism that enables a receptor-like kinase, FERONIA (FER), a positive regulator of auxin-promoted growth, to suppress the abscisic acid (ABA) response through activation of ABI2, a negative regulator of ABA signaling. The FER pathway consists of a FER kinase interacting with guanine exchange factors GEF1, GEF4, and GEF10 that, in turn, activate GTPase ROP11/ARAC10. Arabidopsis mutants disrupted in any step of the FER pathway, including fer, gef1gef4gef10, or rop11/arac10, all displayed an ABAhypersensitive response, implicating the FER pathway in the suppression mechanism. In search of the target for the FER pathway, we found that the ROP11/ARAC10 protein physically interacted with the ABI2 phosphatase and enhanced its activity, thereby linking the FER pathway with the inhibition of ABA signaling.A-type protein phosphatase 2C | signal transduction | small GTPase

SummaryPlant roots are required for the acquisition of water and nutrients, for responses to abiotic and biotic signals in the soil, and to anchor the plant in the ground. Controlling plant root architecture is a fundamental part of plant development and evolution, enabling a plant to respond to changing environmental conditions and allowing plants to survive in different ecological niches. Variations in the size, shape and surface area of plant root systems are brought about largely by variations in root branching. Much is known about how root branching is controlled both by intracellular signalling pathays and by environmental signals. Here, we will review this knowledge, with particular emphasis on recent advances in the field that open new and exciting areas of research. I. BackgroundA plant's root system is the site of water and nutrient uptake from the soil, a sensor of abiotic and biotic stresses, and a structural anchor to support the shoot. The root system communicates with the shoot, and the shoot in turn sends signals to the roots. A plant root system initially consists of a primary root (PR) formed during embryogenesis that has dividing cells in a meristem at its tip. As the seedling develops, certain other cells within the PR acquire the capability to *These authors contributed equally to this work.Key words: abiotic stress, biotic stress, lateral root development, nutrients, plant hormones, root system architecture, transcriptomics. (Fig. 1a). These branch out from the PR, greatly increasing the total surface area and mechanical strength of the root system and allow the plant to explore the soil environment. Ultimately, millions of higher-order root branches can form, resulting in hundreds of miles of root system in a small area of soil (Dittmer, 1937). New roots, called adventitious roots (AR), can also be formed postembryonically at the shoot-root junction, optimizing the exploration of the upper soil layers (Fig. 1a). In cereals such as rice and maize, root structure becomes more complex, with the formation of additional shoot-borne and postembryonic roots, which in turn undergo higher-order branching (Hochholdinger et al., 2004; Hochholdinger & Zimmermann, 2008; Fig. 1b). The root system architecture (RSA) of plants varies hugely between species and also shows extensive natural variation within species, reflecting the plethora of environments in which plants can grow (Cannon, 1949;Loudet et al., 2005;Osmont et al., 2007). Root system architecture manipulation is instrumental in the domestication and breeding of crop plants, because using water and nutrients from the soil in the most efficient manner affects a plant's ability to survive in stressful or poor soils. Changes in RSA can therefore have huge impacts on the final yield of a crop (reviewed in de Dorlodot et al., 2007). Of the factors that control total RSA, LR formation and growth is one of the most important.Many of the hormonal and environmental signals affecting LR development also affect other components that have a bearing on RSA...

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SummaryBarley (Hordeum vulgare) is a crop of global significance. However, a third of the genes of barley are largely inaccessible to conventional breeding programmes as crossovers are localised to the ends of the chromosomes. This work examines whether crossovers can be shifted to more proximal regions simply by elevating growth temperature.We utilised a genome-wide marker set for linkage analysis combined with cytological mapping of crossover events to examine the recombination landscape of plants grown at different temperatures.We found that barley shows heterochiasmy, that is, differences between female and male recombination frequencies. In addition, we found that elevated temperature significantly changes patterns of recombination in male meiosis only, with a repositioning of Class I crossovers determined by cytological mapping of HvMLH3 foci. We show that the length of synaptonemal complexes in male meiocytes increases in response to temperature.The results demonstrate that the distribution of crossover events are malleable and can be shifted to proximal regions by altering the growth temperature. The shift in recombination is the result of altering the distribution of Class I crossovers, but the higher recombination at elevated temperatures is potentially not the result of an increase in Class I events.

Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum,~1.4 and~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.

Auxin signaling relies on ubiquitin ligase SCFTIR1-mediated 26S proteasome-dependent proteolysis of a large family of short-lived transcription regulators, auxin/indole acetic acid (Aux/IAA), resulting in the derepression of auxin-responsive genes. We have shown previously that a subset of Rac GTPases is activated by auxin, and they in turn stimulate auxin-responsive gene expression. We show here that increasing Rac signaling activity promotes Aux/IAA degradation, whereas downregulating that activity results in the reduction of auxin-accelerated Aux/IAA proteolysis. Observations reported here reveal a novel function for these Rac GTPases as regulators for ubiquitin/26S proteasome-mediated proteolysis and further consolidate their role in auxin signaling. Moreover, our study reveals a cellular process whereby auxin induces and Rac GTPases mediate the recruitment of nucleoplasmic Aux/IAAs into proteolytically active nuclear protein bodies, into which components of the SCFTIR1, COP9 signalosome, and 26S proteasome are also recruited.

BackgroundWheat is one of the most widely grown crop in temperate climates for food and animal feed. In order to meet the demands of the predicted population increase in an ever-changing climate, wheat production needs to dramatically increase. Spike and grain traits are critical determinants of final yield and grain uniformity a commercially desired trait, but their analysis is laborious and often requires destructive harvest. One of the current challenges is to develop an accurate, non-destructive method for spike and grain trait analysis capable of handling large populations.ResultsIn this study we describe the development of a robust method for the accurate extraction and measurement of spike and grain morphometric parameters from images acquired by X-ray micro-computed tomography (μCT). The image analysis pipeline developed automatically identifies plant material of interest in μCT images, performs image analysis, and extracts morphometric data. As a proof of principle, this integrated methodology was used to analyse the spikes from a population of wheat plants subjected to high temperatures under two different water regimes. Temperature has a negative effect on spike height and grain number with the middle of the spike being the most affected region. The data also confirmed that increased grain volume was correlated with the decrease in grain number under mild stress.ConclusionsBeing able to quickly measure plant phenotypes in a non-destructive manner is crucial to advance our understanding of gene function and the effects of the environment. We report on the development of an image analysis pipeline capable of accurately and reliably extracting spike and grain traits from crops without the loss of positional information. This methodology was applied to the analysis of wheat spikes can be readily applied to other economically important crop species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-017-0229-8) contains supplementary material, which is available to authorized users.

The Arabidopsis cyclin-dependent kinase G (CDKG) gene defines a clade of cyclin-dependent protein kinases related to CDK10 and CDK11, as well as to the enigmatic Ph1-related kinases that are implicated in controlling homeologous chromosome pairing in wheat. Here we demonstrate that the CDKG1/CYCLINL complex is essential for synapsis and recombination during male meiosis. A transfer-DNA insertional mutation in the cdkg1 gene leads to a temperature-sensitive failure of meiosis in late Zygotene/Pachytene that is associated with defective formation of the synaptonemal complex, reduced bivalent formation and crossing over, and aneuploid gametes. An aphenotypic insertion in the cyclin L gene, a cognate cyclin for CDKG, strongly enhances the phenotype of cdkg1-1 mutants, indicating that this cdk-cyclin complex is essential for male meiosis. Since CYCLINL, CDKG, and their mammalian homologs have been previously shown to affect mRNA processing, particularly alternative splicing, our observations also suggest a mechanism to explain the widespread phenomenon of thermal sensitivity in male meiosis. R eplication and segregation of DNA underpins the reproduction of all cells. In organisms that undergo sexual reproduction, the nucleus carries two copies of each chromosome (or homologs) that replicate and recognize each other before the meiotic reduction division. This process allows the homologs to pair and exchange genetic material before segregation. A proteinaceous structure, known as the synaptonemal complex (SC), forms along the length of each set of paired chromosomes and subsequently forms physical connections between the homologs. Recombination between the homologs involves first the formation of DNA double-strand breaks (DSBs) that are either repaired as noncrossover or crossover (CO) products. Chiasmata, the cytological manifestation of COs, provide a physical connection between the homologs that persists after the SC is disassembled.Many of the proteins involved in meiotic recombination and homologous chromosome synapsis have been identified. At the leptotene stage of prophase I, the chromosome axes are elaborated along the conjoined bases of the sister chromatids. Concomitantly, Spo11-dependent DSBs form and are processed at the axes where the recombination machinery is assembled. This enables the alignment of homologous chromosomes and is dependent on the strand-exchange proteins Rad51 and DMC1. During zygotene, the SC starts to form between the homologs through the polymerization of the central element protein ZYP1 which brings the homologous chromosomes into close apposition. SC formation is complete by pachytene, during which the final stages of recombination are complete. The SC breaks down at the end of pachytene, and the chromosomes condense further during diplotene/diakinesis. At metaphase the bivalents held together by chiasmata are arranged at the metaphase plate, and the first meiotic division occurs.Although many of the structural proteins involved in the progression of meiotic prophase have been identi...