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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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.