Circadian clocks allow the temporal compartmentalization of biological processes. In Arabidopsis, circadian rhythms display organ specificity but the underlying molecular causes have not been identified. We investigated the mechanisms responsible for the similarities and differences between the clocks of mature shoots and roots in constant conditions and in light : dark cycles. We developed an imaging system to monitor clock gene expression in shoots and light- or dark-grown roots, modified a recent mathematical model of the Arabidopsis clock and used this to simulate our new data. We showed that the shoot and root circadian clocks have different rhythmic properties (period and amplitude) and respond differently to light quality. The root clock was entrained by direct exposure to low-intensity light, even in antiphase to the illumination of shoots. Differences between the clocks were more pronounced in conditions where light was present than in constant darkness, and persisted in the presence of sucrose. We simulated the data successfully by modifying those parameters of a clock model that are related to light inputs. We conclude that differences and similarities between the shoot and root clocks can largely be explained by organ-specific light inputs. This provides mechanistic insight into the developing field of organ-specific clocks.
Assimilate partitioning to the root system is a desirable developmental trait to control but little is known of the signaling pathway underlying partitioning. A null mutation in the gene encoding the Gβ subunit of the heterotrimeric G protein complex, a nexus for a variety of signaling pathways, confers altered sugar partitioning in roots. While fixed carbon rapidly reached the roots of wild type and agb1-2 mutant seedlings, agb1 roots had more of this fixed carbon in the form of glucose, fructose, and sucrose which manifested as a higher lateral root density. Upon glucose treatment, the agb1-2 mutant had abnormal gene expression in the root tip validated by transcriptome analysis. In addition, PIN2 membrane localization and level was altered in the agb1-2 mutant. The heterotrimeric G protein complex integrates photosynthesis-derived sugar signaling incorporating both membrane-and transcriptional-based mechanisms. The time constants for these signaling mechanisms are in the same range as photosynthate delivery to the root, raising the possibility that root cells are able to use changes in carbon fixation in real time to adjust growth behavior.
Einkorn, emmer, and spelt are old wheat species that have fed the world for centuries before they have nearly completely been replaced by modern bread wheat. Nowadays, the diversity of these old species lies frozen in gene banks and rare attempts aim to exploit them as a source for genetic diversity in modern wheat breeding. Here, we want to raise a debate on a more holistic exploitation of ancient species via their direct introduction to the consumer market as high quality products. Although exemplified only for ancient wheat species, this innovative self-financing strategy can be directly extended to other species.
The present work investigates the interactions between soil content, rootstock and scion by focusing on the effects of roostocks and nitrogen supply on grape berry content. Scions of Cabernet Sauvignon (CS) and Pinot Noir (PN) varieties were grafted either on Riparia Gloire de Montpellier (RGM) or 110 Richter (110R) rootstock. The 4 rooststock/scion combinations were fertilized with 3 different levels of nitrogen after fruit set. Both in 2013 and 2014, N supply increased N uptake by the plants, and N content both in vegetative and reproductory organs. Rootstock, variety and year affected berry weight at harvest, while nitrogen did not affect significantly this parameter. Grafting on RGM consistently increased berry weight compared to 110R. PN consistently produced bigger berries than CS. CS berries were heavier in 2014 than in 2013, but the year effect was less marked for PN berries. The berries were collected between veraison and maturity, separated in skin and pulp, and their content was analyzed by conventional analytical procedures and untargeted metabolomics. For anthocyanins, the relative quantitation was fairly comparable with both LC-MS determination and HPLC-DAD, which is a fully quantitative technique. The data show complex responses of the metabolite content (sugars, organic acids, amino acids, anthocyanins, flavonols, flavan-3-ols/procyanidins, stilbenes, hydroxycinnamic and hydroxybenzoic acids.) that depend on the rootstock, the scion, the vintage, the nitrogen level, the berry compartment. This opens a wide range of possibilities to adjust the content of these compounds through the choice of the roostock, variety and nitrogen fertilization.
This review presents recent progress in various aspects of plant carotenoids research, along with the knowledge on carotenoid metabolism and regulation in plants. It also covers the most recent progress in the field of carotenoid metabolism, sequestration, and degradation.
Root hairs are fast growing, ephemeral tubular extensions of the root epidermis. They arise in the unsuberized maturation zone of the root, effectively increasing the root surface area in the region over which nutrient and water uptake occur. Variation in root hair length (RHL) between varieties has been shown to be genetically determined, and could, therefore, have consequences for nutrient capture and yield potential in crops. We describe the development of a medium-to-high throughput screening method for assessing RHL in wheat at the seedling stage. This method was used to screen a number of wheat mapping population parental lines for variation in RHL. Parents of two populations derived from inter-varietal crosses differed for RHL: Spark vs Rialto and Charger vs Badger. We identified quantitative trait loci (QTLs) for RHL in the populations derived from these crosses. In Spark × Rialto, QTLs on chromosomes 1A, 2A and 6A were associated with variation in RHL, whilst in Charger × Badger, a QTL for RHL was identified on 2BL. The QTLs on 2A and 6A co-localized with previously described QTLs for yield components. Longer root hairs may confer an advantage by exploiting limiting mineral and water resources. This first QTL analysis of root hair length in wheat identifies loci that could usefully be further investigated for their role in tolerance to limiting conditions.
Mitogen-activated protein kinase (MAPK) cascades play critical roles in signal transduction processes in eukaryotes. The MAPK kinases (MAPKKs) that link MAPKK kinases (MAPKKKs) and MAPKs are key components of MAPK cascades. However, the intricate regulatory mechanisms that control MAPKKs under drought stress conditions are not fully understood, especially in cotton (Gossypium hirsutum). Here, we isolated and characterized the cotton group B MAPKK gene GhMKK3. Overexpressing GhMKK3 in Nicotiana benthamiana enhanced tolerance to drought, and the results of RNA sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR) assays suggest that GhMKK3 plays an important role in responses to abiotic stresses by regulating stomatal responses and root hair growth. Further evidence demonstrated that overexpressing GhMKK3 promoted root growth and ABA-induced stomatal closure. In contrast, silencing GhMKK3 in cotton using virus-induced gene silencing (VIGS) resulted in the opposite phenotypes. More importantly, we identified an ABA- and drought-induced MAPK cascade that is composed of GhMKK3, GhMPK7 and GhPIP1 that compensates for deficiency in the MAPK cascade pathway in cotton under drought stress conditions. Together, these findings significantly improve our understanding of the mechanism by which GhMKK3 positively regulates drought stress responses.
Phytohormone ethylene has previously been known to play an important role in mediating root hair development induced by phosphate starvation; however, the underlying molecular mechanism is not understood. Using combined molecular, genetic, and genomic approaches, we identify a group of genes that affect root hair development by regulating cell wall modifications. Pi starvation increase the stability of EIN3 protein, a key component in the ethylene signaling pathway. The expression of the identified root hair-related genes is enhanced in the EIN3-overexpressing line, but suppressed in the ein3 mutant. Furthermore, EIN3 protein directly binds to the promoter of these genes which are also targeted by a key transcription factor that regulates root hair development. This work not only explains how ethylene mediates root hair responses to phosphate starvation, but may provide a general mechanism for how ethylene regulates root hair development under both stress and non-stress conditions.
Sensitivity to variability in resources has been documented in humans, primates, birds, and social insects, but the fit between empirical results and the predictions of risk sensitivity theory (RST), which aims to explain this sensitivity in adaptive terms, is weak . RST predicts that agents should switch between risk proneness and risk aversion depending on state and circumstances, especially according to the richness of the least variable option . Unrealistic assumptions about agents’ information processing mechanisms and poor knowledge of the extent to which variability imposes specific selection in nature are strong candidates to explain the gap between theory and data. RST’s rationale also applies to plants, where it has not hitherto been tested. Given the differences between animals’ and plants’ information processing mechanisms, such tests should help unravel the conflicts between theory and data. Measuring root growth allocation by split-root pea plants, we show that they favor variability when mean nutrient levels are low and the opposite when they are high, supporting the most widespread RST prediction. However, the combination of non-linear effects of nitrogen availability at local and systemic levels may explain some of these effects as a consequence of mechanisms not necessarily evolved to cope with variance [3 and 4]. This resembles animal examples in which properties of perception and learning cause risk sensitivity even though they are not risk adaptations .
Trichomes are widely distributed on surfaces of different organs in the grape genus Vitis and are of taxonomic utility. To explore the morphology, structure and ontogeny of Vitis trichomes, we investigated the diversity and distribution of trichomes in 34 species of Vitis. Two main types of trichomes in Vitis are documented: non-glandular and glandular. Within non-glandular trichomes, ribbon and simple trichomes are found on different vegetative plant organs. The morphology and ontogeny of these types of trichomes are further examined with light microscopy and scanning electron microscopy. The ultrastructure of the glandular trichomes is explored with transmission electron microscopy. The ribbon trichomes are twisted, greatly elongated and unicellular, and this trichome type may be a morphological synapomorphy of Vitis and its closest tropical relative Ampelocissus and Pterisanthes in Vitaceae. The simple trichomes are documented in most species sampled in the genus. The glandular trichomes are multicellular, non-vascularized and composed of both epidermis and subjacent layers. We show that prickles occurring along the stems and petioles of Vitis davidii are modified glandular trichomes. We observed that glandular trichomes of V. romanetii secrete mucilage and volatile substances which trap insectes on the glands. Transmission electron microscopy indicates that metabolic products accumulate in vacuoles, the cytoplasm and intercellular spaces. We infer that glandular trichomes and young prickles are involved in the secretion of these metabolic products and the intercellular spaces may be the places of temporary storage of these secretions.
Plant natural products are of great value for agriculture, medicine and a wide range of other industrial applications. The discovery of new plant natural product pathways is currently being revolutionized by two key developments. First, breakthroughs in sequencing technology and reduced cost of sequencing are accelerating the ability to find enzymes and pathways for the biosynthesis of new natural products by identifying the underlying genes. Second, there are now multiple examples in which the genes encoding certain natural product pathways have been found to be grouped together in biosynthetic gene clusters within plant genomes. These advances are now making it possible to develop strategies for systematically mining multiple plant genomes for the discovery of new enzymes, pathways and chemistries. Increased knowledge of the features of plant metabolic gene clusters – architecture, regulation and assembly – will be instrumental in expediting natural product discovery. This review summarizes progress in this area.
In this opinion article we examine the relationship between penetrometer resistance and soil depth in the field. Assuming that root growth is inhibited at penetrometer resistances > 2.5 MPa, we conclude that in most circumstances the increases in penetrometer resistance with depth are sufficiently great to confine most deep roots to elongating in existing structural pores. We suggest that deep rooting is more likely related to the interaction between root architecture and soil structure than it is to the ability of a root to deform strong soil. Although the ability of roots to deform strong soil is an important trait, we propose it is more closely related to root exploration of surface layers than deep rooting.
The directional transport of auxin, known as polar auxin transport (PAT), allows asymmetric distribution of this hormone in different cells and tissues. This system creates local auxin maxima, minima, and gradients that are instrumental in both organ initiation and shape determination. As such, PAT is crucial for all aspects of plant development but also for environmental interaction, notably in shaping plant architecture to its environment. Cell to cell auxin transport is mediated by a network of auxin carriers that are regulated at the transcriptional and post-translational levels. Here we review our current knowledge on some aspects of the ‘non-genomic’ regulation of auxin transport, placing an emphasis on how phosphorylation by protein and lipid kinases controls the polarity, intracellular trafficking, stability, and activity of auxin carriers. We describe the role of several AGC kinases, including PINOID, D6PK, and the blue light photoreceptor phot1, in phosphorylating auxin carriers from the PIN and ABCB families. We also highlight the function of some receptor-like kinases (RLKs) and two-component histidine kinase receptors in PAT, noting that there are probably RLKs involved in co-ordinating auxin distribution yet to be discovered. In addition, we describe the emerging role of phospholipid phosphorylation in polarity establishment and intracellular trafficking of PIN proteins. We outline these various phosphorylation mechanisms in the context of primary and lateral root development, leaf cell shape acquisition, as well as root gravitropism and shoot phototropism.
Plants have evolved a remarkable faculty of adaptation to deal with various and changing environmental conditions. In this context, the roots have taken over nutritional aspects and the root system architecture can be modulated in response to nutrient availability or biotic interactions with soil microorganisms. This adaptability requires a fine tuning of gene expression. Indeed, root specification and development are highly complex processes requiring gene regulatory networks involved in hormonal regulations and cell identity. Among the different molecular partners governing root development, microRNAs (miRNAs) are key players for the fast regulation of gene expression. miRNAs are small RNAs involved in most developmental processes and are required for the normal growth of organisms, by the negative regulation of key genes, such as transcription factors and hormone receptors. Here, we review the known roles of miRNAs in root specification and development, from the embryonic roots to the establishment of root symbioses, highlighting the major roles of miRNAs in these processes.
Last September, world leaders made a commitment to end hunger by 2030, as part of the United Nations Sustainable Development Goals (SDGs). It sounds like a massive undertaking. In fact, the world already produces enough food to feed everyone. So why does the problem persist?
Plant cell walls provide stability and protection to plant cells. During growth and development the composition of cell walls changes, but provides enough strength to withstand the turgor of the cells. Hence, cell walls are highly flexible and diverse in nature. These characteristics are important during root growth, as plant roots consist of radial patterns of cells that have diverse functions and that are at different developmental stages along the growth axis. Young stem cell daughters undergo a series of rapid cell divisions, during which new cell walls are formed that are highly dynamic, and that support rapid anisotropic cell expansion. Once the cells have differentiated, the walls of specific cell types need to comply with and support different cell functions. For example, a newly formed root hair needs to be able to break through the surrounding soil, while endodermal cells modify their walls at distinct positions to form Casparian strips between them. Hence, the cell walls are modified and rebuilt while cells transit through different developmental stages. In addition, the cell walls of roots readjust to their environment to support growth and to maximize nutrient uptake. Many of these modifications are likely driven by different developmental and stress signalling pathways. However, our understanding of how such pathways affect cell wall modifications and what enzymes are involved remain largely unknown. In this review we aim to compile data linking cell wall content and re-modelling to developmental stages of root cells, and dissect how root cell walls respond to certain environmental changes.
Breeding crops with more biomass produced per drop of water transpired is a key challenge in the context of climate change. However, the tight coupling between transpiration and carbon assimilation during the day makes it challenging to decrease water loss without altering photosynthesis and reducing crop yield. We tested whether reducing transpiration at night when photosynthesis is inactive could substantially reduce water loss without altering growth—a hypothesis that, to our knowledge, has never been genetically addressed in any species. By studying a whole progeny in grapevine, a major crop for drought-prone areas, we identified genomic regions where selection could be operated to reduce transpiration at night and maintain growth. This opens new horizons for breeding crops with higher water-use efficiency.
In this study we test the hypothesis that maize genotypes with reduced crown root number (CN) will have greater root depth and improved water acquisition from drying soil. Maize recombinant inbred lines with contrasting CN were evaluated under water stress in greenhouse mesocosms and field rainout shelters. CN varied from 25 to 62 among genotypes. Under water stress in the mesocosms, genotypes with low CN had 31% fewer crown roots, 30% deeper rooting, 56% greater stomatal conductance, 45% greater leaf CO2 assimilation, 61% net canopy CO2 assimilation, and 55% greater shoot biomass than genotypes with high CN at 35 days after planting. Under water stress in the field, genotypes with low CN had 21% fewer crown roots, 41% deeper rooting, 48% lighter stem water oxygen isotope enrichment (δ18O) signature signifying deeper water capture, 13% greater leaf relative water content, 33% greater shoot biomass at anthesis, and 57% greater yield than genotypes with high CN. These results support the hypothesis that low CN improves drought tolerance by increasing rooting depth and water acquisition from the subsoil.
Future rice (Oryza sativa) crops will likely experience a range of growth conditions, and root architectural plasticity will be an important characteristic to confer adaptability across variable environments. In this study, the relationship between root architectural plasticity and adaptability (i.e. yield stability) was evaluated in two traditional × improved rice populations (Aus 276 × MTU1010 and Kali Aus × MTU1010). Forty contrasting genotypes were grown in direct-seeded upland and transplanted lowland conditions with drought and drought + rewatered stress treatments in lysimeter and field studies and a low-phosphorus stress treatment in a Rhizoscope study. Relationships among root architectural plasticity for root dry weight, root length density, and percentage lateral roots with yield stability were identified. Selected genotypes that showed high yield stability also showed a high degree of root plasticity in response to both drought and low phosphorus. The two populations varied in the soil depth effect on root architectural plasticity traits, none of which resulted in reduced grain yield. Root architectural plasticity traits were related to 13 (Aus 276 population) and 21 (Kali Aus population) genetic loci, which were contributed by both the traditional donor parents and MTU1010. Three genomic loci were identified as hot spots with multiple root architectural plasticity traits in both populations, and one locus for both root architectural plasticity and grain yield was detected. These results suggest an important role of root architectural plasticity across future rice crop conditions and provide a starting point for marker-assisted selection for plasticity.
Background Morphogenesis depends on the concerted modulation of cell proliferation and differentiation. Such modulation is dynamically adjusted in response to various external and internal signals via complex transcriptional regulatory networks that mediate between such signals and regulation of cell-cycle and cellular responses (proliferation, growth, differentiation). In plants, which are sessile, the proliferation/differentiation balance is plastically adjusted during their life cycle and transcriptional networks are important in this process. MADS-box genes are key developmental regulators in eukaryotes, but their role in cell proliferation and differentiation modulation in plants remains poorly studied.
Methods We characterize the XAL1 loss-of-function xal1-2 allele and overexpression lines using quantitative cellular and cytometry analyses to explore its role in cell cycle, proliferation, stem-cell patterning and transition to differentiation. We used quantitative PCR and cellular markers to explore if XAL1 regulates cell-cycle components and PLETHORA1 (PLT1) gene expression, as well as confocal microscopy to analyse stem-cell niche organization.
Key Results We previously showed that XAANTAL1 (XAL1/AGL12) is necessary for Arabidopsis root development as a promoter of cell proliferation in the root apical meristem. Here, we demonstrate that XAL1 positively regulates the expression of PLT1 and important components of the cell cycle: CYCD3;1, CYCA2;3, CYCB1;1, CDKB1;1 and CDT1a. In addition, we show that xal1-2 mutant plants have a premature transition to differentiation with root hairs appearing closer to the root tip, while endoreplication in these plants is partially compromised. Coincidently, the final size of cortex cells in the mutant is shorter than wild-type cells. Finally, XAL1 overexpression-lines corroborate that this transcription factor is able to promote cell proliferation at the stem-cell niche.
Conclusion XAL1 seems to be an important component of the networks that modulate cell proliferation/differentiation transition and stem-cell proliferation during Arabidopsis root development; it also regulates several cell-cycle components.
GRAS domain genes are a group of important plant-specific transcription factors that have been reported to be involved in plant development. In order to know the roles of GRAS genes in grapevine, a widely cultivated fruit crop, the study on grapevine GRAS (VvGRAS) was carried out, and from which, 43 were identified from 12× assemble grapevine genomic sequences. Further, the genomic structures, synteny, phylogeny, expression profiles in different tissues of these genes, and their roles in response to stress were investigated. Among the genes, two potential target genes (VvSCL15 and VvSCL22) for VvmiR171 were experimentally verified by PPM-RACE and RLM-RACE, in that not only the cleavage sites of miR171 on the target mRNA were mapped but also the cleaved fragments and their expressing patterns were detected. Transgenic Arabidopsis plants over expression VvSCL15 showed lower tolerance to drought and salt treatments.
Long distance transport in plants occurs in sieve tubes of the phloem. The pressure flow hypothesis introduced by Ernst Münch in 1930 describes a mechanism of osmotically generated pressure differentials that are supposed to drive the movement of sugars and other solutes in the phloem, but this hypothesis has long faced major challenges. The key issue is whether the conductance of sieve tubes, including sieve plate pores, is sufficient to allow pressure flow. We show that with increasing distance between source and sink, sieve tube conductivity and turgor increases dramatically in Ipomoea nil. Our results provide strong support for the Münch hypothesis, while providing new tools for the investigation of one of the least understood plant tissues.
Transcriptome data sets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by a lack of metadata or differences in annotation styles of different labs. In this study, we carefully selected and integrated 6057 Arabidopsis microarray expression samples from 304 experiments deposited to the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI). Metadata such as tissue type, growth conditions and developmental stage were manually curated for each sample. We then studied the global expression landscape of the integrated data set and found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome, compared with aerial tissues, but the transcriptome of cultured root is more similar to the transcriptome of aerial tissues, as the cultured root samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating the re-use of plant transcriptome data. As a proof of principle, we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified the accuracy of our predictions with sample metadata provided by the authors.
Arbuscular mycorrhizal fungi (AMF) can transfer nitrogen (N) to host plants, but the ecological relevance is debated, as total plant N and biomass do not generally increase. The extent to which the symbiosis is mutually beneficial is thought to rely on the stoichiometry of N, phosphorus (P) and carbon (C) availability. While inorganic N fertilization has been shown to elicit strong mutualism, characterized by improved plant and fungal growth and mineral nutrition, similar responses following organic N addition are lacking. Using a compartmented microcosm experiment, we determined the significance to a mycorrhizal plant of placing a 15N-labelled, nitrogen-rich patch of organic matter in a compartment to which only AMF hyphae had access. Control microcosms denied AMF hyphal access to the patch compartment. When permitted access to the patch compartment, the fungus proliferated extensively in the patch and transferred substantial quantities of N to the plant. Moreover, our data demonstrate that allowing hyphal access to an organic matter patch enhanced total plant N and P contents, with a simultaneous and substantial increase in plant biomass. Furthermore, we demonstrate that organic matter fertilization of arbuscular mycorrhizal plants can foster a mutually beneficial symbiosis based on nitrogen transfer, a phenomenon previously thought irrelevant.
Salinity is a severe abiotic stress that affects irrigated croplands. Jasmonate (JA) is an essential hormone involved in plant defense against herbivory and in responses to abiotic stress. However, the relationship between the salt stress response and the JA pathway in Arabidopsis thaliana is not well understood at molecular and cellular levels. In this work we investigated the activation of JA signaling by NaCl and its effect on primary root growth. We found that JA-responsive JAZ genes were up-regulated by salt stress in a COI1-dependent manner in the roots. Using a JA-Ile sensor we demonstrated that activation of JA signaling by salt stress occurs in the meristematic zone and stele of the differentiation zone and that this activation was dependent on JAR1 and proteasome functions. Another finding is that the elongation zone (EZ) and its cortical cells were significantly longer in JA-related mutants (AOS, COI1, JAZ3 and MYC2/3/4 genes) compared with wild-type plants under salt stress, revealing the participation of the canonical JA signaling pathway. Noteworthy, osmotic stress – a component of salt stress – inhibited cell elongation in the EZ in a COI1-dependent manner. We propose that salt stress triggers activation of the JA signaling pathway followed by inhibition of cell elongation in the EZ. We have shown that salt-inhibited root growth partially involves the jasmonate signaling pathway in Arabidopsis.
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