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  • Ripening activator turned repressor
    Nat. Plants (IF 10.3) Pub Date : 2017-11-13
    James Giovannoni

    Ripening activator turned repressor Ripening activator turned repressor, Published online: 13 November 2017; doi:10.1038/s41477-017-0062-0 NatureArticleSnippet(type=standfirst, markup= Gene editing reveals that the tomato ripening-inhibitor ( rin ) mutation encodes an active repressor of ripening, refines our understanding of RIN function and highlights strategies for engineering shelf life control. , isJats=true)

    更新日期:2017-11-13
  • Saga rooted in conflict between men and nature
    Nat. Plants (IF 10.3) Pub Date : 2017-11-07
    Anastasia Broadbridge

    Saga rooted in conflict between men and natureSaga rooted in conflict between men and nature, Published online: 07 November 2017; doi:10.1038/s41477-017-0056-y

    更新日期:2017-11-07
  • Precious plants
    Nat. Plants (IF 10.3) Pub Date : 2017-11-07
    Sandra Knapp

    Precious plantsPrecious plants, Published online: 07 November 2017; doi:10.1038/s41477-017-0054-0

    更新日期:2017-11-07
  • Brutal honesty of a life in science
    Nat. Plants (IF 10.3) Pub Date : 2017-11-07
    Laci Gerhart

    Brutal honesty of a life in scienceBrutal honesty of a life in science, Published online: 07 November 2017; doi:10.1038/s41477-017-0052-2

    更新日期:2017-11-07
  • The fruits of imagination
    Nat. Plants (IF 10.3) Pub Date : 2017-11-07

    The fruits of imaginationThe fruits of imagination, Published online: 07 November 2017; doi:10.1038/s41477-017-0058-9NatureArticleSnippet(type=standfirst, markup=The sciences and arts are often described as two separate cultures, but fruitful collaborations across this divide highlight the artificiality of such distinctions., isJats=true)

    更新日期:2017-11-07
  • Sea to summit
    Nat. Plants (IF 10.3) Pub Date : 2017-11-07
    Guillaume Tena

    Sea to summitSea to summit, Published online: 07 November 2017; doi:10.1038/s41477-017-0057-x

    更新日期:2017-11-07
  • Tracing the past and future of a mighty river
    Nat. Plants (IF 10.3) Pub Date : 2017-11-07
    Ryan Scarrow

    Tracing the past and future of a mighty riverTracing the past and future of a mighty river, Published online: 07 November 2017; doi:10.1038/s41477-017-0055-z

    更新日期:2017-11-07
  • Wood from the Heart
    Nat. Plants (IF 10.3) Pub Date : 2017-11-07
    Chris Surridge

    Wood from the HeartWood from the Heart, Published online: 07 November 2017; doi:10.1038/s41477-017-0053-1

    更新日期:2017-11-07
  • Painting with betalains
    Nat. Plants (IF 10.3) Pub Date : 2017-11-06
    Anne Osbourn

    Painting with betalainsPainting with betalains, Published online: 06 November 2017; doi:10.1038/s41477-017-0049-xNatureArticleSnippet(type=standfirst, markup=Investigations of plant metabolism reveal how an enzyme variant with reduced feedback sensitivity may allow plants to switch their pigment palettes., isJats=true)

    更新日期:2017-11-06
  • Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo
    Nat. Plants (IF 10.3) Pub Date : 2017-11-06
    Joakim Palovaara, Shunsuke Saiga, Jos R. Wendrich, Nicole van ‘t Wout Hofland, J. Paul van Schayck, Friederike Hater, Sumanth Mutte, Jouke Sjollema, Mark Boekschoten, Guido J. Hooiveld, Dolf Weijers

    During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered—in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.

    更新日期:2017-11-06
  • Tinker, tailor, soldier, enzyme
    Nat. Plants (IF 10.3) Pub Date : 
    Susanne E. Kohalmi, Emily J. Clayton

    Tinker, tailor, soldier, enzymeTinker, tailor, soldier, enzyme, Published online: 06 November 2017; doi:10.1038/s41477-017-0047-zNatureArticleSnippet(type=standfirst, markup=Enzymes are a great example of the tight link between sequence, structure and function. A recent study of two dehydrogenases shows exactly how small changes in sequence can have great impacts on function., isJats=true)

    更新日期:2017-11-06
  • Photosynthesis booster
    Nat. Plants (IF 10.3) Pub Date : 2017-11-06
    Lei Lei

    Photosynthesis boosterPhotosynthesis booster, Published online: 06 November 2017; doi:10.1038/s41477-017-0050-4

    更新日期:2017-11-06
  • Variation engineering
    Nat. Plants (IF 10.3) Pub Date : 2017-11-06
    Jun Lyu

    Variation engineeringVariation engineering, Published online: 06 November 2017; doi:10.1038/s41477-017-0059-8

    更新日期:2017-11-06
  • Cannabis loves company
    Nat. Plants (IF 10.3) Pub Date : 2017-10-30
    Ryan Scarrow

    Cannabis loves company Nature Plants, Published online: 30 October 2017; doi:10.1038/s41477-017-0051-3

    更新日期:2017-10-30
  • Duplication of an upstream silencer of FZP increases grain yield in rice
    Nat. Plants (IF 10.3) Pub Date : 2017-10-30
    Xufeng Bai, Yong Huang, Yong Hu, Haiyang Liu, Bo Zhang, Cezary Smaczniak, Gang Hu, Zhongmin Han, Yongzhong Xing

    Transcriptional silencer and copy number variants (CNVs) are associated with gene expression. However, their roles in generating phenotypes have not been well studied. Here we identified a rice quantitative trait locus, SGDP7 (Small Grain and Dense Panicle 7). SGDP7 is identical to FZP (FRIZZY PANICLE), which represses the formation of axillary meristems. The causal mutation of SGDP7 is an 18-bp fragment, named CNV-18bp, which was inserted ~5.3 kb upstream of FZP and resulted in a tandem duplication in the cultivar Chuan 7. The CNV-18bp duplication repressed FZP expression, prolonged the panicle branching period and increased grain yield by more than 15% through substantially increasing the number of spikelets per panicle (SPP) and slightly decreasing the 1,000-grain weight (TGW). The transcription repressor OsBZR1 binds the CGTG motifs in CNV-18bp and thereby represses FZP expression, indicating that CNV-18bp is the upstream silencer of FZP. These findings showed that the silencer CNVs coordinate a trade-off between SPP and TGW by fine-tuning FZP expression, and balancing the trade-off could enhance yield potential.

    更新日期:2017-10-30
  • GC-rich coding sequences reduce transposon-like, small RNA-mediated transgene silencing
    Nat. Plants (IF 10.3) Pub Date : 2017-10-30
    Lyudmila V. Sidorenko, Tzuu-fen Lee, Aaron Woosley, William A. Moskal, Scott A. Bevan, P. Ann Owens Merlo, Terence A. Walsh, Xiujuan Wang, Staci Weaver, Todd P. Glancy, PoHao Wang, Xiaozeng Yang, Shreedharan Sriram, Blake C. Meyers

    The molecular basis of transgene susceptibility to silencing is poorly characterized in plants; thus, we evaluated several transgene design parameters as means to reduce heritable transgene silencing. Analyses of Arabidopsis plants with transgenes encoding a microalgal polyunsaturated fatty acid (PUFA) synthase revealed that small RNA (sRNA)-mediated silencing, combined with the use of repetitive regulatory elements, led to aggressive transposon-like silencing of canola-biased PUFA synthase transgenes. Diversifying regulatory sequences and using native microalgal coding sequences (CDSs) with higher GC content improved transgene expression and resulted in a remarkable trans-generational stability via reduced accumulation of sRNAs and DNA methylation. Further experiments in maize with transgenes individually expressing three crystal (Cry) proteins from Bacillus thuringiensis (Bt) tested the impact of CDS recoding using different codon bias tables. Transgenes with higher GC content exhibited increased transcript and protein accumulation. These results demonstrate that the sequence composition of transgene CDSs can directly impact silencing, providing design strategies for increasing transgene expression levels and reducing risks of heritable loss of transgene expression.

    更新日期:2017-10-30
  • Dark night, cold ground
    Nat. Plants (IF 10.3) Pub Date : 2017-10-30
    Thomas Potuschak, Pascal Genschik

    Dark night, cold ground Nature Plants, Published online: 30 October 2017; doi:10.1038/s41477-017-0043-3 Plant growth and development depend on the integration of environmental cues with endogenous signals. Two recent manuscripts provide molecular insights into the mechanism of signal transduction for light and temperature, finding that both impinge on the stability of the PIF3 transcription factor.

    更新日期:2017-10-30
  • Tough GC beats transgene silencing
    Nat. Plants (IF 10.3) Pub Date : 2017-10-30
    Xiuren Zhang

    Tough GC beats transgene silencing Nature Plants, Published online: 30 October 2017; doi:10.1038/s41477-017-0048-y Solid genetic and genomic data now reveal that high guanine–cytosine content can prevent transgenes from RNA silencing, and enhance expression and transgenerational stability.

    更新日期:2017-10-30
  • Arabidopsis BTB/POZ protein-dependent PENETRATION3 trafficking and disease susceptibility
    Nat. Plants (IF 10.3) Pub Date : 2017-10-30
    Hailiang Mao, Bibek Aryal, Tobias Langenecker, Jörg Hagmann, Markus Geisler, Markus Grebe

    The outermost cell layer of plant roots (epidermis) constantly encounters environmental challenges. The epidermal outer plasma membrane domain harbours the PENETRATION3 (PEN3)/ABCG36/PDR8 ATP-binding cassette transporter that confers non-host resistance to several pathogens. Here, we show that the Arabidopsis ENDOPLASMIC RETICULUM-ARRESTED PEN3 (EAP3) BTB/POZ-domain protein specifically mediates PEN3 exit from the endoplasmic reticulum and confers resistance to a root-penetrating fungus, providing prime evidence for BTB/POZ-domain protein-dependent membrane trafficking underlying disease resistance.

    更新日期:2017-10-30
  • Re-evaluation of the rin mutation and the role of RIN in the induction of tomato ripening
    Nat. Plants (IF 10.3) Pub Date : 2017-10-30
    Yasuhiro Ito, Ayako Nishizawa-Yokoi, Masaki Endo, Masafumi Mikami, Yoko Shima, Nobutaka Nakamura, Eiichi Kotake-Nara, Susumu Kawasaki, Seiichi Toki

    Tomato (Solanum lycopersicum) rin mutants completely fail to ripen: they do not produce red pigmentation, soften or induce an ethylene burst. Therefore, RIN has long been believed to function as a major regulator that is essential for the induction of ripening. Here, we provide evidence contradicting this concept of RIN function, showing induction of fruit ripening in the absence of RIN. A CRISPR/Cas9-mediated RIN-knockout mutation did not repress initiation of ripening and the mutant fruits showed moderate red colouring. Moreover, inactivation of the rin mutant allele partially restored the induction of ripening. Therefore, RIN is not required for the initiation of ripening and rin is not a null mutation, but rather is a gain-of-function mutation that produces a protein that actively represses ripening. Since the discovery of the rin mutant a half-century ago, many models have depicted RIN as indispensable for the induction of ripening; these models should be reconsidered in light of these results.

    更新日期:2017-10-30
  • Author Correction: The pattern-recognition receptor CORE of Solanaceae detects bacterial cold-shock protein
    Nat. Plants (IF 10.3) Pub Date : 2017-10-23
    Lei Wang, Markus Albert, Elias Einig, Ursula Fürst, Damaris Krust, Georg Felix

    Author Correction: The pattern-recognition receptor CORE of Solanaceae detects bacterial cold-shock protein Nature Plants, Published online: 23 October 2017; doi:10.1038/s41477-017-0044-2

    更新日期:2017-10-30
  • Publisher Correction: Reassessing apoptosis in plants
    Nat. Plants (IF 10.3) Pub Date : 
    Martin Dickman, Brett Williams, Yurong Li, Paul de Figueiredo, Thomas Wolpert

    Publisher Correction: Reassessing apoptosis in plants Nature Plants, Published online: 16 October 2017; doi:10.1038/s41477-017-0045-1

    更新日期:2017-10-16
  • An even pattern of xylan substitution is critical for interaction with cellulose in plant cell walls
    Nat. Plants (IF 10.3) Pub Date : 
    Nicholas J. Grantham, Joel Wurman-Rodrich, Oliver M. Terrett, Jan J. Lyczakowski, Katherine Stott, Dinu Iuga, Thomas J. Simmons, Mylene Durand-Tardif, Steven. P. Brown, Ray Dupree, Marta Busse-Wicher, Paul Dupree

    Xylan and cellulose are abundant polysaccharides in vascular plants and essential for secondary cell wall strength. Acetate or glucuronic acid decorations are exclusively found on even-numbered residues in most of the glucuronoxylan polymer. It has been proposed that this even-specific positioning of the decorations might permit docking of xylan onto the hydrophilic face of a cellulose microfibril1,2,3. Consequently, xylan adopts a flattened ribbon-like twofold screw conformation when bound to cellulose in the cell wall4. Here we show that ESKIMO1/XOAT1/TBL29, a xylan-specific O-acetyltransferase, is necessary for generation of the even pattern of acetyl esters on xylan in Arabidopsis. The reduced acetylation in the esk1 mutant deregulates the position-specific activity of the xylan glucuronosyltransferase GUX1, and so the even pattern of glucuronic acid on the xylan is lost. Solid-state NMR of intact cell walls shows that, without the even-patterned xylan decorations, xylan does not interact normally with cellulose fibrils. We conclude that the even pattern of xylan substitutions seen across vascular plants enables the interaction of xylan with hydrophilic faces of cellulose fibrils, and is essential for development of normal plant secondary cell walls.

    更新日期:2017-10-11
  • MicroRNA sponge
    Nat. Plants (IF 10.3) Pub Date : 
    Jun Lyu

    MicroRNA sponge Nature Plants, Published online: 5 October 2017; doi:10.1038/s41477-017-0037-1

    更新日期:2017-10-11
  • Geography drives agronomy
    Nat. Plants (IF 10.3) Pub Date : 
    Ryan Scarrow

    Geography drives agronomy Nature Plants, Published online: 5 October 2017; doi:10.1038/s41477-017-0038-0

    更新日期:2017-10-11
  • Maintaining the common grounds
    Nat. Plants (IF 10.3) Pub Date : 

    Maintaining the common grounds Nature Plants, Published online: 5 October 2017; doi:10.1038/s41477-017-0036-2 Cities need green spaces to maintain the well-being of their citizens. But is the realization of their value making them more private luxury than public commons?

    更新日期:2017-10-11
  • European infrastructures for sustainable agriculture
    Nat. Plants (IF 10.3) Pub Date : 
    Jacques Roy, François Tardieu, Michèle Tixier-Boichard, Ulrich Schurr

    European infrastructures for sustainable agriculture Nature Plants, Published online: 5 October 2017; doi:10.1038/s41477-017-0027-3 The European infrastructures EMPHASIS and AnaEE aim to collaborate in bringing innovative solutions for a sustainable intensification of agriculture. By integrating the study of plant phenomics and agricultural ecology they hope to foster the development of novel scientific concepts, sensors and integrated models.

    更新日期:2017-10-11
  • Seeing is believing
    Nat. Plants (IF 10.3) Pub Date : 
    Tamar Azoulay-Shemer, Po-Kai Hsu, Julian I. Schroeder

    Seeing is believing Nature Plants, Published online: 2 October 2017; doi:10.1038/s41477-017-0025-5 Gibberellins (GAs) control key growth and developmental processes in plants. Real-time monitoring of GA concentrations in living tissues is critical for understanding the actions of this hormone class. A first-generation optogenetic GA-nano-indicator now illuminates the effects of GA levels on cell length and light signalling.

    更新日期:2017-10-11
  • Silencing messages in a unique way
    Nat. Plants (IF 10.3) Pub Date : 
    Hiro-oki Iwakawa, Yukihide Tomari

    Silencing messages in a unique way Nature Plants, Published online: 2 October 2017; doi:10.1038/s41477-017-0028-2 A global analysis of translation efficiency and RNA accumulation revealed that microRNAs in the unicellular green alga Chlamydomonas regulate target gene expression via RNA destabilization and translational repression like land plants and metazoans, yet in a different way.

    更新日期:2017-10-11
  • Sometimes a rocker-switch motion
    Nat. Plants (IF 10.3) Pub Date : 
    Karsten Fischer, Andreas P. M. Weber

    Sometimes a rocker-switch motion Nature Plants, Published online: 2 October 2017; doi:10.1038/s41477-017-0026-4 Plastids are integrated into the cellular metabolism by several metabolite and ion transporters. The first crystal structure of one of these transporters, a member of the plastid phosphate transporter family, unravels a rocker-switch transport mode and serves as lead structure for other plastidial and endomembrane system transporters.

    更新日期:2017-10-11
  • Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis
    Nat. Plants (IF 10.3) Pub Date : 
    Chen Chen, Chenlong Li, Ying Wang, Justin Renaud, Gang Tian, Shrikaar Kambhampati, Behnaz Saatian, Vi Nguyen, Abdelali Hannoufa, Frédéric Marsolais, Ze-Chun Yuan, Kangfu Yu, Ryan S. Austin, Jun Liu, Susanne E. Kohalmi, Keqiang Wu, Shangzhi Huang, Yuhai Cui

    Acetyl-coenzyme A (acetyl-CoA) is a central metabolite and the acetyl source for protein acetylation, particularly histone acetylation that promotes gene expression. However, the effect of acetyl-CoA levels on histone acetylation status in plants remains unknown. Here, we show that malfunctioned cytosolic acetyl-CoA carboxylase1 (ACC1) in Arabidopsis leads to elevated levels of acetyl-CoA and promotes histone hyperacetylation predominantly at lysine 27 of histone H3 (H3K27). The increase of H3K27 acetylation (H3K27ac) is dependent on adenosine triphosphate (ATP)-citrate lyase which cleaves citrate to acetyl-CoA in the cytoplasm, and requires histone acetyltransferase GCN5. A comprehensive analysis of the transcriptome and metabolome in combination with the genome-wide H3K27ac profiles of acc1 mutants demonstrate the dynamic changes in H3K27ac, gene transcripts and metabolites occurring in the cell by the increased levels of acetyl-CoA. This study suggests that H3K27ac is an important link between cytosolic acetyl-CoA level and gene expression in response to the dynamic metabolic environments in plants.

    更新日期:2017-09-25
  • Ex situ conservation of plant diversity in the world’s botanic gardens
    Nat. Plants (IF 10.3) Pub Date : 
    Ross Mounce, Paul Smith, Samuel Brockington

    Botanic gardens conserve plant diversity ex situ and can prevent extinction through integrated conservation action. Here we quantify how that diversity is conserved in ex situ collections across the world’s botanic gardens. We reveal that botanic gardens manage at least 105,634 species, equating to 30% of all plant species diversity, and conserve over 41% of known threatened species. However, we also reveal that botanic gardens are disproportionately temperate, with 93% of species held in the Northern Hemisphere. Consequently, an estimated 76% of species absent from living collections are tropical in origin. Furthermore, phylogenetic bias ensures that over 50% of vascular genera, but barely 5% of non-vascular genera, are conserved ex situ. While botanic gardens are discernibly responding to the threat of species extinction, just 10% of network capacity is devoted to threatened species. We conclude that botanic gardens play a fundamental role in plant conservation, but identify actions to enhance future conservation of biodiversity.

    更新日期:2017-09-25
  • Reassessing apoptosis in plants
    Nat. Plants (IF 10.3) Pub Date : 
    Martin Dickman, Brett Williams, Yurong Li, Paul Figueiredo, Thomas Wolpert

    Cell death can be driven by a genetically programmed signalling pathway known as programmed cell death (PCD). In plants, PCD occurs during development as well as in response to environmental and biotic stimuli. Our understanding of PCD regulation in plants has advanced significantly over the past two decades; however, the molecular machinery responsible for driving the system remains elusive. Thus, whether conserved PCD regulatory mechanisms include plant apoptosis remains enigmatic. Animal apoptotic regulators, including Bcl-2 family members, have not been identified in plants but expression of such regulators can trigger or suppress plant PCD. Moreover, plants exhibit nearly all of the biochemical and morphological features of apoptosis. One difference between plant and animal PCD is the absence of phagocytosis in plants. Evidence is emerging that the vacuole may be key to removal of unwanted plant cells, and may carry out functions that are analogous to animal phagocytosis. Here, we provide context for the argument that apoptotic-like cell death occurs in plants.

    更新日期:2017-09-25
  • Quantifying airborne dispersal routes of pathogens over continents to safeguard global wheat supply
    Nat. Plants (IF 10.3) Pub Date : 
    M. Meyer, J. A. Cox, M. D. T. Hitchings, L. Burgin, M. C. Hort, D. P. Hodson, C. A. Gilligan

    Infectious crop diseases spreading over large agricultural areas pose a threat to food security. Aggressive strains of the obligate pathogenic fungus Puccinia graminis f.sp. tritici (Pgt), causing the crop disease wheat stem rust, have been detected in East Africa and the Middle East, where they lead to substantial economic losses and threaten livelihoods of farmers. The majority of commercially grown wheat cultivars worldwide are susceptible to these emerging strains, which pose a risk to global wheat production, because the fungal spores transmitting the disease can be wind-dispersed over regions and even continents1,2,3,4,5,6,7,8,9,10,11. Targeted surveillance and control requires knowledge about airborne dispersal of pathogens, but the complex nature of long-distance dispersal poses significant challenges for quantitative research12,13,14. We combine international field surveys, global meteorological data, a Lagrangian dispersion model and high-performance computational resources to simulate a set of disease outbreak scenarios, tracing billions of stochastic trajectories of fungal spores over dynamically changing host and environmental landscapes for more than a decade. This provides the first quantitative assessment of spore transmission frequencies and amounts amongst all wheat producing countries in Southern/East Africa, the Middle East and Central/South Asia. We identify zones of high air-borne connectivity that geographically correspond with previously postulated wheat rust epidemiological zones (characterized by endemic disease and free movement of inoculum)10,15, and regions with genetic similarities in related pathogen populations16,17. We quantify the circumstances (routes, timing, outbreak sizes) under which virulent pathogen strains such as ‘Ug99’5,6 pose a threat from long-distance dispersal out of East Africa to the large wheat producing areas in Pakistan and India. Long-term mean spore dispersal trends (predominant direction, frequencies, amounts) are summarized for all countries in the domain (Supplementary Data). Our mechanistic modelling framework can be applied to other geographic areas, adapted for other pathogens and used to provide risk assessments in real-time3.

    更新日期:2017-09-25
  • Twenty-first century botany
    Nat. Plants (IF 10.3) Pub Date : 

    Twenty-first century botany Nature Plants, Published online: 6 September 2017; doi:10.1038/s41477-017-0018-4 The recent International Botanical Congress in Shenzhen was the largest meeting in its history. That a gathering rooted in the superficially traditional science of taxonomy is thriving in the age of genomics and biotechnology shows the strength and adaptability of modern botany and botanists.

    更新日期:2017-09-06
  • Plants are not so different
    Nat. Plants (IF 10.3) Pub Date : 
    Stefan Grob

    Plants are not so different Nature Plants, Published online: 6 September 2017; doi:10.1038/s41477-017-0013-9 Hi-C experiments in rice reveal that the rice genome is partitioned into well-defined three-dimensional structures similar to so-called topologically associating domains found in metazoans.

    更新日期:2017-09-06
  • Urban self-sufficiency at risk
    Nat. Plants (IF 10.3) Pub Date : 
    Ryan Scarrow

    Urban self-sufficiency at risk Nature Plants, Published online: 6 September 2017; doi:10.1038/s41477-017-0016-6

    更新日期:2017-09-06
  • Towards a universal model for carbon dioxide uptake by plants
    Nat. Plants (IF 10.3) Pub Date : 
    Han Wang, I. Colin Prentice, Trevor F. Keenan, Tyler W. Davis, Ian J. Wright, William K. Cornwell, Bradley J. Evans, Changhui Peng

    Gross primary production (GPP)—the uptake of carbon dioxide (CO2) by leaves, and its conversion to sugars by photosynthesis—is the basis for life on land. Earth System Models (ESMs) incorporating the interactions of land ecosystems and climate are used to predict the future of the terrestrial sink for anthropogenic CO21. ESMs require accurate representation of GPP. However, current ESMs disagree on how GPP responds to environmental variations1,2, suggesting a need for a more robust theoretical framework for modelling3,4. Here, we focus on a key quantity for GPP, the ratio of leaf internal to external CO2 (χ). χ is tightly regulated and depends on environmental conditions, but is represented empirically and incompletely in today’s models. We show that a simple evolutionary optimality hypothesis5,6 predicts specific quantitative dependencies of χ on temperature, vapour pressure deficit and elevation; and that these same dependencies emerge from an independent analysis of empirical χ values, derived from a worldwide dataset of >3,500 leaf stable carbon isotope measurements. A single global equation embodying these relationships then unifies the empirical light-use efficiency model7 with the standard model of C3 photosynthesis8, and successfully predicts GPP measured at eddy-covariance flux sites. This success is notable given the equation’s simplicity and broad applicability across biomes and plant functional types. It provides a theoretical underpinning for the analysis of plant functional coordination across species and emergent properties of ecosystems, and a potential basis for the reformulation of the controls of GPP in next-generation ESMs.

    更新日期:2017-09-06
  • Crops can be strong and sensitive
    Nat. Plants (IF 10.3) Pub Date : 
    Bruce Walsh

    Crops can be strong and sensitive Nature Plants, Published online: 4 September 2017; doi:10.1038/s41477-017-0012-x The genes in maize that influence environmental sensitivity are largely independent of the genes that influence mean trait values.

    更新日期:2017-09-06
  • Distinct genetic architectures for phenotype means and plasticities in Zea mays
    Nat. Plants (IF 10.3) Pub Date : 
    Aaron Kusmec, Srikant Srinivasan, Dan Nettleton, Patrick S. Schnable

    Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of paramount importance for maintaining and increasing yields in a world experiencing climate change. Here, we report the results of genome-wide association analyses of multiple phenotypes and two measures of phenotypic plasticity in a maize nested association mapping (US-NAM) population grown in multiple environments and genotyped with ~2.5 million single-nucleotide polymorphisms. We show that across all traits the candidate genes for mean phenotype values and plasticity measures form structurally and functionally distinct groups. Such independent genetic control suggests that breeders will be able to select semi-independently for mean phenotype values and plasticity, thereby generating varieties with both high mean phenotype values and levels of plasticity that are appropriate for the target performance environments.

    更新日期:2017-09-06
  • Visualizing fate changes
    Nat. Plants (IF 10.3) Pub Date : 
    Lei Lei

    Visualizing fate changes Nature Plants, Published online: 4 September 2017; doi:10.1038/s41477-017-0014-8

    更新日期:2017-09-06
  • Mechanical regulation of organ asymmetry in leaves
    Nat. Plants (IF 10.3) Pub Date : 
    Jiyan Qi, Binbin Wu, Shiliang Feng, Shouqin Lü, Chunmei Guan, Xiao Zhang, Dengli Qiu, Yingchun Hu, Yihua Zhou, Chuanyou Li, Mian Long, Yuling Jiao

    How appendages, such as plant leaves or animal limbs, develop asymmetric shapes remains a fundamental question in biology. Although ongoing research has revealed the genetic regulation of organ pattern formation, how gene activity ultimately directs organ shape remains unclear. Here, we show that leaf dorsoventral (adaxial-abaxial) polarity signals lead to mechanical heterogeneity of the cell wall, related to the methyl-esterification of cell-wall pectins in tomato and Arabidopsis. Numerical simulations predicate that mechanical heterogeneity is sufficient to produce the asymmetry seen in planar leaves. Experimental tests that alter pectin methyl-esterification, and therefore cell wall mechanical properties, support this model and lead to polar changes in gene expression, suggesting the existence of a feedback mechanism for mechanical signals in morphogenesis. Thus, mechanical heterogeneity within tissue may underlie organ shape asymmetry.

    更新日期:2017-09-06
  • Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis
    Nat. Plants (IF 10.3) Pub Date : 
    Chang Liu, Ying-Juan Cheng, Jia-Wei Wang, Detlef Weigel

    The non-random three-dimensional organization of genomes is critical for many cellular processes. Recently, analyses of genome-wide chromatin packing in the model dicot plant Arabidopsis thaliana have been reported1,2,3,4. At a kilobase scale, the A. thaliana chromatin interaction network is highly correlated with a range of genomic and epigenomic features1,2,3,4. Surprisingly, topologically associated domains (TADs), which appear to be a prevalent structural feature of genome packing in many animal species, are not prominent in the A. thaliana genome1,2,4,5,6. Using a genome-wide chromatin conformation capture approach, Hi-C (ref. 7), we report high-resolution chromatin packing patterns of another model plant, rice. We unveil new structural features of chromatin organization at both chromosomal and local levels compared to A. thaliana, with thousands of distinct TADs that cover about a quarter of the rice genome. The rice TAD boundaries are associated with euchromatic epigenetic marks and active gene expression, and enriched with a sequence motif that can be recognized by plant-specific TCP proteins. In addition, we report chromosome decondensation in rice seedlings undergoing cold stress, despite local chromatin packing patterns remaining largely unchanged. The substantial variation found already in a comparison of two plant species suggests that chromatin organization in plants might be more diverse than in multicellular animals.

    更新日期:2017-09-06
  • The R-loop is a common chromatin feature of the Arabidopsis genome
    Nat. Plants (IF 10.3) Pub Date : 
    Wei Xu, Hui Xu, Kuan Li, Yingxu Fan, Yang Liu, Xuerui Yang, Qianwen Sun

    R-loops are functional structures in chromatin comprising one single-stranded DNA and a DNA:RNA hybrid. Here, we report ssDRIP-seq, a single-strand DNA ligation-based library preparation technique for genome-wide identification of R-loops. When applied in Arabidopsis, ssDRIP-seq exhibits high efficiency, low bias and strand specificity. We found that Arabidopsis R-loops are enriched by both AT and GC skews, and are formed in the sense and antisense orientations. R-loops are strongly enriched in gene promoters and gene bodies, and are highly associated with noncoding RNA and repetitive genomic regions. Furthermore, R-loops are negatively correlated with CG DNA hypermethylation, and are prevalent in regions with multiple chromatin modifications, showing strong correlations with the activated and repressed gene loci. Our analyses indicate that R-loops are common features in the Arabidopsis genome and suggest that the R-loops play diverse roles in genome organization and gene regulation, thereby providing insights into plant nuclear genome formation and function.

    更新日期:2017-09-06
  • Hybrids in the chromatin
    Nat. Plants (IF 10.3) Pub Date : 
    Frédéric Chédin

    Hybrids in the chromatin Nature Plants, Published online: 28 August 2017; doi:10.1038/s41477-017-0011-y New genomic maps reveal that R-loop structures formed upon hybridization of nascent RNA transcripts to the DNA template are a common characteristic of Arabidopsis chromatin that may have a broad impact on gene expression.

    更新日期:2017-09-06
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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