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  • 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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