The Plant Journal

Cover image for Vol. 88 Issue 3

November 2016

Volume 88, Issue 3

Pages 343–518

  1. Issue Information

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. Table of Contents (page 343)

      Version of Record online: 28 NOV 2016 | DOI: 10.1111/tpj.12988

  2. FEATURED ARTICLE

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing (pages 345–360)

      Heqiang Huo, Isabelle M. Henry, Eric R. Coppoolse, Miriam Verhoef-Post, Johan W. Schut, Han de Rooij, Aat Vogelaar, Ronny V.L. Joosen, Leo Woudenberg, Luca Comai and Kent J. Bradford

      Version of Record online: 15 SEP 2016 | DOI: 10.1111/tpj.13267

      Significance Statement

      Bulked segregant analysis and whole genome sequencing are more efficient than conventional mapping strategies, which require large populations. To demonstrate the advantages of this approach, we used two independent allelic mutants to identify the causal mutations conferring thermotolerant seed germination in lettuce.

  3. ORIGINAL ARTICLES

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. You have full text access to this OnlineOpen article
      The role of DNA (de)methylation in immune responsiveness of Arabidopsis (pages 361–374)

      Ana López Sánchez, Joost H.M. Stassen, Leonardo Furci, Lisa M. Smith and Jurriaan Ton

      Version of Record online: 7 SEP 2016 | DOI: 10.1111/tpj.13252

      Significance Statement

      DNA methylation has been implicated in defence priming, but it is not fully understood what types of plant immunity are influenced or to what extent DNA methylation is involved. We addressed these questions by comprehensive phenotypic and transcriptomic analysis of Arabidopsis mutants that are oppositely affected in DNA methylation. We show that DNA (de)methylation processes play critical roles in certain types of innate, and demonstrate acquired immunity and that DNA (de)methylation exerts a global influence on the responsiveness of the defence-related transcriptome, predominantly via trans-regulatory mechanisms.

    2. You have full text access to this OnlineOpen article
      Transient expression in Nicotiana benthamiana for rapid functional analysis of genes involved in non-photochemical quenching and carotenoid biosynthesis (pages 375–386)

      Lauriebeth Leonelli, Erika Erickson, Dagmar Lyska and Krishna K. Niyogi

      Version of Record online: 15 SEP 2016 | DOI: 10.1111/tpj.13268

      Significance Statement

      Transient expression of genes in Nicotiana benthamiana has become a method of choice to quickly assess gene function in planta. Here we illustrate the potential of transient assays in N. benthamiana to provide a medium-throughput platform for assessing gene function with regards to photosynthetic processes. A promising system is described for studying the regulation of NPQ dynamics toward minimizing energy losses and improving photosynthetic yields.

    3. Analysis of transposable elements and organellar DNA in male and female genomes of a species with a huge Y chromosome reveals distinct Y centromeres (pages 387–396)

      Aretuza Sousa, Sidonie Bellot, Jörg Fuchs, Andreas Houben and Susanne S. Renner

      Version of Record online: 14 OCT 2016 | DOI: 10.1111/tpj.13254

      Significance Statement

      In flowering plants, heteromorphic sex chromosomes are known from some 19 species. Here we analysed the repeat composition of Coccinia grandis (Cucurbitaceae), the flowering plant with the largest known Y chromosome. Surprisingly, the centromeric region of this Y chromosome differs from that of all other C. grandis chromosomes, including the X, in that it lacks a highly abundant tandem repeat but has extended histone marks.

    4. Distinct roles of the histone chaperones NAP1 and NRP and the chromatin-remodeling factor INO80 in somatic homologous recombination in Arabidopsis thaliana (pages 397–410)

      Wangbin Zhou, Juan Gao, Jing Ma, Lin Cao, Chi Zhang, Yan Zhu, Aiwu Dong and Wen-Hui Shen

      Version of Record online: 8 SEP 2016 | DOI: 10.1111/tpj.13256

      Significance Statement

      Homologous recombination occurs within the context of a highly complex chromatin structure, so disassembly and reassembly of nucleosomes is needed. Here we show that the H2A/H2B histone chaperones NRP1 and NRP2 act synergistically with the four AtNAP1 histone chaperones to promote somatic homologous recombination. These chaperones are epistatic to another chromatin-remodeling factor, AtINO80, in both spontaneous and damage-induced homologous recombination.

    5. Phenotypic reversion in fas mutants of Arabidopsis thaliana by reintroduction of FAS genes: variable recovery of telomeres with major spatial rearrangements and transcriptional reprogramming of 45S rDNA genes (pages 411–424)

      Veronika Pavlištová, Martina Dvořáčková, Michal Jež, Iva Mozgová, Petr Mokroš and Jiří Fajkus

      Version of Record online: 18 OCT 2016 | DOI: 10.1111/tpj.13257

      Significance Statement

      Arabidopsis thaliana plants dysfunctional in Chromatin Assembly Factor-1 (CAF-1) (FASCIATA or fas mutants) show complex phenotype together with progressive and specific loss of telomere repeats and 45S ribosomal RNA genes (rDNA). Restoration of CAF-1 results in partial or full recovery of telomeres and rDNA and WT phenotype restoration which is independent of these changes. Moreover, revertants show major spatial rearrangements and transcriptional reprogramming of rDNA offering a unique experimental model to address rDNA maintenance and transcriptional control.

    6. The H3 chaperone function of NASP is conserved in Arabidopsis (pages 425–436)

      Vladimir Maksimov, Miyuki Nakamura, Thomas Wildhaber, Paolo Nanni, Margareta Ramström, Jonas Bergquist and Lars Hennig

      Version of Record online: 15 SEP 2016 | DOI: 10.1111/tpj.13263

      Significance statement

      Free histones are toxic for cells and must be guided to DNA by dedicated chaperones. Here we demonstrate that Arabidopsis NASP (named after the mammalian nuclear autoantigenic sperm protein) binds free H3.1 and H3.3 as well as H3-H4 dimers and promotes formation of H3-H4 tetramers and H3-H4-DNA tetrasomes.

    7. Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana (pages 437–451)

      Paulina Lozano-Sotomayor, Ricardo A. Chávez Montes, Marina Silvestre-Vañó, Humberto Herrera-Ubaldo, Raffaella Greco, Jeanneth Pablo-Villa, Bianca M. Galliani, David Diaz-Ramirez, Mieke Weemen, Kim Boutilier, Andy Pereira, Lucia Colombo, Francisco Madueño, Nayelli Marsch-Martínez and Stefan de Folter

      Version of Record online: 27 SEP 2016 | DOI: 10.1111/tpj.13264

      Significance Statement

      Controlling meristematic activity is key determinant for reproductive development and plant growth. Here we document the role of a bZIP transcription factor, bZIP30, which we named DRINK ME, for the shrinking potion in ‘Alice in Wonderland’, in meristem control. Overexpression of DKM results in small plants with short fruits, whereas loss-of-function mutants have longer fruits, more floral buds and larger inflorescence meristems. Our results indicate that DKM is a modulator of meristematic activity and thus of reproductive development and plant growth.

  4. RESOURCE

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp.) into chromosomes and exploring their synteny with wheat (pages 452–467)

      István Molnár, Jan Vrána, Veronika Burešová, Petr Cápal, András Farkas, Éva Darkó, András Cseh, Marie Kubaláková, Márta Molnár-Láng and Jaroslav Doležel

      Version of Record online: 15 SEP 2016 | DOI: 10.1111/tpj.13266

      Significance Statement

      Introgression of desirable genes from wild species (Aegilops sp.) into bread wheat (Triticum aestivum) is hampered by poor knowledge of Aegilops genome structure and lack of molecular tools. Here we used bivariate flow cytometry and microsatellite probes to discriminate and purify Aegilops chromosomes. DNA markers conserved in bread wheat and wild species will be useful in pre-breeding programs to select chromosome segments carrying agronomically useful genes in T. aestivumAegilops recombinant lines.

  5. TECHNICAL ADVANCE

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. KymoRod: a method for automated kinematic analysis of rod-shaped plant organs (pages 468–475)

      Renaud Bastien, David Legland, Marjolaine Martin, Lucien Fregosi, Alexis Peaucelle, Stéphane Douady, Bruno Moulia and Herman Höfte

      Version of Record online: 8 SEP 2016 | DOI: 10.1111/tpj.13255

      Significance Statement

      Connecting molecular networks to organ growth requires a way to automate analysis of intra-organ growth patterns. Here we use KymoRod to uncover previously unsuspected complexity in Arabidopsis hypocotyl growth patterns and to confirm the role of mechano-sensing in the supra-cellular coordination of cell expansion.

    2. Isolation of protein complexes from the model legume Medicago truncatula by tandem affinity purification in hairy root cultures (pages 476–489)

      Jonas Goossens, Nathan De Geyter, Alan Walton, Dominique Eeckhout, Jan Mertens, Jacob Pollier, Jennifer Fiallos-Jurado, Annick De Keyser, Rebecca De Clercq, Jelle Van Leene, Kris Gevaert, Geert De Jaeger, Sofie Goormachtig and Alain Goossens

      Version of Record online: 27 SEP 2016 | DOI: 10.1111/tpj.13258

      Significance Statement

      The model legume Medicago truncatula is widely studied because it produces valuable natural products and engages in endosymbiotic interactions. Here we develop and validate an interactome resource by identifying interactors of bait proteins involved in cell cycle, transcript processing or jasmonate signalling.

    3. New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana (pages 490–504)

      Ryan S. Austin, Shu Hiu, Jamie Waese, Matthew Ierullo, Asher Pasha, Ting Ting Wang, Jim Fan, Curtis Foong, Robert Breit, Darrell Desveaux, Alan Moses and Nicholas J. Provart

      Version of Record online: 5 OCT 2016 | DOI: 10.1111/tpj.13261

      Significance Statement

      Identifying gene sets that are specifically expressed in certain tissues or in response to an environmental stimulus is useful for designing reporter constructs, for generating gene expression markers, and for understanding gene regulatory networks. Here we describe two tools for easily identifying such gene sets and demonstrate the usefulness of these tools using genotoxic stress and pathogen response as test cases.

    4. A liquid chromatography–mass spectrometry platform for the analysis of phyllobilins, the major degradation products of chlorophyll in Arabidopsis thaliana (pages 505–518)

      Bastien Christ, Mareike Hauenstein and Stefan Hörtensteiner

      Version of Record online: 8 SEP 2016 | DOI: 10.1111/tpj.13253

      Significance Statement

      Phyllobilins have similar physiochemical properties and vastly differing abundance in plant extracts, thus accurate identification and quantification is challenging. Here we describe a LC-MS/MS platform that allows their simultaneous detection and quantification within extracts of senescent Arabidopsis thaliana leaves. This MS/MS spectral data can be referenced when analyzing Arabidopsis senescence mutants and ecotypes and should prove useful for comparative analyses of chlorophyll breakdown in other species.

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