• Issue

    The Plant Journal: Volume 103, Issue 1

    1-474
    July 2020

ISSUE INFORMATION

Free Access

Issue Information

  • Pages: 1-4
  • First Published: 29 June 2020
Description unavailable

ORIGINAL ARTICLE

Open Access

Concurrent activation of OsAMT1;2 and OsGOGAT1 in rice leads to enhanced nitrogen use efficiency under nitrogen limitation

  • Pages: 7-20
  • First Published: 05 May 2020
Significance Statement

We report that concurrent activation of OsAMT1;2 and OsGOGAT1 confers better growth and improves the grain yield and quality of rice, especially under nitrogen limitation. Thus, our approach constitutes a promising strategy for improving nitrogen use efficiency in rice.

PERSPECTIVE

Free Access

Multiscale computational models can guide experimentation and targeted measurements for crop improvement

  • Pages: 21-31
  • First Published: 13 February 2020
Significance Statement

Computational plant models increase our comprehension of biological processes and reveal gaps in knowledge. Integrated, multiscale models have the potential to increase our predictive capability for crop response to future environments. This perspective article highlights the need for multiscale modeling for the development of crop ideotypes, and contends that advanced visualization of multiscale model simulations will guide future efforts for experimental measurement and engineering.

ORIGINAL ARTICLES

Open Access

Satellite DNA landscapes after allotetraploidization of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

  • Pages: 32-52
  • First Published: 24 January 2020
Significance Statement

We traced the evolution of allotetraploid quinoa, and followed the emergence, amplification, and reduction of satellite DNA, a fast-evolving sequence class. Using long and short reads, assembled scaffolds as well as Southern, genomic, and fluorescent in situ hybridization, we identified subgenome-specific satellite families, and surprisingly low rates of homoeologous recombination.

Free Access

A long non-coding apple RNA, MSTRG.85814.11, acts as a transcriptional enhancer of SAUR32 and contributes to the Fe-deficiency response

  • Pages: 53-67
  • First Published: 28 January 2020
Significance Statement

LncRNAs are known to be involved in adaptive responses to nutrient stress. In this study we demonstrate that MSTRG.85814.11 promotes SAUR32 expression, which then activates proton extrusion involved in the Fe-deficiency response.

Open Access

Flux balance analysis of metabolism during growth by osmotic cell expansion and its application to tomato fruits

  • Pages: 68-82
  • First Published: 27 January 2020
Significance Statement

In flux balance analysis (FBA), a modelling approach widely used to study plant metabolism, growth is represented by the accumulation of biomass components in fixed proportions, which can be considered to be true during cell division. In plants, however, much of the observable growth results from cell expansion and so, in this paper, we introduce a framework for using FBA to study metabolism during cell expansion and demonstrate its application in predicting metabolic changes during tomato fruit development.

Free Access

The biochemistry of headgroup exchange during triacylglycerol synthesis in canola

  • Pages: 83-94
  • First Published: 28 January 2020
Significance Statement

Relative to the model oilseed Arabidopsis, the canola phosphatidylcholine:diacylglycerol cholinephosphotransferase has a lesser role in the flux of fatty acids during seed oil synthesis, highlighting how pathway fluxes may differ among related species.

Free Access

Tissue-specific study across the stem of Taxus media identifies a phloem-specific TmMYB3 involved in the transcriptional regulation of paclitaxel biosynthesis

  • Pages: 95-110
  • First Published: 30 January 2020
Significance Statement

The composition of taxoids across the whole stem of Taxus media and the stem tissue-specificity of paclitaxel biosynthesis-related enzymes remain largely unknown. We report the involvement of a phloem-specific TmMYB3 in paclitaxel biosynthesis, providing a potential explanation for the phloem-specific accumulation of paclitaxel.

Free Access

Comparative functional analyses of DWARF14 and KARRIKIN INSENSITIVE 2 in drought adaptation of Arabidopsis thaliana

  • Pages: 111-127
  • First Published: 05 February 2020
Significance Statement

The signaling pathways mediated by two paralogous proteins, the strigolactone receptor DWARF14 and the karrikin receptor KARRIKIN INSENSITIVE 2, show both overlapping and specific responses in affecting various physiological and biochemical processes to positively modulate Arabidopsis adaptation to drought. Data obtained from the transcriptome analysis support our findings at a molecular level.

Free Access

Impact of oxidative stress on the function, abundance, and turnover of the Arabidopsis 80S cytosolic ribosome

  • Pages: 128-139
  • First Published: 06 February 2020
Significance Statement

Protein synthesis is critical during abiotic stress, however we know little about the impact of oxidative stress on plant ribosomes. By tracking cytosolic ribosome abundance, turnover, and function, we show the robust maintenance of ribosome function, even when cell growth is significantly slowed, and discover selective patterns of ribosome subunit maintenance in plant cells.

Free Access

COM1, a factor of alternative non-homologous end joining, lagging behind the classic non-homologous end joining pathway in rice somatic cells

  • Pages: 140-153
  • First Published: 05 February 2020
Significance Statement

Double-stranded breaks (DSB) in genomic DNA are potentially lethal lesions that separate parts of chromosome arms from their centromeres. Quite differently to its role in homologous recombination (HR) for meiocytes, here we show that rice COM1 specifically acts in an alternative non-homologous end joining (alt-NHEJ) pathway in somatic cells, based on the Mre11–Rad50–Nbs1 (MRN) complex and facilitated by PI3K-like kinases, and that the NHEJ factors (MRE11, COM1, and LIG4), not the HR factors (RAD51B, RAD51C, and XRCC3), preferentially load onto endogenous DSBs, with the KU70 restricting DSB localization of COM1 and XRCC3 in plant somatic cells.

Open Access

Functional analysis of FRIGIDA using naturally occurring variation in Arabidopsis thaliana

  • Pages: 154-165
  • First Published: 05 February 2020
Significance Statement

The FRI locus is an important determinant of natural variation in flowering time in Arabidopsis. Analysis of natural variants at the FRI locus in more than 1000 accessions provides information about the central domain of the protein.

Free Access

Overexpression of MsGH3.5 inhibits shoot and root development through the auxin and cytokinin pathways in apple plants

  • Pages: 166-183
  • First Published: 07 February 2020
Significance Statement

The auxin-responsive GH3 genes contribute to the maintenance of auxin homeostasis in Arabidopsis and rice; however, little is known about the function of GH3s in apple. Here we demonstrate that MsGH3.5 is an important player in the auxin and cytokinin pathways, affecting shoot and root growth and development by modulating the levels and signaling pathways of these two hormones.

Open Access

A first view on the unsuspected intragenus diversity of N-glycans in Chlorella microalgae

  • Pages: 184-196
  • First Published: 07 February 2020
Description unavailable
Significance Statement

The protein N-glycosylation machinery of green algae has hitherto been considered as being essentially similar to that of land plants. The current work reveals a plethora of yet unknown N-glycan structures only within the Chlorella clade – an economically relevant branch – with considerable repercussions on taxonomy and functional significance.

Open Access

Metabolite/phytohormone–gene regulatory networks in soybean organs under dehydration conditions revealed by integration analysis

  • Pages: 197-211
  • First Published: 18 February 2020
Significance Statement

We analyzed the characteristics of metabolite/phytohormone–gene regulatory networks in dehydration-treated soybean plants. Our analysis revealed the accumulation of raffinose, trehalose, and cZ specifically in dehydration-treated roots, and our integration analysis of metabolite/phytohormone–genes indicated that several metabolite/phytohormone levels, including those of raffinose, trehalose, and cZ, were correlated with transcript levels for these key enzymes at the level of individual plants but not at the organ level under dehydration conditions.

Free Access

Functional analysis of phospholipase Dδ family in tobacco pollen tubes

  • Pages: 212-226
  • First Published: 16 February 2020
Significance Statement

Phosphatidic acid has been demonstrated as an important molecule defining the identity of plasma membrane, but its production from structural phospholipids by phospholipase D is still not completely understood. This study describes a comprehensive bioinformatic, localization and functional analysis of phospholipase Dδ subfamily in tobacco pollen tubes, showing that distinct isoforms have different membrane targeting mechanisms, dynamics, in vivo activity and the effect on cell membrane traffic.

Free Access

Mitochondrial signalling is critical for acclimation and adaptation to flooding in Arabidopsis thaliana

  • Pages: 227-247
  • First Published: 16 February 2020
Significance Statement

Mitochondria provide the energy and metabolic building blocks allowing plants to respond to adverse environmental conditions. Our results show that plant mitochondria also have a function as stress sensors, and that corresponding signalling pathways that lead to the adjustment of gene expression are used for the adaptation to stress.

Free Access

A plastid-localized bona fide geranylgeranyl diphosphate synthase plays a necessary role in monoterpene indole alkaloid biosynthesis in Catharanthus roseus

  • Pages: 248-265
  • First Published: 17 February 2020

Significance Statement

Our study reveals a link between C20 metabolic intermediate (GGPP) and (C10)-monoterpene indole alkaloids (MIA), thus adding new insights into MIA formation in Catharanthus roseus. The findings demonstrate that the plastid-localized bona fide CrGGPPS2 plays an important role in MIA biosynthesis through its potential involvement in providing the precursor for protein-geranylgeranyl-transferase (PGGT) involved in modulation of the MIA pathway

Free Access

Genome-wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure

  • Pages: 266-278
  • First Published: 18 February 2020
Significance Statement

Panicle structure is an important determinant of rice grain yield. This study identified two genes controlling panicle morphology and may help our understanding of the genetic control of panicle structure for achieving high yield in breeding programs.

Open Access

Metabolomics analysis and metabolite-agronomic trait associations using kernels of wheat (Triticum aestivum) recombinant inbred lines

  • Pages: 279-292
  • First Published: 19 February 2020
Significance Statement

This work performed a comprehensive metabolome analysis of kernels from wheat RILs, which, in conjunction with wheat genome data, provided a valuable resource for mQTL analysis, identification of unknown enzymes, and metabolite-agronomic trait correlations.

Free Access

Overexpression of chalcone isomerase in apple reduces phloridzin accumulation and increases susceptibility to herbivory by two-spotted mites

  • Pages: 293-307
  • First Published: 24 February 2020
Description unavailable
Significance Statement

Apples accumulate high levels of the dihydrochalcone glycoside phloridzin due to a metabolic bottleneck in the phenylpropanoid pathway at MdCHI. Release of this bottleneck by constitutive overexpression of AtCHI significantly reduced phloridzin accumulation in transgenic apples and increased susceptibility to herbivory by two-spotted mites, suggesting a role for phloridzin as an antifeedant in apple leaves.

Open Access

ZEITLUPE facilitates the rhythmic movements of Nicotiana attenuata flowers

  • Pages: 308-322
  • First Published: 04 March 2020
Significance Statement

Circadian organ movements are widespread among plants. Yet, the molecular components that operate in these movements have remained unknown. Here, we demonstrate that the growth movements of the pedicel, the organ responsible for the circadian changes in orientation of Nicotiana attenuata flowers, are under the control of the circadian clock and auxin signalling; a result that opens potential avenues to investigate the relationship among different types of movements in plants.

Free Access

WOOLLY, interacting with MYB transcription factor MYB31, regulates cuticular wax biosynthesis by modulating CER6 expression in tomato

  • Pages: 323-337
  • First Published: 04 March 2020
Significance Statement

Our results uncover a novel molecular mechanism whereby a Wo–SlMYB31 complex regulates cuticular wax biosynthesis in tomato.

Free Access

The pulse of the tree is under genetic control: eucalyptus as a case study

  • Pages: 338-356
  • First Published: 06 March 2020
Significance Statement

The ‘pulse’ of the tree that refers to the environmentally induced changes in daily stem radius fluctuation, is a key trait to understand trees’ responses to the environment. This study shows that the ‘pulse’ is associated with genetic variation in a Eucalyptus hybrid and highlights that the dynamics of its genetic architecture is crucial to investigate the genetic bases of tree responses to changes in water availability.

Free Access

Phylogenetic comparison of 5′ splice site determination in central spliceosomal proteins of the U1-70K gene family, in response to developmental cues and stress conditions

  • Pages: 357-378
  • First Published: 04 March 2020
Significance Statement

This study describes a comprehensive analysis to systematically name and identify 115 U1-70K genes from 67 plant species, ranging from algae to angiosperms.

Free Access

Light controls stamen elongation via cryptochromes, phytochromes and COP1 through HY5 and HYH

  • Pages: 379-394
  • First Published: 06 March 2020
Significance Statement

In Arabidopsis auxin-induced stamen elongation is essential for optimizing the transfer of pollen grains onto the pistil to allow successful fertilization. Here we show that different light qualities, via the conserved COP1–HY5/HYH module, finely tune auxin-induced stamen elongation and thus male fertility.

Free Access

Oryza sativa Lysine-Histidine-type Transporter 1 functions in root uptake and root-to-shoot allocation of amino acids in rice

  • Pages: 395-411
  • First Published: 11 March 2020
Significance Statement

Amino acids can serve as important nitrogen sources in agricultural fields, but little is known about the underlying mechanisms of amino acid uptake and allocation in crops. This study conducted genetic association analyses of 15N-aspartate uptake among rice accessions, combined with genetic and biochemical analyses, and revealed that Oryza sativa Lysine-Histidine-type Transporter 1 (OsLHT1) functions in both root uptake and root to shoot allocation of a broad spectrum of amino acids.

Free Access

The rice/maize pathogen Cochliobolus spp. infect and reproduce on Arabidopsis revealing differences in defensive phytohormone function between monocots and dicots

  • Pages: 412-429
  • First Published: 13 March 2020
Significance Statement

Revealing plant mechanisms of non-host resistance (NHR) against Cochliobolus will help to uncover strategies that can be exploited in engineered cereals. Thus, we developed a heterogeneous pathosystem and studied the ability of Cochliobolus to infect various Arabidopsis accessions. Our results indicate distinct defence systems between Arabidopsis and rice to confine Cochliobolus propagation. Moreover, this pathosystem may help to reveal mechanisms of NHR and associated defensive genes against Cochliobolus infection.

Free Access

Survival in the Tropics despite isolation, inbreeding and asexual reproduction: insights from the genome of the world’s southernmost poplar (Populus ilicifolia)

  • Pages: 430-442
  • First Published: 13 March 2020
Significance Statement

Whole-genome sequencing of Populus ilicifolia, a vulnerable and isolated poplar tree from the Tropics that can reproduce both sexually and asexually, was used to explore how population history and reproduction affected its genetic characteristics, genetic load, and its potential for tropical adaptation.

RESOURCE

Open Access

Divergence of 3′ ends as a driver of short interspersed nuclear element (SINE) evolution in the Salicaceae

  • Pages: 443-458
  • First Published: 13 February 2020
Significance Statement

SINEs are heterogeneous retrotransposons, able to affect plant genes and genomes, but are only sparsely described in tree species. We comparatively analyzed 27 077 SINE copies in poplars and willow, focusing on structure, abundance and diversity, representing a valuable resource for the annotation of Salicaceae reference genome sequences. We provide insights into SINE formation and evolution by reshuffling and, characteristic for Salicaceae SINEs, by mutations of the 3′ tail, leading to 3′-end diversification.

TECHNICAL ADVANCE

Open Access

Tissue-specific isolation of Arabidopsis/plant mitochondria – IMTACT (isolation of mitochondria tagged in specific cell types)

  • Pages: 459-473
  • First Published: 14 February 2020
Significance Statement

We propose a new method for ‘transformable’ plant species that allows the user to rapidly isolate highly pure mitochondria from any tissues in any given genotype provided that a tissue-specific promoter is used.