Featured
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Article
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Two orthogonal differentiation gradients locally coordinate fruit morphogenesis
The coordination of cellular behaviors is essential for proper organogenesis. Here the authors show that fruit development in Arabidopsis is governed by time-shifted differentiation gradients that act locally along two perpendicular organ axes.
- Andrea Gómez-Felipe
- , Elvis Branchini
- & Daniel Kierzkowski
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Review Article
| Open Access
Developmental timing in plants
Plants exhibit reproducible timing of developmental events at multiple scales, from switches in cell identity to maturation of the whole plant. Using simplified models to convey key concepts, we review how timing mechanisms interact with the environment to control cyclical and progressive developmental transitions.
- Enrico Coen
- & Przemyslaw Prusinkiewicz
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Article
| Open Access
Autophagy-mediated degradation of integumentary tapetum is critical for embryo pattern formation
A seed consists of an embryo, endosperm, and seed coat. Here the authors show that autophagy plays a crucial role in regulating timely programmed cell death in the innermost seed coat, thereby influencing embryo pattern formation and seed viability.
- Lin-lin Zhao
- , Ru Chen
- & Peng Zhao
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Article
| Open Access
Spatiotemporal formation of glands in plants is modulated by MYB-like transcription factors
The spatiotemporal formation of glands in tomato trichomes is regulated by two MYB-like transcription factors, named as GCR1 and 2, whose expression is tightly restricted by SlTOE1B. GCR1 and 2 inhibit gland formation by repressing LFS expression.
- Jiang Chang
- , Shurong Wu
- & Shuang Wu
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Article
| Open Access
Core clock genes adjust growth cessation time to day-night switches in poplar
Alique et al. show that poplar trees adjust their seasonal growth timing by finely tuning the daily expression level of the photoperiodic integrator FT2 through a mechanism governed by the circadian clock’s core genes.
- Daniel Alique
- , Arturo Redondo López
- & Mariano Perales
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Article
| Open Access
Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition
Seed germination in plants is a tightly controlled process relying on translation of stored RNAs. Here, Tremblay et al. show that nascent transcriptome and epigenome reprogramming are detected from initial stages of germination.
- Benjamin J. M. Tremblay
- , Cristina P. Santini
- & Julia I. Qüesta
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Article
| Open Access
Genetic control of thermomorphogenesis in tomato inflorescences
Mechanisms underlying changes in inflorescence development in response to high ambient temperature remain unclear. Here, the authors report the cloning of the MIB2, encoding a homology of SPATULA, and its activation of CONSTANS-Like1 for determining tomato inflorescence branching at high ambient temperature.
- Shuai Sun
- , Zhiqiang Liu
- & Xia Cui
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Article
| Open Access
Petal abscission is promoted by jasmonic acid-induced autophagy at Arabidopsis petal bases
In angiosperms, petal abscission is crucial for reproductive success and seed dispersion. However, the regulation of this abscission remains unclear. Here, the authors identify a process of petal abscission regulated by jasmonic acid via autophagy at the base of Arabidopsis petals.
- Yuki Furuta
- , Haruka Yamamoto
- & Nobutoshi Yamaguchi
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Article
| Open Access
BCL7A and BCL7B potentiate SWI/SNF-complex-mediated chromatin accessibility to regulate gene expression and vegetative phase transition in plants
This study uncovers the specialized function of previously elusive BCL7 subunits of SWI/SNF complexes in eukaryotes and reveals the mechanism whereby plants memorize the juvenile identity through SWI/SNF-mediated control of chromatin accessibility.
- Yawen Lei
- , Yaoguang Yu
- & Chenlong Li
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Article
| Open Access
A CYBDOM protein impacts iron homeostasis and primary root growth under phosphate deficiency in Arabidopsis
Iron deposition in cell walls inhibits Arabidopsis root growth under phosphate deficiency. A protein with iron reductase activity belonging to an uncharacterized CYBDOM family was identified which modulates this process and affects iron homeostasis.
- Joaquín Clúa
- , Jonatan Montpetit
- & Yves Poirier
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Article
| Open Access
Ferric reduction by a CYBDOM protein counteracts increased iron availability in root meristems induced by phosphorus deficiency
The study identified an Arabidopsis ascorbate-dependent metalloreductase belonging to the CYBDOM family, which functions in maintaining cell elongation and meristem integrity by preventing iron-dependent root growth arrest under phosphate deficiency.
- Rodolfo A. Maniero
- , Cristiana Picco
- & Ricardo F. H. Giehl
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Article
| Open Access
BPG4 regulates chloroplast development and homeostasis by suppressing GLK transcription factors and involving light and brassinosteroid signaling
The authors identify BPG4, a novel regulator of chloroplast development. BPG4 directly suppresses transcriptional activity of GLK to fine-tune photosynthesis associated nuclear gene expression, and regulates chloroplast development and homeostasis.
- Ryo Tachibana
- , Susumu Abe
- & Takeshi Nakano
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Article
| Open Access
MADS1-regulated lemma and awn development benefits barley yield
HvMADS1 in barley positively regulates awn length and lemma width by promoting cell proliferation through direct action on the expression of HvSHI and HvDL. In wheat, MADS1 conservatively regulates awn length.
- Yueya Zhang
- , Chaoqun Shen
- & Dabing Zhang
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Article
| Open Access
Decoding the gene regulatory network of endosperm differentiation in maize
The cereal endosperm constitutes most of the grain by volume. Here the authors use single-cell analysis of maize developing endosperm to decode gene regulatory networks that likely control endosperm growth and offer a framework for crop improvement.
- Yue Yuan
- , Qiang Huo
- & Zeyang Ma
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Article
| Open Access
Primase promotes the competition between transcription and replication on the same template strand resulting in DNA damage
Resolving R-loops caused by transcription-replication conflicts (TRCs) is vital to genome stability in organisms. Here, the authors show that the chloroplast-localized primase ATH intensifies template strand competition and exacerbates the Head-On TRCs induced DNA damage.
- Weifeng Zhang
- , Zhuo Yang
- & Qianwen Sun
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Article
| Open Access
Cell geometry regulates tissue fracture
The epidermal surface of leaves and flower petals often display cells with wavy geometries. Here the authors provide evidence that this pattern represents an energy-efficient mechanism to protect plants from deleterious surface fissures and toughen the plants’ protective surface.
- Amir J. Bidhendi
- , Olivier Lampron
- & Anja Geitmann
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Article
| Open Access
Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat
The analysis of wheat cultivars reveals that variations in histone modification, rather than DNA sequence, are closely linked to the expression of nitrogen metabolism genes and distinct agronomic traits. The findings suggest that epigenetic regulation plays a crucial role in cultivar-specific adaptation to low nitrogen conditions in wheat.
- Hao Zhang
- , Zhiyuan Jin
- & Jun Xiao
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Article
| Open Access
Control of compound leaf patterning by MULTI-PINNATE LEAF1 (MPL1) in chickpea
Pinnate compound leaves sequentially produce their leaflets along the longitudinal axes. The study identifies the MPL1 gene as a key regulator in orchestrating an acropetal pattern of leaflet formation during the chickpea pinnate leaf development.
- Ye Liu
- , Yuanfan Yang
- & Liangliang He
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Article
| Open Access
A micro RNA mediates shoot control of root branching
Plant shoots and roots act in concert to ensure access to soil nutrients by adapting root growth. The manuscript identifies a key shoot signal, a mobile micro RNA, that systemically controls lateral root initiation to optimize nitrate supply.
- Moritz Sexauer
- , Hemal Bhasin
- & Katharina Markmann
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Article
| Open Access
Nitric oxide controls shoot meristem activity via regulation of DNA methylation
The authors show that gaseous Nitric Oxide (NO) promotes transit amplifying cell fate in the Arabidopsis shoot meristem. NO acts by modifying AGO4-WUSCHEL protein interactions in stem cells, directly linking NO signaling with DNA methylation.
- Jian Zeng
- , Xin’Ai Zhao
- & Jan U. Lohmann
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Article
| Open Access
Soybean reduced internode 1 determines internode length and improves grain yield at dense planting
Many cereal crops have been bred to be more compact to allow high-density planting, but soybean has remained relatively overlooked. Here, the authors describe a compact soybean mutant, reduced internode 1, that significantly enhances grain yield under high-density planting conditions compared to an elite cultivar.
- Shichen Li
- , Zhihui Sun
- & Sijia Lu
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Article
| Open Access
Petal size is controlled by the MYB73/TPL/HDA19-miR159-CKX6 module regulating cytokinin catabolism in Rosa hybrida
Expression of MIR159 is attenuated by a MYB73/TPL/HDA19 repression complex during rose petal development. Reduced MIR159 levels lead to accumulation of Cytokinin Oxidase 6, causing cytokinin clearance and subsequent arrest of cell division.
- Weikun Jing
- , Feifei Gong
- & Nan Ma
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Article
| Open Access
A silicon transporter gene required for healthy growth of rice on land
Rice actively accumulates silicon as amorphous silica (phytoliths), which protects the plant from various stresses. Here, the authors show that SlET4, a polarly localizes Si transporter, exports Si from leaf cells to the leaf surface and is required for healthy growth of rice on land.
- Namiki Mitani-Ueno
- , Naoki Yamaji
- & Jian Feng Ma
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Article
| Open Access
Natural plant growth and development achieved in the IPK PhenoSphere by dynamic environment simulation
The PhenoSphere is a unique plant cultivation facility in which field-like environments can be simulated. Here, the authors find that a single season simulation is superior to an averaged season and to a climatized glasshouse cultivation to elicit field-like phenotypes evaluated in 11 maize lines.
- Marc C. Heuermann
- , Dominic Knoch
- & Thomas Altmann
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Article
| Open Access
Arabidopsis TCP4 transcription factor inhibits high temperature-induced homeotic conversion of ovules
Global warming threatens food security and plant survival. This paper demonstrates that Class II TCP transcription factors are critical for specifying ovule identity and inhibiting the conversion of ovules into carpelloids under high temperature.
- Jingqiu Lan
- , Ning Wang
- & Genji Qin
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Article
| Open Access
QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize
The lack of large-scale QTL cloning method hampers systematic dissection of genetic base of quantitative traits. Here, the authors develop a multi-omics data-based technique for large-scale and rapid cloning of quantitative genes of tassel branch number and discovery of selection signatures in maize breeding.
- Xi Wang
- , Juan Li
- & Lin Li
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Article
| Open Access
A BLADE-ON-PETIOLE orthologue regulates corolla differentiation in the proximal region in Torenia fournieri
Flowers manifest enormous diversity and shape is determined by morphogenesis along different independent axes. Here Su et al. report a shared BOP-ALOG module that regulates corolla differentiation in the proximal region axis.
- Shihao Su
- , Yawen Lei
- & Tetsuya Higashiyama
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Article
| Open Access
A maize epimerase modulates cell wall synthesis and glycosylation during stomatal morphogenesis
Dynamic cell walls enable stomata rapidly responding to the environment. Here the authors report that a maize epimerase is involved in cell wall polysaccharide biosynthesis and glycosylation modulation during stomatal morphogenesis.
- Yusen Zhou
- , Tian Zhang
- & Chun-Peng Song
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Article
| Open Access
Fertilization controls tiller numbers via transcriptional regulation of a MAX1-like gene in rice cultivation
Here the authors show that fertilization controls rice tiller numbers through the transcription of a rice MAX1-like gene involved in strigolactone biosynthesis. Promoter variation lines have the potential to improve yield when fertilizer is limited.
- Jinying Cui
- , Noriko Nishide
- & Takeshi Izawa
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Article
| Open Access
ACL and HAT1 form a nuclear module to acetylate histone H4K5 and promote cell proliferation
Xu et al. showed that a histone acetyltransferase interacts with an acetyl-CoA synthetic enzyme for histone acetylation to stimulate gene expression and endosperm cell division, pointing to a mechanism coupling energy metabolism to epigenetics.
- Qiutao Xu
- , Yaping Yue
- & Dao-Xiu Zhou
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Article
| Open Access
Coordinated regulation of vegetative phase change by brassinosteroids and the age pathway in Arabidopsis
Zhou et al. reveal a novel role for brassinosteroids in regulation of vegetative phase change in Arabidopsis. Brassinosteroids regulate this process by simultaneously stabilizing SPL9 and TOE1 through the BIN2-mediated phosphorylation process.
- Bingying Zhou
- , Qing Luo
- & Gang Wu
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Article
| Open Access
Chemical imaging reveals diverse functions of tricarboxylic acid metabolites in root growth and development
Chemical imaging of maize roots reveals differential patterns of TCA cycle metabolites along the axis of development. Root growth is affected in distinct ways by exogenous treatments and tissue-specific genetic manipulation of TCA metabolites.
- Tao Zhang
- , Sarah E. Noll
- & Alexandra J. Dickinson
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Article
| Open Access
OBERON3 and SUPPRESSOR OF MAX2 1-LIKE proteins form a regulatory module driving phloem development
The phloem tissue is the main transport route for sugars in plant bodies. This study reveals a nuclear protein complex consisting of SMXL5 and OBE3 to be essential for phloem development by establishing a phloem-specific chromatin conformation.
- Eva-Sophie Wallner
- , Nina Tonn
- & Thomas Greb
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Article
| Open Access
Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum
Chrysanthemum is an important ornamental species with great economic value. Here, the authors assemble the haploid genome of C. morifolium, reveal its segmental allopolyploid genomic composition (AA’B), and identify candidate genes associated with flower development, petal shape, and flower colour.
- Aiping Song
- , Jiangshuo Su
- & Fadi Chen
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Article
| Open Access
The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine
DNA methylation level declines during aging of mammals. Here, the authors report single-base resolution landscape of cytosine DNA methylation at different ages of Chinese pine and show that the global cytosine DNA methylation gradually increases as age progresses.
- Jiang Li
- , Fangxu Han
- & Shihui Niu
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Article
| Open Access
An integrase toolbox to record gene-expression during plant development
Synthetic circuits that can record in vivo signaling networks is critical in elucidating developmental process. Here, the authors describe the engineering and application of synthetic in vivo recorders with different promoters that can drive spatiotemporally-specific integrase switching during lateral root initiation.
- Sarah Guiziou
- , Cassandra J. Maranas
- & Jennifer L. Nemhauser
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Article
| Open Access
CEP peptide and cytokinin pathways converge on CEPD glutaredoxins to inhibit root growth
C-terminally encoded peptide (CEP) and cytokinin (CK) hormones modulate plant root architecture in response to environmental cues. The results show that CEP and CK pathways utilise CEPD glutaredoxins in separate organs to curb primary root growth.
- Michael Taleski
- , Kelly Chapman
- & Michael A. Djordjevic
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Article
| Open Access
Optimization of rice panicle architecture by specifically suppressing ligand–receptor pairs
Rice panicle architecture dominates grain yield. In this study, the authors demonstrate a method for rationally overcoming the trade-off between yield traits and optimizing rice panicle architecture by specifically manipulating ligand–receptor pairs.
- Tao Guo
- , Zi-Qi Lu
- & Hong-Xuan Lin
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Article
| Open Access
Directed growth and fusion of membrane-wall microdomains requires CASP-mediated inhibition and displacement of secretory foci
Casparian strips are extracellular diffusion barriers in plant roots. Here, Barbosa et al. provide evidence that CASP proteins shape Casparian strips by displacing vesicle tethering factors and organizing cell wall formation
- Inês Catarina Ramos Barbosa
- , Damien De Bellis
- & Niko Geldner
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Article
| Open Access
MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis
Plants respond to light and temperature changes via the photoreceptor phytochrome B and the phytohormone auxin. Here the authors reveal microRNA156 as a previously uncharacterized developmental signal that gates environmentally regulated plant growth by licensing auxin sensitivity.
- Qing Sang
- , Lusheng Fan
- & Xuemei Chen
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Article
| Open Access
The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis
Torreya grandis is a gymnosperm species that produces edible seeds with high level of sciadonic acid (SCA). Here, the authors assemble the genome of this species, preform methylone analysis of seeds at different developmental stages, and reveal two key genes involved in SCA biosynthesis.
- Heqiang Lou
- , Lili Song
- & Jiasheng Wu
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Article
| Open Access
Epidermal injury-induced derepression of key regulator ATML1 in newly exposed cells elicits epidermis regeneration
In many plants, only the outermost cells are specified into the epidermis, with underlying mechanisms unknown. Here, the authors show that a key epidermis identity gene is activated in surface cells, via positional cues involving mechanical signals.
- Hiroyuki Iida
- , Ari Pekka Mähönen
- & Shinobu Takada
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Article
| Open Access
Tiller Number1 encodes an ankyrin repeat protein that controls tillering in bread wheat
Tiller number is an important agronomic trait of wheat. Here, the authors clone a positive regulator of wheat tiller number and show that the encoded ankyrin repeat protein can promote tiller bud outgrowth through inhibiting ABA biosynthesis and signaling.
- Chunhao Dong
- , Lichao Zhang
- & Xu Liu
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Article
| Open Access
Dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat root growth
Introgression of the short arm of rye chromosome one into common wheat increases root biomass and drought tolerance, but the underlying genetic basis is unknown. Here, the authors report that dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate the differences of wheat root architecture.
- Gilad Gabay
- , Hanchao Wang
- & Jorge Dubcovsky
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Article
| Open Access
A phosphoinositide hub connects CLE peptide signaling and polar auxin efflux regulation
In this paper the authors demonstrate that auxin efflux in the phloem vascular tissue of plants is determined by antagonism between CLE peptide signaling pathways and phosphoinositide kinases.
- Qian Wang
- , A. Cecilia Aliaga Fandino
- & Christian S. Hardtke
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Article
| Open Access
Common evolutionary trajectory of short life-cycle in Brassicaceae ruderal weeds
Understanding origin and adaptation of weeds is important for their management. Here, via genome assembly, population genomics, and QTL mapping, the authors establish Cardamine occulta as a model to study weed ruderality and show FLC and CRY2 as genetic drivers for the establishment of short life cycle.
- Ling-Zi Li
- , Zhou-Geng Xu
- & Jia-Wei Wang
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Article
| Open Access
Arabidopsis DXO1 activates RNMT1 to methylate the mRNA guanosine cap
Arabidopsis DXO1 is a member of the eukaryotic DXO family of decapping enzymes for NAD-capped RNAs. Here the authors show that DXO1 is an essential component in canonical m7G capping of mRNA and activates RNMT1 which methylates the guanosine cap to form the m7G cap.
- Chen Xiao
- , Kaien Li
- & Yiji Xia
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Article
| Open Access
Evidence that endosperm turgor pressure both promotes and restricts seed growth and size
Using computational simulations and experiments, the authors propose a mechanical model of seed growth where endosperm pressure directly induces growth but indirectly inhibits it through force-dependent testa wall stiffening.
- Audrey Creff
- , Olivier Ali
- & Benoit Landrein
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Article
| Open Access
High-frequency synthetic apomixis in hybrid rice
Previously, a proof-of-concept for low frequency synthetic apomixis was established in a laboratory strain of rice by combining MiMe mutations with the egg cell expression of the embryogenic trigger - BBM1. Here, the authors achieve clonal seed formation in hybrid rice with almost full penetrance and higher fertility.
- Aurore Vernet
- , Donaldo Meynard
- & Emmanuel Guiderdoni
Rewiring of a KNOXI regulatory network mediated by UFO underlies the compound leaf development in Medicago truncatula