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| Open AccessA fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics
Plants utilize transcriptional dynamics to adapt to cold stress. Here, Zhang et al. describe a network of chromatin interactions between gene promoters across the Arabidopsis genome that could facilitate co-regulation of gene expression during cold stress.
- Yueying Zhang
- , Qianli Dong
- & Huakun Zhang
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Article
| Open AccessA transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination
Japonica rice generally has greater capacity for low temperatures germination (LTG) than indica rice. Here, the authors report an E2 ubiquitin-conjugating enzyme-encoding gene OsUBC12 can increase LTG in japonica rice by negatively regulate ABA signaling via promoting the proteasomal degradation of OsSnRK1.1.
- Chuanzhong Zhang
- , Hongru Wang
- & Jun Fang
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| Open AccessA 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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| Open AccessFerric 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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| Open AccessProximity to Photosystem II is necessary for activation of Plastid Terminal Oxidase (PTOX) for photoprotection
Plastid terminal oxidase (PTOX) is efficient in photoprotection in stress-tolerant plants. Transferring this activity to different species requires modifications to the thylakoid structure to allow PTOX access to the Photosystem II acceptor pool.
- Pablo Ignacio Calzadilla
- , Junliang Song
- & Giles Nicholas Johnson
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| Open AccessAdaptive traits of cysts of the snow alga Sanguina nivaloides unveiled by 3D subcellular imaging
Sanguina nivaloides thrives in red snowfields worldwide. It cannot be cultivated. Using environmental samples, 3D electron microscopy combined with functional analyzes revealed unique cell architecture features adapted to life in a snowy environment.
- Jade A. Ezzedine
- , Clarisse Uwizeye
- & Eric Maréchal
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| Open AccessA mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice
Cold stress hampers rice growth and yield. This paper demonstrates that mitochondrial superoxide plays a key role in cold responses, and identifies a pentatricopeptide repeat protein which modulates mitochondrial superoxide and rice cold tolerance.
- Xiaofeng Zu
- , Lilan Luo
- & Xiaofeng Cao
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Article
| Open AccessA 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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| Open AccessThe CBL1/9-CIPK1 calcium sensor negatively regulates drought stress by phosphorylating the PYLs ABA receptor
ABA signaling and Ca2+ signaling regulatory networks are crucial for how plants respond to drought stress. Here, the authors reported that the functional module of the CBL1/9-CIPK1-PYLs regulatory network plays a negative role in ABA signaling and its response to drought stress.
- Zhang You
- , Shiyuan Guo
- & Cun Wang
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Article
| Open AccessFunctional annotation of proteins for signaling network inference in non-model species
An artificial-intelligence network is used to generate highly accurate predictions of proteins’ functionality. The predictions on the identity of regulatory proteins is used to create regulatory networks and make discoveries about complex biological systems.
- Lisa Van den Broeck
- , Dinesh Kiran Bhosale
- & Rosangela Sozzani
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| Open AccessThe OsSGS3-tasiRNA-OsARF3 module orchestrates abiotic-biotic stress response trade-off in rice
Gu et al. report that the OsSGS3-tasiRNA-OsARF3 module plays an important role in coordinating the trade-off between heat tolerance and disease resistance, which positively regulates thermotolerance but negatively modulates immunity in rice.
- Xueting Gu
- , Fuyan Si
- & Junzhong Liu
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Article
| Open AccessFlavodiiron-mediated O2 photoreduction at photosystem I acceptor-side provides photoprotection to conifer thylakoids in early spring
Generally, net O2 consumption becomes dominant when photosynthesis is suppressed at night in green organisms. Here, Bag et al. show that Scots pine and Norway spruce needles display strong O2 consumption when extremely low temperatures coincide with high solar irradiation during early spring.
- Pushan Bag
- , Tatyana Shutova
- & Stefan Jansson
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| Open AccessCross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses
How plants respond to multiple stresses occurring simultaneously is poorly understood. Here the authors describe how gene expression in Marchantia polymorpha responds to different combinations of seven abiotic stresses and provide online resources to facilitate data visualization and usability.
- Qiao Wen Tan
- , Peng Ken Lim
- & Marek Mutwil
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Article
| Open AccessPotassium nutrient status drives posttranslational regulation of a low-K response network in Arabidopsis
Potassium is essential for plant growth and development. Here the authors present evidence that plants respond to low potassium availability by modulating the abundance and phosphorylation status of proteins in CBL-CIPK-channel modules.
- Kun-Lun Li
- , Ren-Jie Tang
- & Sheng Luan
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Article
| Open AccessGenome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass
Paspalum vaginatum is a stress tolerant wild relative of maize and sorghum. Here, the authors assemble its genome at pseudomolecule level and reveal the role of trehalose mediated autophagy in increasing maize biomass productivity under nutrient-deficit conditions.
- Guangchao Sun
- , Nishikant Wase
- & James C. Schnable
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Article
| Open AccessTranslational fidelity and growth of Arabidopsis require stress-sensitive diphthamide biosynthesis
Diphthamide is a post-translationally modified histidine residue present in animal and yeast TRANSLATION ELONGATION FACTOR2. Here the authors show that diphthamide modification of eEF2 is conserved in Arabidopsis thaliana and contributes to translational fidelity and growth via cell proliferation.
- Hongliang Zhang
- , Julia Quintana
- & Ute Krämer
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Article
| Open AccessA natural uORF variant confers phosphorus acquisition diversity in soybean
Improving phosphorus (P) acquisition efficiency is important for sustainable agriculture. Here, the authors report a natural variation in an upstream open reading frame of a SEC12-like gene GmPHF1 is crucial for protein abundance and spatial distribution of GmPHF1, which contribute to P acquisition diversity in soybean.
- Zilong Guo
- , Hongrui Cao
- & Hong Liao
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Article
| Open AccessCloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii
The Aegilops tauschii-derived leaf rust resistance gene Lr42 has been widely used for breeding resistance wheat cultivars, but the molecular basis is unknown. Here, the authors show that Lr42 encodes an NLR-type of disease resistance gene by bulked segregant mapping in Ae. tauschii and confirm its function in common wheat.
- Guifang Lin
- , Hui Chen
- & Sanzhen Liu
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Article
| Open AccessApoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature
Arabidopsis root hair growth is enhanced at low temperatures. Here the authors show that the class III peroxidases PRX62 and PRX69 modulate ROS homeostasis and cell wall characteristics, and promote root hair elongation at low temperature.
- Javier Martínez Pacheco
- , Philippe Ranocha
- & José M. Estevez
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| Open AccessPhloem iron remodels root development in response to ammonium as the major nitrogen source
Ammonium affects plant root development through different mechanisms than nitrate. Here, the authors show that the Arabidopsis cell wall-localized ferroxidase LPR2 is required to attenuate root growth in response to ammonium.
- Xing Xing Liu
- , Hai Hua Zhang
- & Chong Wei Jin
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| Open AccessInterdependent iron and phosphorus availability controls photosynthesis through retrograde signaling
Iron deficiency induces chlorosis in plants but only when phosphate supply is sufficient. Here, the authors show that phosphate-dependency is governed by a ROS-mediated retrograde signaling pathway involving the PHT4;4 chloroplast ascorbate transporter and the bZIP58 nuclear transcription factor.
- Hye-In Nam
- , Zaigham Shahzad
- & Hatem Rouached
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| Open AccessA giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean
While multiple resistance-to-Phytophthora sojae loci/alleles have been mapped in soybean, many of them have become ineffective to newly evolved isolates. Here, the authors show that a 27.7-kb nucleotide-binding site-leucine-rich repeat gene confers broad-spectrum resistance to P. sojae in soybean.
- Weidong Wang
- , Liyang Chen
- & Jianxin Ma
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| Open AccessNatural variation in a type-A response regulator confers maize chilling tolerance
The genetic basis of low-temperature tolerance in maize is unclear. Here, the authors show that the type-A Response Regulator 1 (ZmRR1) and mitogen-activated protein kinase (MPK8) are positive and negative regulators of maize chilling tolerance, and ZmRR1 is phosphorylated by ZmMPK8 during cold treatment.
- Rong Zeng
- , Zhuoyang Li
- & Shuhua Yang
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| Open AccessThe Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts
Welwitschia mirabilis is a unique plant that only has two leaves, but it can survive in hostile conditions of the African desert. Here, the authors report its chromosome-level genome assembly and discuss how gene function and regulation have given rise to its unique morphology and environmental adaptions.
- Tao Wan
- , Zhiming Liu
- & Qingfeng Wang
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| Open AccessInitiation and amplification of SnRK2 activation in abscisic acid signaling
SnRK2 kinase activity is rapidly activated in response to ABA. Here the authors show that initial activation of SnRK2s is achieved by B2 and B3 RAF kinase-mediated phosphorylation of the activation loop and that transphosphorylation between SnRK2s then amplifies the response.
- Zhen Lin
- , Yuan Li
- & Pengcheng Wang
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Article
| Open AccessA molecular switch in sulfur metabolism to reduce arsenic and enrich selenium in rice grain
Contamination of paddy soils can lead to toxic arsenic accumulation in rice grains and low levels of the micronutrient selenium. Here the authors show that a gain of function mutant affecting an O-acetylserine (thiol) lyase enhances sulfur and selenium assimilation while reducing arsenic accumulation in grains.
- Sheng-Kai Sun
- , Xuejie Xu
- & Fang-Jie Zhao
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| Open AccessPlant Raf-like kinases regulate the mRNA population upstream of ABA-unresponsive SnRK2 kinases under drought stress
SnRK2 protein kinases play key roles in signaling during plant responses to abiotic stress. Here Soma et al. report three Arabidopsis Raf-like MAP kinase kinase kinases phosphorylate and activate a subclass of SnRK2s that rapidly respond to osmotic stress independently of ABA signaling.
- Fumiyuki Soma
- , Fuminori Takahashi
- & Kazuko Yamaguchi-Shinozaki
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| Open AccessA RAF-SnRK2 kinase cascade mediates early osmotic stress signaling in higher plants
Rapid activation of SnRK2 kinases is central to plant responses to osmotic stress and abscisic acid. Here the authors show that a group of Raf-like kinases are very quickly activated by osmotic stress, and then phosphorylate and activate SnRK2s.
- Zhen Lin
- , Yuan Li
- & Pengcheng Wang
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| Open AccessVariation of a major facilitator superfamily gene contributes to differential cadmium accumulation between rice subspecies
Grain of indica rice accumulates more toxic cadmium (Cd) than japonica, but the underlying genetic basis is unclear. Here, the authors show that natural variation of OsCd1 contributes to divergence in grain Cd accumulation and transferring japonica allele to indica rice leads to reduced Cd accumulation.
- Huili Yan
- , Wenxiu Xu
- & Zhenyan He
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Article
| Open AccessNetwork Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions
Temporal control of transcriptional networks enables organisms to adapt to changing environment. Here, the authors use a scaled-up cell-based assay to identify direct targets of nitrogen-early responsive transcription factors and validate a network path mediating dynamic nitrogen signaling in Arabidopsis.
- Matthew D. Brooks
- , Jacopo Cirrone
- & Gloria M. Coruzzi
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Article
| Open AccessCalcium-activated 14-3-3 proteins as a molecular switch in salt stress tolerance
Salinity triggers an increase in cytosolic Ca2+ concentration in plants. Here, the authors propose a model whereby 14-3-3 proteins decode this calcium signature and regulate Na+ extrusion via Ca2+-dependent regulation of PKS5 and SOS2 kinases that in turn regulate the Na+/H+ antiporter SOS1 and PM H+-ATPase
- Zhijia Yang
- , Chongwu Wang
- & Yan Guo
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Article
| Open AccessThe genome of broomcorn millet
Broomcorn millet is one of the earliest domesticated plants and has the highest water use efficiency among cereals. Here, the authors report its genome assembly and annotation, which provides a valuable resource for breeders and paves the way for studying plant drought tolerance and C4 photosynthesis.
- Changsong Zou
- , Leiting Li
- & Heng Zhang
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| Open AccessChromosome conformation capture resolved near complete genome assembly of broomcorn millet
Broomcorn millet is one of the oldest crops cultivated by human that has strong abiotic stress tolerance. To facilitate genome assisted breeding of this and related species, the authors report its genome assembly and conduct comparative genome structure and evolution analyses with foxtail millet.
- Junpeng Shi
- , Xuxu Ma
- & Jinsheng Lai
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Article
| Open AccessProteasomal degradation of BRAHMA promotes Boron tolerance in Arabidopsis
Boron is essential for plant survival but high levels can impair growth and cause DNA damage. Here the authors show that Arabidopsis can ameliorate Boron toxicity via proteasomal degradation of BRAHMA to minimize open chromatin and reduce the likelihood of DNA double strand breaks.
- Takuya Sakamoto
- , Yayoi Tsujimoto-Inui
- & Toru Fujiwara
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Article
| Open AccessStructure of the hyperosmolality-gated calcium-permeable channel OSCA1.2
In plants, hyperosmolality stimuli triggers opening of the osmosensitive channels, leading to a rapid downstream signaling cascade. Here, the authors solve the cryo-EM structure of an osmosensitive channel from Arabidopsis OSCA1.2 in its inactivated state.
- Xin Liu
- , Jiawei Wang
- & Linfeng Sun
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| Open AccessEarly selection of bZIP73 facilitated adaptation of japonica rice to cold climates
Japonica rice can grow further north than wild or indica rice and is more tolerant of cold climates. Here, the authors show that bZIP73 likely underwent selection in the early phase of rice domestication to facilitate cold tolerance in japonica by modulating ABA and ROS homeostasis.
- Citao Liu
- , Shujun Ou
- & Chengcai Chu
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Article
| Open AccessRice actin binding protein RMD controls crown root angle in response to external phosphate
The orientation of plant roots responds to gravity and influences nutrient acquisition. Here the authors show that the formin RMD buffers movement of specialized gravity-sensing organelles and report enhanced RMD expression during phosphate deficiency that could alter root angle to improve phosphate uptake.
- Guoqiang Huang
- , Wanqi Liang
- & Dabing Zhang
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Article
| Open AccessRice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate
Plant root architecture can adapt to different nutrient conditions in the soil. Here Giri et al. show that the rice auxin influx carrier AUX1 mobilizes auxin from the root apex to the differentiation zone and promotes root hair elongation when roots encounter low external phosphate.
- Jitender Giri
- , Rahul Bhosale
- & Malcolm J. Bennett
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| Open AccessA mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate
Plant root hairs elongate in response to low soil phosphate. Here Bhosale et al. show that root hair elongation requires auxin synthesis mediated by TAA1, auxin transport by AUX1 in the lateral root cap and epidermis, and signaling via the auxin-inducible ARF19, RSL2 and RSL4 transcription factors.
- Rahul Bhosale
- , Jitender Giri
- & Ranjan Swarup
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Article
| Open AccessResource acquisition and reproductive strategies of tropical forest in response to the El Niño–Southern Oscillation
It has been suggested that tree phenology may be regulated by climatic oscillations. Here, Detto et al. present a 30 year tropical forest dataset that suggests leaf and fruit production is coordinated with ENSO cycles, with greater leaf fall observed prior to El Niño followed by greater seed production.
- Matteo Detto
- , S. Joseph Wright
- & Helene C. Muller-Landau
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Article
| Open AccessCombining chemical and genetic approaches to increase drought resistance in plants
Plants respond to abiotic stress via the phytohormone ABA. Here, Cao et al. report a series of new ABA receptor agonists, named AMFs, which have higher receptor-binding affinities and show that, when employed in tandem with ABA receptor overexpression, can significantly increase drought resistance
- Min-Jie Cao
- , Yu-Lu Zhang
- & Jian-Kang Zhu
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Article
| Open AccessArabidopsis R1R2R3-Myb proteins are essential for inhibiting cell division in response to DNA damage
Inhibition of cell division maintains genome integrity in response to DNA damage. Here Chen et al. propose that DNA damage causes cell cycle arrest in the Arabidopsis root via Rep-MYB transcription factor-mediated repression of G2/M-specific gene expression in response to reduced cyclin-dependent kinase activity.
- Poyu Chen
- , Hirotomo Takatsuka
- & Masaaki Umeda
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Article
| Open AccessNatural allelic variation of FRO2 modulates Arabidopsis root growth under iron deficiency
Iron is an essential micronutrient for plants and a lack of iron availability limits crop yield in many parts of the world. Here the authors show that natural variation in root growth ofArabidopsis plants under iron deficiency can be caused by allelic variation at the FRO2locus.
- Santosh B. Satbhai
- , Claudia Setzer
- & Wolfgang Busch
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Article
| Open AccessLow phosphate activates STOP1-ALMT1 to rapidly inhibit root cell elongation
Low Pi availability inhibits primary root growth, but the sensory mechanisms are not known. Here the authors uncover a signalling pathway regulating Pi-mediated root growth inhibition inArabidopsis, involving the transcription factor STOP1, its direct target ALMT1, a malate channel, and ferroxidase LPR1.
- Coline Balzergue
- , Thibault Dartevelle
- & Thierry Desnos
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| Open AccessNatural variation in CTB4a enhances rice adaptation to cold habitats
Low temperature is a major factor limiting productivity in rice. Here the authors show that theCTB4a gene confers cold tolerance to japonicavarieties adapted to cold habitats at the booting stage of development, and propose that CTB4a acts via an interaction with the beta subunit of ATP synthase.
- Zhanying Zhang
- , Jinjie Li
- & Zichao Li
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Article
| Open AccessEnvironmental conditions regulate the impact of plants on cloud formation
Volatile organic compounds (VOC) emitted by vegetation influence cloud formation, yet the impact of environmental stresses remains little known. Here, manipulation experiments reveal insect infestation and heat stress are linked to induced VOC and constitutive VOC emissions shifts, respectively.
- D. F. Zhao
- , A. Buchholz
- & Th. F. Mentel
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| Open AccessA novel thiol-reductase activity of Arabidopsis YUC6 confers drought tolerance independently of auxin biosynthesis
YUC6 is a flavin monooxygenase required for the synthesis of the plant hormone auxin. Chaet al. discover that in Arabidopsis, this enzyme also plays a role in combatting oxidative stress independently of auxin biosynthesis, by acting as a thiol-reductase.
- Joon-Yung Cha
- , Woe-Yeon Kim
- & Dae-Jin Yun
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Article |
Natural variation in arsenate tolerance identifies an arsenate reductase in Arabidopsis thaliana
Arsenic tolerance in plants is critical for their adaptation to some soils and has therefore played an important role in plant distribution. Here, the authors identify a quantitative trait locus encoding an arsenate reductase enzyme that confers arsenic tolerance in plants.
- Eduardo Sánchez-Bermejo
- , Gabriel Castrillo
- & Antonio Leyva