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| Open AccessHaplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus
Trait introgression requires universal markers, but cross-species transferability of current SNP markers can be as low as 2%. Here, the authors use an AmpSeq haplotype strategy targeting the collinear core genome for marker development and show transferability increases to 91.4% in the Vitis genus.
- Cheng Zou
- , Avinash Karn
- & Lance Cadle-Davidson
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Article
| Open AccessNatural variation of an EF-hand Ca2+-binding-protein coding gene confers saline-alkaline tolerance in maize
Saline-alkaline stress affects worldwide crops production, but the tolerance mechanisms have not been fully elucidated. Here, the authors show that EF-hand Ca2 + -binding-protein coding gene ZmNSA1 can regulate root H + efflux, Na + homeostasis, and saline-alkaline tolerance in maize.
- Yibo Cao
- , Ming Zhang
- & Caifu Jiang
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Article
| Open AccessLong-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
The South African quality protein maize (QPM) cultivars have the desired high lysine content and kernel hardness due to o2 mutation and the introgression of modifiers of o2 (Mo2) QTLs, respectively. Here, the authors assemble the genome of a QPM line and identify candidate genes underlying Mo2 QTLs.
- Changsheng Li
- , Xiaoli Xiang
- & Wenqin Wang
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Article
| Open AccessAn artificial metalloenzyme biosensor can detect ethylene gas in fruits and Arabidopsis leaves
Existing methods to detect ethylene in plant tissue typically require gas chromatography or use ethylene-dependent gene expression as a proxy. Here Vong et al. show that an artificial metalloenzyme-based ethylene probe can be used to detect ethylene in plants with improved spatiotemporal resolution.
- Kenward Vong
- , Shohei Eda
- & Katsunori Tanaka
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Article
| Open AccessThe tin1 gene retains the function of promoting tillering in maize
Unlike the other domesticated maize, sweet maize and popcorn retain tillering growth habit, but the underlying mechanism is unknown. Here, the authors identify a transcription factor tin1 that maintains outgrowth of tiller independent of tb1 and show its conservation in foxtail millet and rice.
- Xuan Zhang
- , Zhelong Lin
- & Zhongwei Lin
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Article
| Open AccessGenome-wide associated study identifies NAC42-activated nitrate transporter conferring high nitrogen use efficiency in rice
Improving crop nitrogen use efficiency can facilitate sustainable production, however, the genetic mechanisms have not been fully revealed. Here, the authors discover the NAC42-NPF6.1 signaling cascade mainly derives from indica and wild rice and demonstrate the potential of using the allele for cultivar improvement.
- Weijie Tang
- , Jian Ye
- & Jianmin Wan
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Article
| Open AccessThe indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency
Indica rice has higher nitrate assimilation and nitrogen use efficiency (NUE) than japonica rice, but the mechanism is unclear. Here, the authors reveal that the difference is partly due to allelic variation of a nitrate reductase encoding gene and this indica allele can increase yield potential and NUE.
- Zhenyu Gao
- , Yufeng Wang
- & Qian Qian
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Article
| Open AccessPathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases
Steroidal glycoalkaloids (SGAs) accumulate in Solanum, but their hydroxylating enzymes are unknown. Here, the authors report 2-OXOGLUTARATE DEPENDENT DIOXYGENASE enzymes that catalyze the committed hydroxylation steps in the biosynthesis of leptinine insecticidal compounds in wild potato or non-bitter SGAs in cultivated tomato.
- Pablo D. Cárdenas
- , Prashant D. Sonawane
- & Asaph Aharoni
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Article
| Open AccessChloroplastic metabolic engineering coupled with isoprenoid pool enhancement for committed taxanes biosynthesis in Nicotiana benthamiana
Engineering Taxol pathway in microbes needs to overcome the difficulty of expressing plant P450 enzymes. Here, the authors use a compartmentalized metabolic engineering strategy to construct the taxanes production pathway in chloroplasts of Nicotiana benthamiana and realize the production of taxadience-5α-ol.
- Jianhua Li
- , Ishmael Mutanda
- & Yong Wang
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Article
| Open AccessThe chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis
Black pepper (Piper nigrum) belongs to the long-isolated lineage of basal angiosperm and its fruit has been used for food spice and phytomedicines for thousands of years. Here, the authors assemble the reference genome of this species and analyze gene families associated with piperine biosynthesis.
- Lisong Hu
- , Zhongping Xu
- & Shuangxia Jin
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Article
| Open AccessMeiotic crossovers characterized by haplotype-specific chromosome painting in maize
Meiotic crossovers (COs) are essential for proper chromosome segregation and generating novel combinations of alleles. Here, the authors develop haplotype-specific oligos on maize chromosome 10 for fluorescence in situ hybridization and analyze CO patterns in an intermated recombinant population derived from B73 and Mo17.
- Lívia do Vale Martins
- , Fan Yu
- & Jiming Jiang
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Article
| Open AccessSoybean antiviral immunity conferred by dsRNase targets the viral replication complex
Soybean mosaic virus (SMV) is a potyvirus that reduces soybean yield and seed quality worldwide. Here, the authors reveal that the resistance gene Rsv4 encodes an RNase H family protein with dsRNA-degrading activity, and it can enter the viral replication compartment and degrade viral dsRNA.
- Kazuhiro Ishibashi
- , Masayasu Saruta
- & Akito Kaga
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Article
| Open AccessAn ancestral NB-LRR with duplicated 3′UTRs confers stripe rust resistance in wheat and barley
Stripe rust is a serious threat to wheat production. Here, the authors reveal that the resistance gene, only present in the wheat progenitor Aegilops tauschii and its derived synthetic wheat, encodes a nucleotide oligomerization domain-like receptor and confers resistance in common wheat and barley.
- Chaozhong Zhang
- , Lin Huang
- & Daolin Fu
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Article
| Open AccessGSNOR provides plant tolerance to iron toxicity via preventing iron-dependent nitrosative and oxidative cytotoxicity
How plants deal with iron toxicity is still unclear. Here, the authors reveal that S-nitrosoglutathione-reductase (GSNOR) provides tolerance to iron toxicity by preventing iron-dependent nitrosative and oxidative cytotoxicity in Arabidopsis, legumes, and rice.
- Baohai Li
- , Li Sun
- & Wolfgang Busch
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Article
| Open AccessThe grain yield modulator miR156 regulates seed dormancy through the gibberellin pathway in rice
Pre-harvest sprouting reduces the yield of agriculturally important crops such as rice. Here, the authors show that mutating specific members of the MIR156 gene family can suppress pre-harvest sprouting in rice without negative effects on plant architecture, suggesting a practical route to elite crop varieties.
- Chunbo Miao
- , Zhen Wang
- & Jian-Kang Zhu
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Article
| Open AccessChromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation
Three-dimensional genome organization and its effect on transcription remain elusive in rice. Here, the authors map promoter–promoter interactions and heterochromatin interactions using ChIA-PET and reveal spatial correlation between the genetic regulation of eQTLs and e-traits.
- Lun Zhao
- , Shuangqi Wang
- & Xingwang Li
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Article
| Open AccessEngineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria
The root microbiota is critical for promoting crop yield. Here, the authors create a synthetic pathway for the production of the rhizopine scyllo-inosamine in Medicago truncatula and barley, and show its perception by rhizosphere bacteria for targeted regulation of bacterial gene expression.
- Barney A. Geddes
- , Ponraj Paramasivan
- & Philip S. Poole
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Article
| Open AccessSequencing of Chinese castor lines reveals genetic signatures of selection and yield-associated loci
Castor is an important industrial oil crop, but knowledge on its genetic diversity is limited. Here, Fan et al. show geographic pattern of Chinese castors that have developed during domestication by population genetic analyses, and reveal candidate genes associated with agronomically important traits.
- Wei Fan
- , Jianjun Lu
- & Peng Cui
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Article
| Open AccessExtensive intraspecific gene order and gene structural variations in upland cotton cultivars
While multiple cotton genomes are available, genome wide variation comparison between allotetraploid upland cotton cultivars remain unexplored. Here, the authors assemble two upland cotton cultivars and reveal large scale structural variations on chromosome A08.
- Zhaoen Yang
- , Xiaoyang Ge
- & Fuguang Li
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Article
| Open AccessDissecting a heterotic gene through GradedPool-Seq mapping informs a rice-improvement strategy
Developing hybrid rice cultivars requires time consuming random crossing. Here, the authors develop a new next generation sequencing-based quantitative trait locus mapping method to dissect heterotic gene OsMADS1 and demonstrate the feasibility of pyramiding two genes to achieve large heterotic effect.
- Changsheng Wang
- , Shican Tang
- & Bin Han
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Article
| Open AccessChromatin interaction maps reveal genetic regulation for quantitative traits in maize
Spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, the authors construct maize chromatin interaction maps using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and show their associations with gene expression and agronomic traits.
- Yong Peng
- , Dan Xiong
- & Xingwang Li
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Article
| Open AccessLong-range interactions between proximal and distal regulatory regions in maize
Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can discover specific protein-centered chromatin interactions in high resolution. Here, the authors use ChIA-PET to reveal the complex and dynamic interactions between proximal and distal regulatory regions of genes in maize.
- En Li
- , Han Liu
- & Jinsheng Lai
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Article
| 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 AccessAn asymmetric allelic interaction drives allele transmission bias in interspecific rice hybrids
Our limited understanding of the hybrid sterility (HS) mechanism in Asian–African rice hybrids hampers utilization of the interspecific heterosis for rice production. Here, the authors identify S1-mediated HS-related tripartite gamete killer-protector system, and explore their evolutionary relationship.
- Yongyao Xie
- , Jintao Tang
- & Letian Chen
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Article
| Open AccessNatural variation of OsGluA2 is involved in grain protein content regulation in rice
Grain protein content determines rice nutrition quality. Here, the authors show that a single nucleotide polymorphism in the promoter region of OsGluA2, encoding a glutelin type-A2 precursor, is responsible for glutelin content difference between the indica and japonica rice subspecies.
- Yihao Yang
- , Min Guo
- & Changjie Yan
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Article
| Open AccessMeta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor
Flavor is one of the most important traits for improving tomato sensory quality and consumer acceptability. Here, the authors report meta-analysis of genome-wide association studies of flavor related traits and show genetic insights into the influence of human selection during domestication and improvement.
- Jiantao Zhao
- , Christopher Sauvage
- & Mathilde Causse
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Article
| Open AccessA high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour
Existing apple genome assemblies all derive from Golden Delicious. Here, the authors combine different sequencing technologies to assemble a high quality genome of an anther-derived homozygous genotype HFTH1 and find the association of a retrotransposon and red fruit colour.
- Liyi Zhang
- , Jiang Hu
- & Peihua Cong
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Article
| Open AccessWater impacts nutrient dose responses genome-wide to affect crop production
Scarcity of water and nutrients limit crop yields. Here Swift et al. show that gene expression in rice responds differently to changes in the absolute amount of nitrogen available compared to nitrogen concentration and identify expression profiles associated with crop performance in arid, low-nutrient soils.
- Joseph Swift
- , Mark Adame
- & Gloria M. Coruzzi
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Article
| Open AccessA reference-grade wild soybean genome
Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al. report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci.
- Min Xie
- , Claire Yik-Lok Chung
- & Hon-Ming Lam
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Article
| Open AccessWhole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement
Brassica napus is a globally important oil crop, but the origin of the allotetraploid genome and its improvement process are largely unknown. Here, the authors take a population genetic approach to resolve its origin and evolutionary history, and identify candidate genes related to important agricultural traits.
- Kun Lu
- , Lijuan Wei
- & Jiana Li
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Article
| Open AccessCytosolic lipid droplets as engineered organelles for production and accumulation of terpenoid biomaterials in leaves
Cytosolic lipid droplets are ER-derived organelles that accumulate in seeds to fuel germination. Here, Sadre et al. show that by boosting lipid production and anchoring key terpenoid biosynthetic enzymes to the droplet surface, an efficient terpenoid production platform can be established in leaves.
- Radin Sadre
- , Peiyen Kuo
- & Bjoern Hamberger
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Article
| Open AccessSite-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems
Few approaches for targeted manipulation of the epigenome are available in plants. Here, the authors adapt the dCas9-SunTag system to engineer targeted gene activation and site-specific manipulation of DNA methylation in Arabidopsis.
- Ashot Papikian
- , Wanlu Liu
- & Steven E. Jacobsen
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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 AccessOrigin and evolution of qingke barley in Tibet
The origin of Tibetan barley (qingke) has been a controversial issue for many years. Here, the authors conduct population genomics study to support that qingke is derived from eastern domesticated barley instead of Tibetan wild barley and suggest southern Tibetan Plateau as its introduction route.
- Xingquan Zeng
- , Yu Guo
- & Nyima Tashi
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Article
| Open AccessA common genetic mechanism underlies morphological diversity in fruits and other plant organs
Remarkable organ shape morphological diversity exists in fruits, vegetables and seeds. Here, the authors establish a link between OVATE Family Proteins and TONNEAU1 Recruiting Motif family proteins in the development pathway that governs fruit shape of tomato, melon, and cucumber as well as potato tuber shape.
- Shan Wu
- , Biyao Zhang
- & Esther van der Knaap
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Article
| Open AccessOverexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth
Drought resistant plants typically have reduced growth. Here the authors show that overexpression of the BRL3 brassinosteroid receptor confers drought tolerance and accumulation of osmoprotectant metabolites without penalizing growth, demonstrating that drought response and growth can be uncoupled.
- Norma Fàbregas
- , Fidel Lozano-Elena
- & Ana I. Caño-Delgado
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Article
| Open AccessDeletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice
Plant architecture transition is one of the great consequences during rice domestication. Here, the authors find that chromosomal deletions linked to the previously known PROG1 gene also participate in plant architecture domestication in both Asian and African cultivated rice.
- Yongzhen Wu
- , Shuangshuang Zhao
- & Lubin Tan
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Article
| Open AccessA PECTIN METHYLESTERASE gene at the maize Ga1 locus confers male function in unilateral cross-incompatibility
Unilateral cross-incompatibility between certain varieties of maize prevents cross-fertilization and can facilitate hybrid breeding. Here the authors show that a PECTIN METHYLESTERASE gene is able to overcome this reproductive barrier and confer fertility when expressed in pollen of the male parent.
- Zhaogui Zhang
- , Baocai Zhang
- & Huabang Chen
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Article
| Open AccessCarboxysome encapsulation of the CO2-fixing enzyme Rubisco in tobacco chloroplasts
Previous efforts to assemble Rubisco within a cyanobacterial carboxysome-derived protein shell in plant chloroplasts to concentrate CO2 have been unsuccessful. Here, Long et al. produce carboxysomes in tobacco chloroplasts that encapsulate the introduced Rubisco and enable autotrophic growth at elevated CO2.
- Benedict M. Long
- , Wei Yih Hee
- & G. Dean Price
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Article
| Open AccessMolecular basis for the production of cyclic peptides by plant asparaginyl endopeptidases
Asparaginyl endopeptidases (AEPs) are plant proteases that can also function as ligases, catalyzing the production of cyclic plant peptides. Here, the authors identify structural features that govern AEP ligase activity, providing insights to aid the discovery and engineering of ligase-type AEPs.
- M. A. Jackson
- , E. K. Gilding
- & D. J. Craik
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Article
| Open AccessCRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation
Efficient gene targeting in higher plants remains challenging. Here, the authors develop a sequential transformation method for CRISPR/Cas9-mediated gene targeting in Arabidopsis and demonstrate its functionality at five genomic sites in two endogenous loci.
- Daisuke Miki
- , Wenxin Zhang
- & Jian-Kang Zhu
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Article
| Open AccessImproving wood properties for wood utilization through multi-omics integration in lignin biosynthesis
A systematic analysis of lignin biosynthetic genes to quantitatively understand their effect on wood properties is still lacking. Here, the authors integrate transcriptomic, proteomic, fluxomic and phenomic data to quantify the impact of perturbations of transcript abundance on lignin biosynthesis and wood properties.
- Jack P. Wang
- , Megan L. Matthews
- & Vincent L. Chiang
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Article
| Open AccessGS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality
Rice grain shape or size is an important trait associated with both yield and appearance quality. Here, the authors identify GS9 as a negative transcription regulator of slender grain and show it can improve grain shape and appearance independently from other previously identified grain size genes.
- Dong-Sheng Zhao
- , Qian-Feng Li
- & Qiao-Quan Liu
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Article
| Open AccessPhotosystem II Subunit S overexpression increases the efficiency of water use in a field-grown crop
Availability of irrigation water will be an increasing barrier to global crop yield increases. Here the authors show transgenic tobacco plants overexpressing Photosystem II Subunit S have less stomatal opening in response to light and a 25% reduction in water loss per CO2 assimilated under replicated field trials.
- Katarzyna Głowacka
- , Johannes Kromdijk
- & Stephen P. Long
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Article
| Open AccessG-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice
Cereal crops' grain yield and quality are traits that are usually considered to be negatively correlated. Here, the authors show that interaction of G-protein βγ subunits with an alternatively spliced MADS1lgy3 protein can increase rice grain yield and quality simultaneously in field conditions.
- Qian Liu
- , Ruixi Han
- & Xiangdong Fu
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Article
| Open AccessMSD1 regulates pedicellate spikelet fertility in sorghum through the jasmonic acid pathway
Inflorescence architecture affects crop grain yield. Here, the authors deploy whole-genome sequencing-based bulk segregant analysis to identify the causal gene of a sorghum multi-seeded (msd) mutant and suggest MSD1 regulating the fertility of the pedicellate spikelets through jasmonic acid pathway.
- Yinping Jiao
- , Young Koung Lee
- & Zhanguo Xin
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Article
| Open AccessGenetic variations in ARE1 mediate grain yield by modulating nitrogen utilization in rice
Understanding the regulatory mechanisms of nitrogen assimilation is crucial for developing crop cultivars with improved nitrogen utilization efficiency (NUE). Here the authors identify a new negative regulator of NUE and mutation of this gene increases 10–20% rice grain yield under nitrogen-limiting field conditions.
- Qing Wang
- , Jinqiang Nian
- & Jianru Zuo
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Article
| Open AccessA defensin-like protein drives cadmium efflux and allocation in rice
Crops that allocate heavy metals to leaves rather than grains could allow phytoremediation of polluted soil while producing food that is safe to eat. Here, the authors show that a defensin-like protein promotes cadmium secretion from rice cells and allocation to leaves without causing accumulation in grain.
- Jin-Song Luo
- , Jing Huang
- & Ji-Ming Gong