Article
|
Open Access
Featured
-
-
Article
| Open AccessAugmented CO2 tolerance by expressing a single H+-pump enables microalgal valorization of industrial flue gas
Microalgae used for CO2 removal in an industrial exhaust gas stream usually has low CO2 tolerance. Here, the authors increase CO2 tolerance by expressing a single H + -pump and enable microalgal valorization of industrial flue gas.
- Hong Il Choi
- , Sung-Won Hwang
- & Sang Jun Sim
-
Comment
| Open AccessBiotechnological development of plants for space agriculture
The logistical and practical challenges of supplying food for long-term space missions are substantial. In this comment, the authors discuss potential biotechnological approaches that could be used to aid the production of food crops in space.
- Yongming Liu
- , Gengxin Xie
- & Maozhi Ren
-
Article
| Open AccessRETRACTED ARTICLE: Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis
Unlike insects and mice, CRISPR/Cas9-based gene drives have not been achieved in plants. Here, the authors demonstrate homozygous F1 Arabidopsis plants can be obtained through zygotic conversion using CRISPR/Cas9-mediated homology-directed repair.
- Tao Zhang
- , Michael Mudgett
- & Yunde Zhao
-
Article
| Open AccessA Bacillus thuringiensis Cry protein controls soybean cyst nematode in transgenic soybean plants
Genetic resistance to soybean cyst nematode (SCN) is beginning to decline. Here, the authors report that soybean lines expressing the Bacillus thuringiensis protein Cy14Ab have significant levels of protection from SCN in both greenhouse and field trials.
- Theodore W. Kahn
- , Nicholas B. Duck
- & Julia Daum
-
Article
| Open AccessA recombined Sr26 and Sr61 disease resistance gene stack in wheat encodes unrelated NLR genes
The tall wheat grass-derived stem rust resistance genes Sr26 and Sr61 are among a few ones that are effective to all current dominant races of stem rust, including Ug99. Here, the authors show that the two genes are present in a small non-recombinogenic segment but encode two unrelated NLR proteins.
- Jianping Zhang
- , Timothy C. Hewitt
- & Evans S. Lagudah
-
Article
| Open AccessThe regulatory landscape of Arabidopsis thaliana roots at single-cell resolution
Existing studies of the chromatin accessibility, the primary mark of regulatory DNA, in Arabidopsis are based mainly on bulk samples. Here, the authors report the regulatory landscape of Arabidopsis thaliana roots at single-cell resolution.
- Michael W. Dorrity
- , Cristina M. Alexandre
- & Josh T. Cuperus
-
Article
| Open AccessEctopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase
The ability to target DNA methylation to specific loci is important for both basic and applied research. Here, the authors fuse CG-specific methyltransferase SssI with an artificial zinc finger protein for DNA methylation targeting and show the chromatin features favorable for efficient gain of methylation.
- Wanlu Liu
- , Javier Gallego-Bartolomé
- & Steven E. Jacobsen
-
Article
| Open AccessContrasting epigenetic control of transgenes and endogenous genes promotes post-transcriptional transgene silencing in Arabidopsis
Accumulating evidences point to a discrepancy in the epigenetic behaviour of transgenes and endogenous genes. Here, via characterization of mutants impaired in histone demethylases JMJ14 and IBM1, the authors show that transgenes and endogenous genes are regulated by different epigenetic mechanisms in Arabidopsis.
- Nicolas Butel
- , Agnès Yu
- & Hervé Vaucheret
-
Article
| Open AccessSubtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals
The genomic organization and origin of the avenacin biosynthetic gene cluster remain unknown. Here, the authors assemble the genome of diploid oat Avena strigosa, reveal the structure and organization of the consecutive genes, characterize the last two missing pathway steps, and investigate the origin of the pathway in cereals.
- Yan Li
- , Aymeric Leveau
- & Anne Osbourn
-
Article
| Open AccessAn Arabidopsis AT-hook motif nuclear protein mediates somatic embryogenesis and coinciding genome duplication
Plant somatic embryogenesis (SE) can be triggered by hormone application or overexpression of certain transcription factors such as BBM. Here Karami et al. show that AHL15 is required for induction of downstream BBM targets and promotes heterochromatin decondensation and endomitosis during the induction of SE.
- Omid Karami
- , Arezoo Rahimi
- & Remko Offringa
-
Article
| Open AccessO-linked N-acetylglucosamine transferase is involved in fine regulation of flowering time in winter wheat
Little is known about genes that regulate flowering time difference among winter wheat cultivars. Here, via map-based cloning, the authors show the role of an O-linked N-acetylglucosamine (O-GlcNAc) transferase TaOGT1 in regulating flowering time difference among winter wheat cultivars.
- Min Fan
- , Fang Miao
- & Liuling Yan
-
Article
| Open AccessVersatility in acyltransferase activity completes chicoric acid biosynthesis in purple coneflower
Biosynthetic pathway of chicoric acid in purple coneflower has not been fully elucidated, though the compound has been shown to have potential health benefits. Here, the authors report the involvement of both BAHD and SCPL acyltransferases in its biosynthesis and show the pathway is unique to Echinacea species.
- Rao Fu
- , Pingyu Zhang
- & Yang Zhang
-
Article
| Open AccessGenome-wide association studies provide insights into the genetic determination of fruit traits of pear
Studies of fruit quality traits in pears are lagging behind the other major fruit trees. Here, the authors conduct GWAS of fruit quality and phenological traits in a panel of 312 sand pear accessions using SNPs called from resequencing data, and reveal the involvement of a lignin formation-related protein in regulating stone cell development.
- Ming-Yue Zhang
- , Cheng Xue
- & Jun Wu
-
Article
| Open AccessTowards plant resistance to viruses using protein-only RNase P
New approaches to plant disease control are important for pathogens that are difficult to control by existing methods. Here, the authors report a potential strategy to combat plant viruses by cytosolic expressed protein-only RNase P and show its ability for in vitro cleavage of tRNA-like structures existing in many plant viruses.
- Anthony Gobert
- , Yifat Quan
- & Philippe Giegé
-
Article
| Open AccessPlasma membrane H+-ATPase overexpression increases rice yield via simultaneous enhancement of nutrient uptake and photosynthesis
Improved utilisation of nitrogen and carbon could boost agricultural productivity. Here Zhang et al. show that overexpression of a single gene, encoding the plasma membrane H+ -ATPase 1 OSA1, is able to increase both carbon fixation via photosynthesis and nitrogen assimilation via ammonium uptake in rice.
- Maoxing Zhang
- , Yin Wang
- & Yiyong Zhu
-
Article
| Open AccessChromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis
Ophiorrhiza pumila is a medicinal plant that can produce the anti-cancer monoterpene indole alkaloid (MIA) camptothecin. Here, the authors report its genome assembly and propose a working model for MIA evolution and biosynthesis through comparative genomics, synteny, and metabolic gene cluster analyses.
- Amit Rai
- , Hideki Hirakawa
- & Mami Yamazaki
-
Article
| Open AccessCondensation of Rubisco into a proto-pyrenoid in higher plant chloroplasts
Introducing the pyrenoid-based CO2-concentrating mechanism of green algae into crops could greatly improve photosynthesis. Here, the authors show that expression of the algal linker protein EPYC1 and a plant-algal hybrid Rubisco in Arabidopsis chloroplasts leads to formation of a phase separated algal-like proto-pyrenoid.
- Nicky Atkinson
- , Yuwei Mao
- & Alistair J. McCormick
-
Article
| Open AccessAn epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas
Strong transgene suppression has been observed in Chlamydomonas reinhardtii, but the underlying mechanism is unknown. Here, the authors identify a sirtuin-type histone deacetylase that selectively acts on transgenic DNA to repress gene expression by assembling a repressive chromatin structure composed of deacetylated histones.
- Juliane Neupert
- , Sean D. Gallaher
- & Ralph Bock
-
Article
| Open AccessCloning of wheat keto-acyl thiolase 2B reveals a role of jasmonic acid in grain weight determination
It has been reported that several phytohormones are involved in the regulation of grain weight, but the role of jasmonic acids (JA) remains elusive. Here, via bulked segregant analysis (BSA)-based cloning, the authors show keto-acyl thiolase 2B involved in β-oxidation during JA synthesis is a positive regulator of wheat grain weight.
- Yun Chen
- , Yan Yan
- & Jin-Ying Gou
-
Article
| Open AccessDocking of acetyl-CoA carboxylase to the plastid envelope membrane attenuates fatty acid production in plants
In plants, light-dependent activation fatty acid synthesis (FAS) is mediated in part by acetyl-CoA carboxylase (ACCase). Here the authors identify a family of genes encoding carboxyltransferase interactors that attenuate FAS in the light by docking acetyl-CoA carboxylase to the plastid envelope.
- Yajin Ye
- , Krisztina Nikovics
- & Jay J. Thelen
-
Article
| Open AccessTwo nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming
Plant pathogens secrete various effectors to manipulate host immunity. Here, Kim et al. describe two Magnaporthe oryzae effectors that translocate into the nuclei of infected rice cells and reprogram expression of immunity-associated genes, increasing susceptibility to hemibiotrophic pathogens.
- Seongbeom Kim
- , Chi-Yeol Kim
- & Yong-Hwan Lee
-
Article
| Open AccessPlant hairy roots enable high throughput identification of antimicrobials against Candidatus Liberibacter spp.
The putative causal agent of citrus greening Candidatus Liberibacter asiaticus (CLas) cannot be cultured, which hampers finding new therapies to control this devastating disease. Here, the authors show that hairy roots support CLas propagation and enable high throughput antimicrobial screening.
- Sonia Irigoyen
- , Manikandan Ramasamy
- & Kranthi K. Mandadi
-
Article
| Open AccessA cellulose synthase-derived enzyme catalyses 3-O-glucuronosylation in saponin biosynthesis
Saponins such as glycyrrhizin, a natural sweetener found in licorice root, are a class of triterpenoids synthesized that are characterized by a glucoronic acid moiety at the C-3 position. Here the authors show that saponin glucuronosylation is catalyzed by cellulose-synthase like enzymes and reconstitute glycyrrhizin synthesisin yeast.
- Soo Yeon Chung
- , Hikaru Seki
- & Toshiya Muranaka
-
Article
| Open AccessNatural variations of SLG1 confer high-temperature tolerance in indica rice
Understanding the mechanism of high-temperature tolerance will help to breed crops adaptive to warming climate. Here, the authors show SLG1, a cytosolic tRNA 2-thiolation protein 2 encoding gene, is differentiated between the two Asian cultivated rice subspecies and confers high temperature tolerance of indica rice.
- Yufang Xu
- , Li Zhang
- & Shanguo Yao
-
Article
| Open AccessGenome biology of the paleotetraploid perennial biomass crop Miscanthus
The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus.
- Therese Mitros
- , Adam M. Session
- & Daniel S. Rokhsar
-
Article
| Open AccessCarotenoids modulate kernel texture in maize by influencing amyloplast envelope integrity
Very little is known about how vitreous endosperm in the mature maize kernel is created. Here, via map-based cloning, the authors find that mutation of a β-carotene hydroxylase 3 encoding gene Ven1 affects carotenoids and lipids composition, which consequently influences amyloplast envelope integrity.
- Haihai Wang
- , Yongcai Huang
- & Yongrui Wu
-
Article
| Open AccessMSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants
The meiotic transmissibility and progeny phenotypic influence of graft-mediated epigenetic changes remain unclear. Here, the authors use the msh1 mutant in the rootstock to trigger heritable enhanced growth vigor in Arabidopsis and tomato, and show it is associated with the RNA-directed DNA methylation pathway.
- Hardik Kundariya
- , Xiaodong Yang
- & Sally A. Mackenzie
-
Article
| Open AccessChromosome-level genome assembly of a parent species of widely cultivated azaleas
Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.
- Fu-Sheng Yang
- , Shuai Nie
- & Jian-Feng Mao
-
Perspective
| Open AccessMultiplying the efficiency and impact of biofortification through metabolic engineering
Biofortification is an effective means to reduce micronutrient malnutrition. Here, the authors review recent advances in biofortification and propose stacking multiple micronutrient traits into high-yielding varieties through the combination of conventional breeding and genetic engineering approaches.
- Dominique Van Der Straeten
- , Navreet K. Bhullar
- & Howarth Bouis
-
Article
| Open AccessOrigin and adaptation to high altitude of Tibetan semi-wild wheat
Mechanism of high altitude adaptation of wheat remains unknown. Here, the authors assemble the draft genome of a Tibetan semi-wild wheat accession and resequence 245 wheat accessions to reveal that Tibetan semi-wild wheat has been de-domesticated from local landraces to adapt to high altitude.
- Weilong Guo
- , Mingming Xin
- & Qixin Sun
-
Article
| Open AccessTailoring poplar lignin without yield penalty by combining a null and haploinsufficient CINNAMOYL-CoA REDUCTASE2 allele
Plants with reduced amounts of lignin typically suffer from dwarfed growth, which offsets their gain in fermentable sugar yield. Here, the authors show that genome-edited poplar lines with a null and a haploinsufficient allele of CINNAMOYL-COA REDUCTASE2 (CCR2) can be obtained that have a reduced lignin level and normal growth.
- Barbara De Meester
- , Barbara Madariaga Calderón
- & Wout Boerjan
-
Article
| Open AccessResequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns
Hybrid rice cultivars are widely planted around the world. Here, the authors resequence 1,143 indica accessions, focusing on the parents of superior hybrid rice lines in China, and reveal genetic loci that are associated with heterosis via measuring frequency of parental variation difference (FPVD).
- Qiming Lv
- , Weiguo Li
- & Dingyang Yuan
-
Article
| Open AccessDiversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints
Genebanks hold comprehensive collections of wild species, wild relatives, and landraces that are useful for genetic improvement. Here, the authors report the genotype of nearly 80,000 wheat accessions using DArTseq technology to show the less explored genetic diversity.
- Carolina Sansaloni
- , Jorge Franco
- & Kevin Pixley
-
Article
| Open AccessFonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate
Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.
- Michael Abrouk
- , Hanin Ibrahim Ahmed
- & Simon G. Krattinger
-
Article
| Open AccessChanging local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering
The heterochromatic knob (hk4S) on Arabidopsis chromosome 4 prevents the recombination between accessions with and without hk4S. Here, via egg-cell specific expression of the Cas9 nuclease, the authors demonstrate targeted reversal of the 1.1 Mb long hk4S-inversion in Col-0 and restore the crossovers with Ler-1.
- Carla Schmidt
- , Paul Fransz
- & Holger Puchta
-
Article
| Open AccessA protein-independent fluorescent RNA aptamer reporter system for plant genetic engineering
Fluorescent RNA aptamers could potentially be used as protein-independent reporters of transgene expression in plants. Here, the authors report that an optimized RNA aptamer, developed from Broccoli, can be used to detect transgene expression in stable and transiently transformed plant tissue.
- Jiuyuan Bai
- , Yao Luo
- & Yun Zhao
-
Article
| Open AccessGenome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties
Wild teas are considered as valuable resource for studying domestication and breeding. Here, Zhang et al. report genome of wild tea DASZ and transcriptome of 217 accessions, which clarify pedigree of Chinese tea cultivars and show tea may not have undergone long-term artificial directional selection on flavor-related metabolites.
- Weiyi Zhang
- , Youjun Zhang
- & Weiwei Wen
-
Article
| Open AccessIntegrative analysis of reference epigenomes in 20 rice varieties
Comprehensive epigenomic maps of various rice varieties are still unavailable. Here, the authors report the development of eChIP as a fast and low-input upgrade of regular plant ChIP-seq protocol for epigenome analysis of 20 rice varieties and annotate over 80% of the genome with different epigenome properties for transcriptional regulation.
- Lun Zhao
- , Liang Xie
- & Xingwang Li
-
Article
| Open AccessUDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice
Increasing grain yield needs to be put in the context of environmental stress. Here, the authors reveal that a UDP-glucosyltransferase is associated with regulation of rice grain size, abiotic stress tolerance, flavonoid-mediated auxin signaling, and redirection of carbon flux to flavonoid glycosides synthesis.
- Nai-Qian Dong
- , Yuwei Sun
- & Hong-Xuan Lin
-
Article
| Open AccessAllele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa
Alfalfa is an important forage crop, but genetic improvement is challenging due to the lack of a reference genome and an efficient genome editing protocol. Here, the authors report the chromosome-level assembly of the autotetraploid genome and a CRISPR/Cas9-based transgene-free genome editing protocol.
- Haitao Chen
- , Yan Zeng
- & Qiang Qiu
-
Article
| Open AccessIntegrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth
An increase in genomic selection (GS) accuracy can accelerate genetic gain by shortening the breeding cycles. Here, the authors introduce a network-based GS method that uses metabolic models and improves the prediction accuracy of Arabidopsis growth within and across environments.
- Hao Tong
- , Anika Küken
- & Zoran Nikoloski
-
Article
| Open AccessEffect of sequence depth and length in long-read assembly of the maize inbred NC358
Sequence depth and read length determine the quality of genome assembly. Here, the authors leverage a set of PacBio reads to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as an example.
- Shujun Ou
- , Jianing Liu
- & Doreen Ware
-
Article
| Open AccessTargeted delivery of nanomaterials with chemical cargoes in plants enabled by a biorecognition motif
Targeted delivery of nanomaterials to subcellular compartments could allow precision engineering of plant function. Here, Santana et al. show that quantum dots functionalized with a rationally-designed targeting peptide are preferentially delivered to chloroplasts where they can be used to tune organellar redox status.
- Israel Santana
- , Honghong Wu
- & Juan Pablo Giraldo
-
Article
| Open AccessIdentification and characterization of N9-methyltransferase involved in converting caffeine into non-stimulatory theacrine in tea
Kucha is a rare variety of tea tree that produces the non-stimulatory theacrine instead of caffeine. Here the authors show that theacrine synthase from Kucha has N9-methyltransferase activity resulting from amino acid substitutions that explain substrate specificity and could potentially guide production of caffeine-free tea.
- Yue-Hong Zhang
- , Yi-Fang Li
- & Rong-Rong He
-
Article
| Open AccessMarker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9
Existing examples of targeted gene insertion in plants either rely on a selectable marker gene or result in short DNA inserts. Here, the authors use an optimized CRISPR-Cas9 method to insert a 5.2 kb carotenoid biosynthesis cassette into genomic safe harbors in rice, and obtain marker-free lines with high carotenoid content.
- Oliver Xiaoou Dong
- , Shu Yu
- & Pamela C. Ronald
-
Article
| Open AccessThe genome evolution and low-phosphorus adaptation in white lupin
White lupin is a legume crop that develops cluster roots for efficient phosphate acquisition. Here, the authors assemble its triplicated genome, reveal gene expression difference among sub-genomes, and characterize possible pathways related to high phosphorus-use efficiency.
- Weifeng Xu
- , Qian Zhang
- & Feng Cheng
-
Article
| Open AccessA serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 regulates maize grain yield
Selection of kernel number per ear has improved maize yield, but the genetic base is unclear. Here, the authors reveal that a serine/threonine protein kinase KNR6 is a positive regulator of the trait and show in vitro evidences that KNR6 may function through phosphorylating an Arf GTPase-activating protein.
- Haitao Jia
- , Manfei Li
- & Zuxin Zhang
-
Article
| Open AccessExceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff
Teff is an indigenous cereal critical to food security in the Horn of Africa. Here, the authors report an improved genome assembly and observe the surprisingly low levels of large-scale structural rearrangement, homoeologous exchanges, or bias gene loss after the formation of this tetraploid species.
- Robert VanBuren
- , Ching Man Wai
- & Todd P. Michael
-
Article
| Open AccessNeo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice
A transposon insertion in the regulatory region of maize Tb1 gene leads to increased apical dominance and a reduction of tillering. Here, the authors showed that a duplicated rice Tb1 orthologue, OsTb2, has gained a regulatory effect on tillering opposite that of OsTb1 during artificial selection only in upland japonica rice.
- Jun Lyu
- , Liyu Huang
- & Fengyi Hu