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| Open AccessDeep learning the cis-regulatory code for gene expression in selected model plants
This study explores the variation in gene regulation across plant species and genotypes using interpretable deep learning on DNA sequence and RNA-seq data, demonstrating the models’ utility in functional genomics and phenotypic trait prediction.
- Fritz Forbang Peleke
- , Simon Maria Zumkeller
- & Jędrzej Szymański
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Matters Arising
| Open AccessThe wheat stripe rust resistance gene YrNAM is Yr10
- Katherine Dibley
- , Matthias Jost
- & Peng Zhang
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Article
| Open AccessA pair of atypical NLR-encoding genes confers Asian soybean rust resistance in soybean
Asian soybean rust (ASR) is a devastating disease of soybean. Here, the author report the identification of an atypical pair of nucleotide-binding leucine-rich repeat (NLR) encoding genes and how they function together to confer broad-spectrum resistance to ASR.
- Qingnan Hao
- , Hongli Yang
- & Xinan Zhou
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Article
| Open AccessAn ARF gene mutation creates flint kernel architecture in dent maize
The mutation of ARFTF17 results in the development of flint kernel architecture in dent maize by reducing excessive pericarp length. This discovery holds significant potential for enhancing grain quality in elite, high-yielding dent maize hybrids.
- Haihai Wang
- , Yongcai Huang
- & Yongrui Wu
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Article
| Open AccessWheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein
Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. Here, the authors report the cloning of powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima encoding a mixed lineage kinase domain-like (MLKL) protein.
- Huanhuan Li
- , Wenqiang Men
- & Wenxuan Liu
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Article
| Open AccessDynamics of extrachromosomal circular DNA in rice
Comparing to other biological systems, our understanding of plant extrachromosomal circular DNA (eccDNA) is limited. Here, the authors profile eccDNA from six rice tissues and investigate eccDNA characteristics, formation mechanisms, distribution, and functional implications.
- Jundong Zhuang
- , Yaoxin Zhang
- & Tingting Lu
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Article
| Open AccessRecurrent evolutionary switches of mitochondrial cytochrome c maturation systems in Archaeplastida
Cytochrome c maturation (CCM) is the process of covalent attachment of a heme group to the conserved cysteines to form the holocytochrome. Here, the authors report that the non-adaptive convergent evolution at the pathway level leads to mosaic distribution of CCM systems I and III among Archaeplastida species.
- Huang Li
- , Soujanya Akella
- & Jeffrey P. Mower
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Article
| Open AccessDysfunction of duplicated pair rice histone acetyltransferases causes segregation distortion and an interspecific reproductive barrier
Loss of function alleles of two genetically interacting loci mediate both segregation distortion and interspecific hybrid incompatible via epigenetic regulation in rice.
- Ben Liao
- , You-Huang Xiang
- & Hong-Xuan Lin
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Article
| Open AccessA chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm
Coffea arabica is an allotetraploid hybrid of C. eugenioides and C. canephora and contributes to approximately 60% of world coffee production. Here, the authors report its chromosome-level genome assembly and identify that chromosomal abnormalities and introgression from C. canephora may contribute to diversity and pathogen resistance.
- Simone Scalabrin
- , Gabriele Magris
- & Michele Morgante
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Article
| Open AccessWheat Pm55 alleles exhibit distinct interactions with an inhibitor to cause different powdery mildew resistance
Powdery mildew threatens worldwide wheat production. Here, the authors report the cloning of two powdery mildew resistant Pm55 alleles and show that they exhibit distinct interactions with the inhibitor SuPm55 to cause different resistance.
- Chuntian Lu
- , Jie Du
- & Ruiqi Zhang
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Article
| Open AccessSoybean 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 AccessLoss-of-function of an α-SNAP gene confers resistance to soybean cyst nematode
Here, the authors show that the soybean GmSNAP02 gene confers a unique mode of resistance to the soybean cyst nematode Heterodera glycines through loss-of-function mutations that implicate GmSNAP02 as a nematode virulence target.
- Mariola Usovsky
- , Vinavi A. Gamage
- & Andrew M. Scaboo
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Article
| Open AccessLHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat
The regulation of genetic diversity resulting from polyploidization and its impact on environmental adaptability remain unclear. Here, the authors show that LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat.
- Zijuan Li
- , Yuyun Zhang
- & Yijing Zhang
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Article
| Open AccessTranscriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks
Panicle architecture significantly determines rice grain yield. Here, the authors investigate the transcriptome of young panicles from 275 rice varieties and propose a method to identify causal genes for panicle traits and construct regulatory networks.
- Luchang Ming
- , Debao Fu
- & Weibo Xie
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Article
| Open AccessA toxin-antidote system contributes to interspecific reproductive isolation in rice
Orzya meridionalis is a wild rice species that has reproductive isolation with Asian cultivated rice. Here, the authors report the cloning of the second locus controlling hybrid male sterility between the two species and show the encoded toxin-antidote system provides stacked reproductive isolation for maintaining species identity.
- Shimin You
- , Zhigang Zhao
- & Jianmin Wan
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Article
| Open AccessPan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits
A pan-genome can reduce bias in genetic diversity analysis inherent in using a single reference genome. Here, the authors assemble genomes of 10 diverse apple accessions, conduct pan-genome analysis together with three existing genomes, and reveal the role of mitogen-activated protein kinase homolog MMK2 in fruit coloration.
- Ting Wang
- , Shiyao Duan
- & Ting Wu
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Article
| Open AccessEvolution of a ZW sex chromosome system in willows
Investigation of heterogametic transitions in sex chromosomes is challenging but fascinating from an evolutionary perspective. Here, Hu et al. have identified a transition from an XY to a ZW system in the genus Salix (willows) where both the Z and W chromosomes have originated from the ancestral Y.
- Nan Hu
- , Brian J. Sanderson
- & Matthew S. Olson
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Article
| Open AccessMSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism
Interhomolog polymorphism, which is detected by MSH2-containing heterodimers, may affect crossover outcomes during meiosis. Here, the authors revealed antagonistic effects of MSH2 on interfering and non-interfering crossover pathways in Arabidopsis.
- Julia Dluzewska
- , Wojciech Dziegielewski
- & Piotr A. Ziolkowski
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Article
| Open AccessRobotized indoor phenotyping allows genomic prediction of adaptive traits in the field
Robotized indoor phenotyping allows measuring of plant physiological traits at high throughput, but is often considered as non-relevant for field conditions. Here, the authors show that maize traits measured indoor translate to the field and can be inferred via genomic prediction.
- Jugurta Bouidghaghen
- , Laurence Moreau
- & François Tardieu
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Article
| Open AccessPaternal DNA methylation is remodeled to maternal levels in rice zygote
Liu et al. show that zygotic remodelling of paternal DNA methylation is matched to maternal levels in hybrids and that parental-specific epigenomes are re-established during embryogenesis, highlighting genetic control of epigenetic inheritance.
- Qian Liu
- , Xuan Ma
- & Dao-Xiu Zhou
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Article
| Open AccessA global-temporal analysis on Phytophthora sojae resistance-gene efficacy
Rps genes are used to manage the major soybean pathogen Phytophthora sojae, which causes Phytophthora stem and root rot (PRR). Here, the authors show that widely used Rps genes are no longer effective for managing PRR in the United States, Canada and Argentina.
- Austin G. McCoy
- , Richard R. Belanger
- & Martin I. Chilvers
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Article
| Open AccessExtrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants
Epigenetic control of extrachromosomal circular DNA (eccDNA) compartment and the relationships between eccDNA and plant genome stability remain unclear. Here, the authors investigate eccDNA and structural variations in Arabidopsis epigenetic mutants to reveal the eccDNA repertoire and its impact on genome stability.
- Panpan Zhang
- , Assane Mbodj
- & Marie Mirouze
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Article
| Open AccessSCFRMF mediates degradation of the meiosis-specific recombinase DMC1
In eukaryotes the recombinase DMC1 is required for meiotic recombination, but it remains unclear how DMC1 stability is regulated. Here the authors identify a SCF complex which mediates ubiquitination and proteasomal degradation of DMC1.
- Wanyue Xu
- , Yue Yu
- & Yingxiang Wang
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Article
| Open AccessTwo complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice
The mechanisms of the partial reproductive isolation between the two subspecies of rice remains obscure. Here, the authors show that the two adjacent genes form a killer-protector system to induce hybrid male sterility and reproductive isolation between indica and japonica.
- Daiqi Wang
- , Hongru Wang
- & Ziqiang Liu
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Article
| Open AccessThe allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits
Horseradish is a spicy root vegetable and it also produces horseradish peroxidase, an enzyme widely used in biochemistry applications. Here, the authors report its telomere-to-telomere reference genome, reveal subgenome diversification and the effect on the biosynthesis of glucosinolates and horseradish peroxidases.
- Fei Shen
- , Shixiao Xu
- & Martin A. Lysak
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Article
| Open AccessComparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae
Asteraceae is the largest family of flowering plants. Here, the authors assemble the genomes of stem lettuce (within Asteraceae) and beach cabbage (within Goodeniaceae) for evolutionary genomics analyses and reveal the absence of the core regulatory gene of nitrogen and carbon assimilation in Asteraceae.
- Fei Shen
- , Yajuan Qin
- & Xiaozeng Yang
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Article
| Open AccessSequencing trait-associated mutations to clone wheat rust-resistance gene YrNAM
Wheat stripe (yellow) rust is a devastating disease posing a threat to global production. Here, the authors report the cloning of a wheat stripe rust resistance gene encoding a protein with a NAM domain and a ZnF-BED domain using a strategy called sequencing trait-associated mutations (STAM).
- Fei Ni
- , Yanyan Zheng
- & Jiajie Wu
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Article
| Open AccessManipulating microRNA miR408 enhances both biomass yield and saccharification efficiency in poplar
Modifying plant lignin pathway to enhance saccharification efficiency is often associated with growth penalty. Here, the authors show that overexpression of Pag-miR408 in poplar leads to enhanced saccharification efficiency and growth in both laboratory and field conditions, and laccase genes are the targets of Pag-miR408.
- Yayu Guo
- , Shufang Wang
- & Jinxing Lin
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Article
| Open AccessThe MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation
It has generally been considered that MOM1, a transcriptional silencing factor in plants, mediated silencing is independent or downstream of DNA methylation. Here, the authors show that MOM1 complex recruits the RdDM machinery through MORC6 to establish de novo DNA methylation in Arabidopsis.
- Zheng Li
- , Ming Wang
- & Steven E. Jacobsen
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Article
| Open AccessJoint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids
Genetic dissection of hybrids is more difficult than inbreds as nonadditive effects are involved. Here, the authors report a pipeline for joint analysis of phenotypes, effects, and generations and demonstrate its usefulness in identification of loci associated with quality traits and improving predict accuracy in genomic selection of hybrid rice.
- Lanzhi Li
- , Xingfei Zheng
- & Zhongli Hu
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Article
| Open AccessMG1 interacts with a protease inhibitor and confers resistance to rice root-knot nematode
Rice root-knot nematode is a major threat to rice production. Here, the authors identify an R gene MG1 in rice that confers resistance against nematodes and encodes a protein that interacts with a protease inhibitor.
- Xiaomin Wang
- , Rui Cheng
- & Xiaoli Guo
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Article
| Open AccessSingle-gene resolution of diversity-driven overyielding in plant genotype mixtures
Biodiversity often increases the functioning and productivity of ecosystems or communities. This work shows that such a positive diversity effect, namely overyielding in mixtures of two divergent Arabidopsis thaliana genotypes, can be genetically mapped and resolved to a single gene.
- Samuel E. Wuest
- , Lukas Schulz
- & Pascal A. Niklaus
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Article
| Open AccessLong-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana
Transposons can be co-transcribed with genes in plant genomes. Here, the authors show the global production of chimeric transposon-gene transcripts and their epigenetic regulation in Arabidopsis thaliana.
- Jérémy Berthelier
- , Leonardo Furci
- & Hidetoshi Saze
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Article
| Open AccessAn E2-E3 pair contributes to seed size control in grain crops
Researchers identify an E3 ligase SGD1 and its E2 partner responsible for grain yield control using foxtail millet, and reveal its conserved role in wheat, maize, and rice. Furthermore, SGD1 ubiquitinates the brassinosteroid receptor BRI1 thus stabilizing it and promoting grain yield in crops.
- Sha Tang
- , Zhiying Zhao
- & Xianmin Diao
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Article
| Open AccessThe 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 AccessOptimization 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 AccessPan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
Pan-genomes provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Here, the authors report a new rice pan-genome including 73 Asian rice and two wild relatives (Oryza rufipogon and O. punctata), and reveal the prevalence and scale of large inversions across the pan-genome.
- Yong Zhou
- , Zhichao Yu
- & Rod A. Wing
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Article
| Open AccessHistone H2A monoubiquitination marks are targeted to specific sites by cohesin subunits in Arabidopsis
How histone H2A monoubiquitination (H2Aub1) is established at specific genomic locations remains unclear. Here, the authors report that Arabidopsis cohesin subunits SCC3 and SYN4 are involved in H2Aub1 through their direct or indirect interaction with BMI1A/B/C subunits of PRC1, the E3 ligases in PRC1 for H2Aub1.
- Yu Zhang
- , Min Ma
- & Yuda Fang
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Article
| Open AccessClimate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles
The interplay of migration and adaptation was key in shaping species’ responses to Quaternary climate change. Illustrating this, Luqman et al. show that adaptive responses in a plant species emerged from climate-induced range shifts due to heterogenous sieving of adaptive alleles across space and time.
- Hirzi Luqman
- , Daniel Wegmann
- & Alex Widmer
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Article
| Open AccessTandemly duplicated CYP82Ds catalyze 14-hydroxylation in triptolide biosynthesis and precursor production in Saccharomyces cerevisiae
Hydroxylation at the C-14 position of triptolide is critical for its potent antitumor activity. Here, the authors report two CYP82Ds catalyze the 14-hydroxylation reaction via metabolic grid and achieve heterologous bioproduction of triptolide precursor in engineered Saccharomyces cerevisiae.
- Yifeng Zhang
- , Jie Gao
- & Luqi Huang
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Article
| Open AccessDosage 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 AccessThe effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids
The effect of sequence polymorphisms on recombination is not fully understood. Here, the authors develop the seed-typing method to map crossovers (COs) by sequencing and show that COs occur preferentially within polymorphic hotspots and that this effect depends on the mismatch repair gene MSH2 in Arabidopsis.
- Maja Szymanska-Lejman
- , Wojciech Dziegielewski
- & Piotr A. Ziolkowski
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Article
| Open AccessHistone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis
Histone chaperones and chromatin remodelers control nucleosome dynamics. Here the authors show that the Arabidopsis ASF1 chaperone primarily supplies histone variants to the HIRA complex to ensure proper epigenetic gene regulation.
- Zhenhui Zhong
- , Yafei Wang
- & Steven E. Jacobsen
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Article
| Open AccessChromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops
Genome evolution of Allium genus and genomic basis underlying the pungency flavor formation remain poorly understood. Here, the authors assemble the genome of bunching onion and conduct population genetics analyses to reveal Allium genome evolution, flavor formation and domestication history.
- Nanqiao Liao
- , Zhongyuan Hu
- & Jing-Quan Yu
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Article
| Open AccessN6-methyladenosine RNA modification promotes viral genomic RNA stability and infection
Wheat production is threatened by wheat yellow mosaic virus (WYMV). Here, via genome-wide association study, the authors report that a putative methyltransferase B positively regulates WYMV infection through enhancing viral genomic RNA stability by N6-methyladenosine RNA modification.
- Tianye Zhang
- , Chaonan Shi
- & Jian Yang
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Article
| Open AccessConserved signalling components coordinate epidermal patterning and cuticle deposition in barley
The leaf epidermis is sealed by a lipid-rich cuticle to prevent water loss and interspersed with stomatal pores to allow gas exchange. Here the authors provide evidence that two barley proteins, HvYDA1 and HvBRX-Solo, regulate both processes linking epidermal patterning with cuticular properties in a cereal crop.
- Linsan Liu
- , Sarah B. Jose
- & Sarah M. McKim
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Article
| Open AccessJoint control of meiotic crossover patterning by the synaptonemal complex and HEI10 dosage
During meiosis, the number and distribution of crossovers (COs) are tightly controlled, but the mechanistic basis of this control is unclear. Here, by combining experimental data and mathematical modeling, the study advocates a CO patterning model via coarsening through the diffusion of HEI10 along the synaptonemal complex.
- Stéphanie Durand
- , Qichao Lian
- & Raphael Mercier
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Article
| Open AccessGenome-wide association study identifies a gene responsible for temperature-dependent rice germination
Physiology of seed germination has been optimized for various climatic conditions. Here, the authors report a 14-3-3 protein encoding gene GF14h is responsible for temperature-dependent rice germination by regulating ABA-responsive genes and contributes to the geographical adaptation of rice.
- Hideki Yoshida
- , Ko Hirano
- & Makoto Matsuoka
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Article
| Open AccessRegain flood adaptation in rice through a 14-3-3 protein OsGF14h
Waterlogging tolerance is important in direct seeding rice cultivation practice. Here, the authors identify a 14-3-3 protein-coding gene OsGF14h in weedy rice that confers anaerobic germination and anaerobic seedling development tolerance by balancing ABA signaling and GA biosynthesis.
- Jian Sun
- , Guangchen Zhang
- & Wenfu Chen