ORCID Profile
0000-0003-3181-9812
Current Organisations
Shanghai Jiao Tong University
,
University of Adelaide
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Publisher: Springer Science and Business Media LLC
Date: 28-06-2021
Publisher: Wiley
Date: 06-10-2020
DOI: 10.1111/NPH.16161
Abstract: In flowering plants, pollen wall is a specialized extracellular cell-wall matrix surrounding male gametophytes and acts as a natural protector of pollen grains against various environmental and biological stresses. The formation of pollen wall is a complex but well-regulated process, which involves the action of many different genes. However, the genetic and molecular mechanisms underlying this process remain largely unknown. In this study, we isolated and characterized a novel rice male sterile mutant, defective pollen wall3 (dpw3), which displays smaller and paler anthers with aborted pollen grains. DPW3 encodes a novel membrane-associated alpha integrin-like protein conserved in land plants. DPW3 is ubiquitously expressed in anther developmental stages and its protein is localized to the plasma membrane, endoplasmic reticulum (ER) and Golgi. Anthers of dpw3 plants exhibited unbalanced anther cuticular profile, abnormal Ubisch bodies, disrupted callose deposition, defective pollen wall formation such as abnormal microspore plasma membrane undulation and defective primexine formation, resulting in pollen abortion and complete male sterility. Our findings revealed a novel and vital role of alpha integrin-like proteins in plant male reproduction.
Publisher: Wiley
Date: 02-2022
DOI: 10.1111/PBI.13776
Abstract: Molecular characterization of genetically modified organisms (GMOs) yields basic information on exogenous DNA integration, including integration sites, entire inserted sequences and structures, flanking sequences and copy number, providing key data for biosafety assessment. However, there are few effective methods for deciphering transgene integration, especially for large DNA fragment integration with complex rearrangement, inversion and tandem repeats. Herein, we developed a universal L arge I ntegrated DNA F ragments E nrichment strategy combined with PacBio Seq uencing (LIFE‐Seq) for deciphering transgene integration in GMOs. Universal tilling DNA probes targeting transgenic elements and exogenous genes facilitate specific enrichment of large inserted DNA fragments associated with transgenes from plant genomes, followed by PacBio sequencing. LIFE‐Seq were evaluated using six GM events and four crop species. Target DNA fragments averaging ~6275 bp were enriched and sequenced, generating ~26 352 high fidelity reads for each s le. Transgene integration structures were determined with high repeatability and sensitivity. Compared with next‐generation whole‐genome sequencing, LIFE‐Seq achieved better data integrity and accuracy, greater universality and lower cost, especially for transgenic crops with complex inserted DNA structures. LIFE‐Seq could be applied in molecular characterization of transgenic crops and animals, and complex DNA structure analysis in genetics research.
Publisher: Springer Science and Business Media LLC
Date: 08-06-2020
Publisher: Oxford University Press (OUP)
Date: 19-07-2016
DOI: 10.1105/TPC.16.00108
Publisher: Springer Science and Business Media LLC
Date: 09-10-2022
DOI: 10.1007/S00299-022-02920-8
Abstract: Genome resequencing uncovers genome-wide DNA polymorphisms that are useful for the development of high-density InDel markers between two barley cultivars. Discovering genomic variations and developing genetic markers are crucial for genetics studies and molecular breeding in cereal crops. Although InDels (insertions and deletions) have become popular because of their abundance and ease of detection, discovery of genome-wide DNA polymorphisms and development of InDel markers in barley have lagged behind other cereal crops such as rice, maize and wheat. In this study, we re-sequenced two barley cultivars, Golden Promise (GP, a classic British spring barley variety) and Hua30 (a Chinese spring barley variety), and mapped clean reads to the reference Morex genome, and identified in total 13,933,145 single nucleotide polymorphisms (SNPs) and 1,240,456 InDels for GP with Morex, 11,297,100 SNPs and 781,687 InDels for Hua30 with Morex, and 13,742,399 SNPs and 1,191,597 InDels for GP with Hua30. We further characterized distinct types, chromosomal distribution patterns, genome location, functional effect, and other features of these DNA polymorphisms. Additionally, we revealed the functional relevance of these identified SNPs/InDels regarding different flowering times between Hua30 and GP within 17 flowering time genes. Furthermore, we developed a series of InDel markers and validated them experimentally in 43 barley core accessions, respectively. Finally, we rebuilt population structure and phylogenetic tree of these 43 barley core accessions. Collectively, all of these genetic resources will facilitate not only the basic research but also applied research in barley.
Publisher: Springer Science and Business Media LLC
Date: 13-04-2020
Publisher: Oxford University Press (OUP)
Date: 03-01-2017
DOI: 10.1104/PP.16.01726
Publisher: Wiley
Date: 07-10-2021
DOI: 10.1111/TPJ.15496
Abstract: Jasmonates (JAs) are key phytohormones that regulate plant responses and development. JASMONATE‐ZIM DOMAIN (JAZ) proteins safeguard JA signaling by repressing JA‐responsive gene expression in the absence of JA. However, the interaction and cooperative roles of JAZ repressors remain unclear during plant development. Here, we found that OsJAZ6 interacts with OsJAZ1 depending on a single amino acid in the so‐called ZIM domain of OsJAZ6 in rice JA signaling transduction and JA‐regulated rice spikelet development. In vivo protein distribution analysis revealed that the OsJAZ6 content is efficiently regulated during spikelet development, and biochemical and genetic evidence showed that OsJAZ6 is more sensitive to JA‐mediated degradation than OsJAZ1. Through over‐ and mis‐expression experiments, we further showed that the protein stability and levels of OsJAZ6 orchestrate the output of JA signaling during rice spikelet development. A possible mechanism, which outlines how OsJAZ repressors interact and function synergistically in specifying JA signaling output through degradation titration, is also discussed.
Publisher: Oxford University Press (OUP)
Date: 22-10-2020
DOI: 10.1105/TPC.20.00551
Publisher: Springer Science and Business Media LLC
Date: 26-07-2021
DOI: 10.1007/S00122-021-03911-1
Abstract: Several QTLs and genes responsible for seed dormancy were detected and SNP candidates were shown to cause changes in seed germination. Seed dormancy is a key agricultural trait to prevent pre-harvest sprouting in crop plants such as rice (Oryza sativa L.), wheat (Triticum aestivum), and barley (Hordeum vulgare L.). However, our knowledge of seed dormancy is h ered by the complexities of studying a trait that changes over time after seed harvest, and is complicated by interactions between phytohormones, seed coat components and the environment. Here, we have conducted a genome-wide association study using a panel of 311 natural accessions of cultivated rice, examining a total of 519,158 single nucleotide polymorphisms (SNPs). Eight quantitative trait loci (QTLs) were found to associate with seed dormancy in the whole panel and five in the Japonica and Indica subpanel expression of candidate genes within 100 kb of each QTL was examined in two published, germination-specific transcriptomic datasets. Ten candidate genes, differentially expressed within the first four days post-imbibition, were identified. Five of these genes had previously been associated with awn length, heading date, yield, and spikelet length phenotypes. Two candidates were validated using Quantitative Reverse Transcription (qRT)-PCR. In addition, previously identified genes involved in hormone signaling during germination were found to be differentially expressed between a japonica and an indica line SNPs in the promoter of Os9BGlu33 were associated with germination index, with qRT-PCR validation. Collectively, our results are useful for future characterization of seed dormancy mechanism and crop improvement, and suggest haplotypes for further analysis that may be of use to boost PHS resistance in rice.
Publisher: Wiley
Date: 30-11-2022
DOI: 10.1111/NPH.17849
Abstract: Organ size is determined mainly by cell ision and cell expansion. Several genetic factors regulating development of plant lateral organs have been characterized, but those involved in determining reproductive organ size and separation in rice (Oryza sativa) remain unknown. We have isolated the rice gene SMALL REPRODUCTIVE ORGANS (SRO) encoding a nucleus-localized Cys2His2 (C
Publisher: Oxford University Press (OUP)
Date: 23-12-2015
DOI: 10.1104/PP.15.01561
Publisher: Wiley
Date: 12-2022
DOI: 10.1111/NPH.18551
Abstract: In cereal plants, the size of the panicle (inflorescence) is a critical factor for yield. Panicle size is determined by a complex interplay of genetic and environmental factors, but the mechanisms underlying adaptations to temperature stress during panicle development remain largely unknown. We identify the rice THERMOSENSITIVE BARREN PANICLE (TAP) gene, which encodes a transposase-derived FAR1-RELATED SEQUENCE (FRS) protein and is responsible for regulating panicle and spikelet development at high ambient temperature. The tap mutants display high temperature-dependent reproductive abnormalities, including compromised secondary branch and spikelet initiation and pleiotropic floral organ defects. Consistent with its thermosensitive phenotype, TAP expression is induced by high temperature. TAP directly promotes the expression of OsYABBY3 (OsYAB3), OsYAB4, and OsYAB5, which encode key transcriptional regulators in panicle and spikelet development. In addition, TAP physically interacts with OsYAB4 and OsYAB5 proteins phenotypic analysis of osyab4 tap-1 and osyab5 tap-1 double mutants indicates that TAP-OsYAB4/OsYAB5 complexes act to maintain normal panicle and spikelet development. Taken together, our study reveals the novel role of a TE-derived transcription factor in controlling rice panicle development under high ambient temperatures, shedding light on the molecular mechanism underlying the adaptation of cereal crops to increasing environmental temperatures.
Publisher: Oxford University Press (OUP)
Date: 07-12-2017
DOI: 10.1104/PP.17.00704
Publisher: Oxford University Press (OUP)
Date: 21-09-2023
Publisher: Oxford University Press (OUP)
Date: 05-2018
DOI: 10.1104/PP.18.00017
Publisher: Oxford University Press (OUP)
Date: 26-03-2018
DOI: 10.1104/PP.17.01759
Publisher: The Company of Biologists
Date: 2019
DOI: 10.1242/DEV.173419
Abstract: Jasmonates (JAs) are crucial to the coordination of plant stress responses and development. JA signaling depends on JASMONATE-ZIM DOMAIN (JAZ) proteins that are destroyed by the SCF
Publisher: Oxford University Press (OUP)
Date: 02-05-2018
DOI: 10.1104/PP.18.00110
Abstract: Aminoacyl-tRNA synthetases (aaRSs) have housekeeping roles in protein synthesis, but little is known about how these aaRSs are involved in organ development. Here, we report that a rice (Oryza sativa) glutamyl-tRNA synthetase (OsERS1) maintains proper somatic cell organization and limits the overproliferation of male germ cells during early anther development. The expression of OsERS1 is specifically detectable in meristematic layer 2-derived cells of the early anther, and osers1 anthers exhibit overproliferation and disorganization of layer 2-derived cells, producing fused lobes and extra germ cells in early anthers. The conserved biochemical function of OsERS1 in ligating glutamate to tRNAGlu is enhanced by its cofactor aaRS OsARC. Furthermore, metabolomics profiling revealed that OsERS1 is an important node for multiple metabolic pathways, indicated by the accumulation of amino acids and tricarboxylic acid cycle components in osers1 anthers. Notably, the anther defects of the osers1 mutant are causally associated with the abnormal accumulation of hydrogen peroxide, which can reconstitute the osers1 phenotype when applied to wild-type anthers. Collectively, these findings demonstrate how aaRSs affect male organ development in plants, likely through protein synthesis, metabolic homeostasis, and redox status.
Publisher: Springer Science and Business Media LLC
Date: 06-09-2021
DOI: 10.1186/S12284-021-00520-W
Abstract: Panicle architecture is one of the major factors influencing productivity of rice crops. The regulatory mechanisms underlying this complex trait are still unclear and genetic resources for rice breeders to improve panicle architecture are limited. Here, we have performed a genome-wide association study (GWAS) to analyze and identify genetic determinants underlying three panicle architecture traits. A population of 340 rice accessions from the 3000 Rice Genomes Project was phenotyped for panicle length, primary panicle number and secondary branch number over two years GWAS was performed across the whole panel, and also across the japonica and indica sub-panels. A total of 153 quantitative trait loci (QTLs) were detected, of which 5 were associated with multiple traits, 8 were unique to either indica or japonica sub-panels, while 37 QTLs were stable across both years. Using haplotype and expression analysis, we reveal that genetic variations in the OsSPL18 promoter significantly affect gene expression and correlate with panicle length phenotypes. Three new candidate genes with putative roles in determining panicle length were also identified. Haplotype analysis of OsGRRP and LOC_Os03g03480 revealed high association with panicle length variation. Gene expression of DSM2 , involved in abscisic acid biosynthesis, was up-regulated in long panicle accessions. Our results provide valuable information and resources for further unravelling the genetic basis determining rice panicle architecture. Identified candidate genes and molecular markers can be used in marker-assisted selection to improve rice panicle architecture through molecular breeding.
Publisher: Oxford University Press (OUP)
Date: 20-05-2016
DOI: 10.1104/PP.16.00016
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.TPLANTS.2022.01.009
Abstract: Gene editing using clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) has revolutionized biotechnology and provides genetic tools for medicine and life sciences. However, the application of this technology to miRNAs, with the function as negative gene regulators, has not been extensively reviewed in plants. Here, we summarize the evolution, biogenesis, and structure of miRNAs, as well as their interactions with mRNAs and computational models for predicting target genes. In addition, we review current advances in CRISPR/Cas for functional analysis and for modulating miRNA genes in plants. Extending our knowledge of miRNAs and their manipulation with CRISPR will provide fundamental understanding of the functions of plant miRNAs and facilitate more sustainable and publicly acceptable genetic engineering of crops.
Publisher: Wiley
Date: 05-11-2021
DOI: 10.1111/PBI.13718
Publisher: Wiley
Date: 17-06-2021
DOI: 10.1111/NPH.17512
Abstract: Photoperiod‐dependent male fertility is a critical enabler of modern hybrid breeding. A MYB transcription factor, CSA , is a key regulator of sugar partitioning in rice anthers, disruption of which causes photoperiod‐sensitive male sterility. However, little is known about the molecular mechanisms governing plant fertility in response to photoperiod. Here, we have obtained another rice photoperiod‐sensitive male sterile mutant, csa2 , which exhibits semi‐sterility under long‐day (LD) conditions, with normal fertility under short‐day (SD) conditions. CSA2 specifically expressed in anthers, and here is shown to be indispensable for sugar partitioning to anthers under LD conditions. The CSA2 protein can restore the fertility of csa mutants under SD conditions when expressed in a CSA‐specific pattern, indicating that the two proteins share common downstream regulatory targets. Transcriptomic analyses also reveal discrete regulatory targets in anthers. Furthermore, the regulatory role of CSA2 in sugar transport was influenced by the photoperiod conditions during floral initiation, not simply during anther development. Collectively, we propose that rice evolved at least two MYB proteins, CSA2 and CSA, that regulate sugar transport in anthers under LD and SD conditions, respectively. This finding provides insight into the molecular mechanisms that regulate male fertility in response to photoperiod.
Publisher: Oxford University Press (OUP)
Date: 19-07-2016
DOI: 10.1104/PP.16.00625
Publisher: Wiley
Date: 24-02-2022
DOI: 10.1111/NPH.18008
Abstract: Rice inflorescence development determines yield and relies on the activity of axillary meristems (AMs) however, high-resolution analysis of its early development is lacking. Here, we have used high-throughput single-cell RNA sequencing to profile 37 571 rice inflorescence cells and constructed a genome-scale gene expression resource covering the inflorescence-to-floret transition during early reproductive development. The differentiation trajectories of florets and AMs were reconstructed, and discrete cell types and groups of regulators in the highly heterogeneous young inflorescence were identified and then validated by in situ hybridization and with fluorescent marker lines. Our data demonstrate that a WOX transcription factor, DWARF TILLER1, regulates flower meristem activity, and provide evidence for the role of auxin in rice inflorescence branching by exploring the expression and biological role of the auxin importer OsAUX1. Our comprehensive transcriptomic atlas of early rice inflorescence development, supported by genetic evidence, provides single-cell-level insights into AM differentiation and floret development.
Publisher: Wiley
Date: 30-11-2021
DOI: 10.1111/NPH.17855
Abstract: The spatiotemporal control of meristem identity is critical for determining inflorescence architecture, and thus yield, of cereal plants. However, the precise mechanisms underlying inflorescence and spikelet meristem determinacy in cereals are still largely unclear. We have generated loss‐of‐function and overexpression mutants of the paralogous OsMADS5 and OsMADS34 genes in rice ( Oryza sativa ), and analysed their panicle phenotypes. Using chromatin immunoprecipitation, electrophoretic mobility‐shift and dual‐luciferase assays, we have also identified RICE CENTRORADIALIS 4 ( RCN4 ), a TFL1 ‐like gene, as a direct downstream target of both OsMADS proteins, and have analysed RCN4 mutants. The osmads5 osmads34 mutant lines had significantly enhanced panicle branching with increased secondary, and even tertiary and quaternary, branches, compared to wild‐type (WT) and osmads34 plants. The osmads34 mutant phenotype could largely be rescued by also knocking out RCN4 . Moreover, transgenic panicles overexpressing RCN4 had significantly increased branching, and initiated development of c . 7× more spikelets than WT. Our results reveal a role for OsMADS5 in panicle development, and show that OsMADS5 and OsMADS34 play similar functions in limiting branching and promoting the transition to spikelet meristem identity, in part by repressing RCN4 expression. These findings provide new insights to better understand the molecular regulation of rice inflorescence architecture.
Publisher: Oxford University Press (OUP)
Date: 15-11-2023
Abstract: Research into crop yield and resilience has underpinned global food security, evident in yields tripling in the past 5 decades. The challenges that global agriculture now faces are not just to feed 10+ billion people within a generation, but to do so under a harsher, more variable, and less predictable climate, and in many cases with less water, more expensive inputs, and declining soil quality. The challenges of climate change are not simply to breed for a “hotter drier climate,” but to enable resilience to floods and droughts and frosts and heat waves, possibly even within a single growing season. How well we prepare for the coming decades of climate variability will depend on our ability to modify current practices, innovate with novel breeding methods, and communicate and work with farming communities to ensure viability and profitability. Here we define how future climates will impact farming systems and growing seasons, thereby identifying the traits and practices needed and including exemplars being implemented and developed. Critically, this review will also consider societal perspectives and public engagement about emerging technologies for climate resilience, with participatory approaches presented as the best approach.
Publisher: Springer Science and Business Media LLC
Date: 18-06-2019
Publisher: Oxford University Press (OUP)
Date: 09-2022
Abstract: Cellulose and lignin are critical cell wall components for plant morphogenesis and adaptation to environmental conditions. The cytoskeleton supports cell wall deposition, but much of the underpinning regulatory components remain unknown. Here, we show that an APETALA2/ETHYLENE RESPONSE FACTOR (ERF) family transcription factor, OsERF34, directly promotes the expression of the actin- and microtubule-binding protein Rice Morphology Determinant (RMD) in rice (Oryza sativa) peduncles. OsERF34 and RMD are highly expressed in sclerenchymatous peduncle cells that are fortified by thick secondary cell walls (SCWs) that provide mechanical peduncle strength. erf34 and rmd-1 mutants contained lower cellulose and lignin contents and thinner SCWs, while ERF34 over-expressing (OE) lines maintained high cellulose and lignin content with thicker SCWs. These characteristics impacted peduncle mechanical strength, that is, reduced strength in erf34 and rmd-1 and increased strength of ERF34 OE plants. Taken together, our results demonstrate that the OsERF34-RMD cascade positively regulates SCW synthesis and mechanical strength in rice peduncles, which is important for yield, and provide a potential guide for improved peduncle breeding efforts in rice.
Publisher: Springer Science and Business Media LLC
Date: 07-2022
DOI: 10.1007/S00299-022-02873-Y
Abstract: Novel alleles of two reported tiller angle genes and eleven candidate genes for rice tiller angle were identified by combining GWAS with transcriptomic, qRT-PCR and haplotype analysis. Rice tiller angle is a key agronomic trait determining rice grain yield. Several quantitative trait loci (QTLs) affecting rice tiller angle have been mapped in the past decades. Little is known about the genetic base of tiller angle in rice, because rice tiller angle is a complex polygenic trait. In this study, we performed genome-wide association study (GWAS) on tiller angle in rice using a population of 164 japonica varieties derived from the 3 K Rice Genomes Project (3 K RGP). We detected a total of 18 QTLs using 1135519 single-nucleotide polymorphisms (SNP) based on three GWAS models (GLM, FastLMM and FarmCPU). Among them, two identified QTLs, qTA8.3 and qTA8.4, overlapped with PAY1 and TIG1, respectively, and additional 16 QTLs were identified for the first time. Combined with haplotype and expression analyses, we further revealed that PAY1 harbors one non-synonymous variation at its coding region, likely leading to variable tiller angle in the population, and that nature variations in the promoter of TIG1 significantly affect its expression, closely correlating with tiller angle phenotypes observed. Similarly, using qRT-PCR and haplotype analysis, we identified 1 and 7 candidate genes in qTA6.1 and qTA8.1 that were commonly detected by two GWAS models, respectively. In addition, we identified 3 more candidate genes in the remaining 14 novel QTLs after filtering by transcriptome analysis and qRT-PCR. In summary, this study provides new insights into the genetic architecture of rice tiller angle and candidate genes for rice breeding.
Publisher: Springer Science and Business Media LLC
Date: 25-01-2022
DOI: 10.1186/S12284-022-00554-8
Abstract: Formins are actin-binding proteins that are key to maintaining the actin cytoskeleton in cells. However, molecular mechanisms controlling the stability of formin proteins in plants remain unknown. Here, we have identified six rice SIAH-type E3 ligases, named RIP1-6 (RMD Interacting Protein 1–6) respectively, with ubiquitination enzyme activity in vitro. All six proteins can form homo- and hetero-dimers with themselves, and hetero-dimers with type II formin RMD/OsFH5. In vivo assays showed that RIP1-6 proteins localize in the cytoplasm with a punctate distribution, and all of them interact with RMD to change its native diffuse cytoplasmic localization to match that of RIP1-6. To our surprise, degradation experiments revealed that RIP1, RIP5, and RIP6 decrease rather than increase the degradation rate of RMD. Genetic analyses revealed redundancy between these six genes either single or double mutants did not show any obvious phenotypes. However, the sextuple rip1-6 mutant displayed dwarf height, wrinkled seeds and wider leaves that were similar to the previously reported rmd mutant, and defective microfilaments and increased flag leaf angles that were not reported in rmd mutant. Collectively, our study provides insights into the mechanisms determining formin protein stability in plants.
Publisher: The Company of Biologists
Date: 15-06-2022
DOI: 10.1242/DEV.200415
Abstract: Rice (Oryza sativa) is one of our main food crops, feeding ∼3.5 billion people worldwide. An increasing number of studies note the importance of the cytoskeleton, including actin filaments and microtubules, in rice development and environmental responses. Yet, reliable in vivo cytoskeleton markers are lacking in rice, which limits our knowledge of cytoskeletal functions in living cells. Therefore, we generated bright fluorescent marker lines of the actin and microtubule cytoskeletons in rice, suitable for live-cell imaging in a wide variety of rice tissues. Using these lines, we show that actin bundles and microtubules engage and co-function during pollen grain development, how the cytoskeletal components are coordinated during root cell development, and that the actin cytoskeleton is robust and facilitates microtubule responses during salt stress. Hence, we conclude that our cytoskeletal marker lines, highlighted by our findings of cytoskeletal associations and dynamics, will substantially further future investigations in rice biology.
Location: China
Location: China
No related grants have been discovered for Dabing Zhang.