152 results on '"Wanqi Liang"'
Search Results
2. <scp>THERMOSENSITIVE BARREN PANICLE</scp> ( <scp>TAP</scp> ) is required for rice panicle and spikelet development at high ambient temperature
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Peng Zhang, Wanwan Zhu, Yi He, Junyi Fan, Jin Shi, Ruifeng Fu, Jianping Hu, Li Li, Dabing Zhang, and Wanqi Liang
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Hot Temperature ,Gene Expression Regulation, Plant ,Physiology ,Temperature ,Oryza ,Plant Science ,Inflorescence ,Edible Grain ,Plant Proteins - 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.
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- 2022
3. How price labeling strategy affects consumers' purchase intention? The role of perceived price difference in price assessment
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Wanqi Liang, Deyi Zhou, Muhammad Rizwan, and Samir Huseynov
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General Medicine - Abstract
PurposeBy conducting an online experiment, this paper proposes and tests a conceptual model about the impact of price labeling strategy on consumers' perceived price difference and purchase intention. The authors also analyze differential influences of shopping channels and price levels on documented effects. The paper provides strategic suggestions for online grocery store managers to adopt profit-maximizing labeling decisions.Design/methodology/approachIn a between-subject experiment, the authors simulated a shopping task with eight scenarios by exogenously manipulating price labeling strategies (unit price/retail price), sales channels (online/offline) and price levels (higher/lower than the average price). Participants are randomly assigned to one of the eight scenarios and asked to report their perceived price difference between the stimuli product and the average market price and their purchase intention on the stimuli product.FindingsExperimental results show that compared to the unit price, the retail price increases the perceived price difference. It shows that the unit price increases consumers' purchase intention when the product price is higher than the average market price. However, these effects only exist in the online shopping context.Originality/valueThis paper extends the study of price labeling strategy to an online shopping context and examines the mediation effect of the perceived price difference.
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- 2023
4. Genetic architecture of seed glycerolipids in Asian cultivated rice
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Jun Hong, Leah Rosental, Yang Xu, Dawei Xu, Isabel Orf, Wengsheng Wang, Zhiqiang Hu, Su Su, Shaoxing Bai, Mohammed Ashraf, Chaoyang Hu, Changquan Zhang, Zhikang Li, Jianlong Xu, Qiaoquan Liu, Hui Zhang, Fengli Zhang, Zhijing Luo, Mingjiao Chen, Xiaofei Chen, Natalie Betts, Alisdair Fernie, Wanqi Liang, Guanqun Chen, Yariv Brotman, Dabing Zhang, and Jianxin Shi
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Physiology ,Plant Science - Abstract
Glycerolipids are essential for rice development and grain quality but its genetic regulation remains unknown. Here we report its genetic base using metabolite-based genome-wide association study and metabolite-based quantitative traits locus (QTL) analyses based on lipidomic profiles of seeds from 587 Asian cultivated rice accessions and 103 chromosomal segment substitution lines, respectively. We found that two genes encoding phosphatidylcholine (PC):diacylglycerol cholinephosphotransferase (OsLP1) and granule-bound starch synthase I (Waxy) contribute to variations in saturated triacylglycerol (TAG) and lyso-PC contents, respectively. We demonstrated that allelic variation in OsLP1 sequence between indica and japonica results in different enzymatic preference for substrate PC-16:0/16:0 and different saturated TAG levels. Further evidence demonstrated that OsLP1 also affects heading date, and that co-selection of OsLP1 and a flooding-tolerant QTL in Aus results in the abundance of saturated TAGs associated with flooding tolerance. Moreover, we revealed that the sequence polymorphisms in Waxy has pleiotropic effects on lyso-PC and amylose content. We proposed that rice seed glycerolipids have been unintentionally shaped during natural and artificial selection for adaptive or import seed quality traits. Collectively, our findings provide valuable genetic resources for rice improvement and evolutionary insights into seed glycerolipid variations in rice.
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- 2022
5. Rice HEAT SHOCK PROTEIN60-3B maintains male fertility under high temperature by starch granule biogenesis
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Sen Lin, Ze Liu, Shiyu Sun, Feiyang Xue, Huanjun Li, Askar Tursun, Lichun Cao, Long Zhang, Zoe A Wilson, Dabing Zhang, and Wanqi Liang
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Physiology ,Genetics ,Plant Science - Abstract
Heat stress has a deleterious effect on male fertility in rice (Oryza sativa), but mechanisms to protect against heat stress in rice male gametophytes are poorly understood. Here, we have isolated and characterized a heat-sensitive male-sterile rice mutant, heat shock protein60-3b (oshsp60-3b), that shows normal fertility at optimal temperatures but decreasing fertility as temperatures increase. High temperatures interfered with pollen starch granule formation and reactive oxygen species (ROS) scavenging in oshsp60-3b anthers, leading to cell death and pollen abortion. In line with the mutant phenotypes, OsHSP60-3B was rapidly upregulated in response to heat shock and its protein products were localized to the plastid. Critically, overexpression of OsHSP60-3B enhanced the heat tolerance of pollen in transgenic plants. We demonstrated that OsHSP60-3B interacted with FLOURY ENDOSPERM6(FLO6) in plastids, a key component involved in the starch granule formation in the rice pollen. Western blot results showed that FLO6 level was substantially decreased in oshsp60-3b anthers at high temperature, indicating that OsHSP60-3B is required to stabilize FLO6 when temperatures exceed optimal conditions. We suggest that in response to high temperature, OsHSP60-3B interacts with FLO6 to regulate starch granule biogenesis in rice pollen and attenuates ROS levels in anthers to ensure normal male gametophyte development in rice.
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- 2023
6. The regulatory role of CARBON STARVED ANTHER-mediated photoperiod-dependent male fertility in rice
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Jingbin Li, Duoxiang Wang, Shiyu Sun, Linlin Sun, Jie Zong, Yaqi Lei, Jing Yu, Wanqi Liang, and Dabing Zhang
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Fertility ,Gene Expression Regulation, Plant ,Physiology ,Photoperiod ,Genetics ,food and beverages ,Oryza ,Plant Science ,Sugars ,Plant Proteins - Abstract
Environmental signals, especially daylength, play important roles in determining fertility in photoperiod-sensitive genic male sterile (PGMS) lines that are critical to sustain production of high-yielding hybrid rice (Oryza sativa) varieties. However, the mechanisms by which PGMS lines perceive changes in photoperiod and transmit those signals to elicit downstream effects are not well understood. In this study, we compared the transcriptomes from the leaves and anthers of carbon starved anther (csa), a PGMS line, to wild-type (WT) tissues under different photoperiods. Components of circadian clock in the leaves, including Circadian Clock-Associated 1 and Pseudo-Response Regulator (PRR95), played vital roles in sensing the photoperiod signals. Photoperiod signals were weakly transduced to anthers, where gene expression was mainly controlled by the CSA allele. CSA played a critical role in regulating sugar metabolism and cell wall synthesis in anthers under short-day conditions, and transcription of key genes inducing csa-directed sterility was upregulated under long-day (LD) conditions though not to WT levels, revealing a mechanism to explain the partial restoration of fertility in rice under LD conditions. Eight direct targets of CSA regulation were identified, all of which were genes involved in sugar metabolism and transport (cell wall invertases, SWEETs, and monosaccharide transporters) expressed only in reproductive tissues. Several hub genes coordinating the effects of CSA regulation were identified as critical elements determining WT male fertility and further analysis of these and related genes will reveal insights into how CSA coordinates sugar metabolism, cell wall biosynthesis, and photoperiod sensing in rice anther development.
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- 2022
7. Rice SIAH E3 Ligases Interact with RMD Formin and Affect Plant Morphology
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Shuwei Chang, Guoqiang Huang, Duoxiang Wang, Wanwan Zhu, Jianxin Shi, Litao Yang, Wanqi Liang, Qi Xie, and Dabing Zhang
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RMD ,Height ,Location ,fungi ,Soil Science ,food and beverages ,Plant culture ,Plant Science ,macromolecular substances ,SB1-1110 ,Degradation ,Seeds ,Morphogenesis ,Original Article ,Rice ,Agronomy and Crop Science ,SIAH ,E3 ligase - 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.
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- 2022
8. Multi-omics analysis reveals a link between Brassica -specific miR1885 and rapeseed tolerance to low temperature
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Xiang Yu, Pengfei Xu, Wenting Zhang, Xuan Wang, Yantao Zhu, Wanqi Liang, and Yuke He
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Brassica crops include various edible vegetable and plant oil crops, and their production is limited by low temperature beyond their tolerant capability. The key regulators of low-temperature resistance in Brassica remain largely unexplored. To identify post-transcriptional regulators of plant response to low temperature, we performed small RNA profiling, and found that 16 known miRNAs were responsive to cold treatment in Brassica rapa. The cold response of seven of those miRNAs were further confirmed by qRT-PCR and/or northern blotting analyses. In parallel, a genome-wide association study of 220 accessions of Brassica napus identified four candidate MIRNA genes, all of which were cold-responsive, at the loci associated with low temperature resistance. Specifically, these large-scale data analyses revealed a link between miR1885 and the plant response to low temperature in both B. rapa and B. napus. Using 5′ rapid amplification of cDNA ends approach, we validated that miR1885 can cleave its putative target transcripts, Bn.TIR.A09 and Bn.TNL.A03, in B. napus. Furthermore, overexpression of miR1885 in Semi-winter type B. napus decreased the mRNA abundance of Bn.TIR.A09 and Bn.TNL.A03, resulting in increased sensitivity to low temperature. Knocking down of miR1885 in Spring type B. napus led to increased mRNA abundance of its targets and improved rapeseed tolerance to low temperature. Together, our results suggested that the loci of miR1885 and its targets could be potential candidates for the molecular breeding of low temperature-tolerant Spring type Brassica crops.
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- 2023
9. OsPRD2 is essential for double-strand break formation, but not spindle assembly during rice meiosis
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Chong Wang, Shuying Qu, Jie Zhang, Ming Fu, Xiaofei Chen, and Wanqi Liang
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Plant Science - Abstract
Meiotic recombination starts with the programmed formation of double-strand breaks (DSB) in DNA, which are catalyzed by SPO11, a type II topoisomerase that is evolutionarily conserved, and several other accessary proteins. Homologs of MEIOSIS INHIBITOR 4 (MEI4/REC24/PRD2) are proteins that are also essential for the generation of meiotic DSBs in budding yeast, mice and Arabidopsis thaliana. In Arabidopsis, the protein ARABIDOPSIS THALIANA PUTATIVE RECOMBINATION INITIATION DEFECTS 2/MULTIPOLAR SPINDLE 1 (AtPRD2/MPS1) has been shown to have additional roles in spindle assembly, indicating a functional diversification. Here we characterize the role of the rice MEI4/PRD2 homolog in meiosis. The osprd2 mutant was completely male and female sterile. In male meiocytes of osprd2, no γH2AX foci were detected and twenty-four univalents were produced at diakinesis, suggesting that OsPRD2 is essential for DSB generation. OsPRD2 showed a dynamic localization during meiosis. For instance, OsPRD2 foci first appeared as discrete signals across chromosome at leptotene, and then became confined to the centromeres during zygotene, suggesting that they might be involved in assembly of the spindle. However we did not observe any obvious aberrant morphologies in neither the organization of the bipolar spindle nor in the orientation of the kinetochore in the mutant. These findings suggest that in rice PRD2 might not be required for spindle assembly and organization, as it does in Arabidopsis. Taken together our results indicate that plant MEI4/PRD2 homologs do play a conserved role in the formation of meiotic DSBs in DNA, but that their involvement in bipolar spindle assembly is rather species-specific.
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- 2023
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10. Rice Glucose 6-Phosphate/Phosphate Translocator 1 is required for tapetum function and pollen development
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Huanjun Li, Wanqi Liang, Feiyang Xue, and Weidan Zhang
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Gametophyte ,Tapetum ,Agriculture (General) ,Stamen ,Heterotrophic plastids ,food and beverages ,Agriculture ,Plant Science ,Biology ,medicine.disease_cause ,Pollen exine formation ,Cell biology ,S1-972 ,medicine.anatomical_structure ,Sporopollenin ,Tapetal PCD ,Pollen ,Male fertility ,medicine ,Gamete ,Glucose-6-Phosphate/Phosphate Translocator ,Plastid ,Agronomy and Crop Science - Abstract
In plants, non-green plastids in heterotrophic tissues are sites for starch and fatty acids biosynthesis, which are essential for plant development and reproduction. Distinct from chloroplasts, the metabolites for these processes in non-green plastids have to be imported through specific transporters. Glucose 6-Phosphate/Phosphate Translocator 1 is required for the uptake of cytosolic Glucose 6-Phosphate into non-green plastids. In Arabidopsis, GPT1 has been demonstrated to play essential roles in male, female gametophyte and embryo development. However, the roles of GPTs in other species are yet largely unknown. Here, we reported that rice OsGPT1 is indispensable for normal tapetal degeneration and pollen exine formation during anther and pollen development. OsGPT1 is localized in the plastid and distributed in the anther wall layers and late-stage pollen grains. Different from the gametic defects caused by mutation in AtGPT1, disruption of OsGPT1 does not affect male and female gamete transmission as well as embryo development. On the contrary, osgpt1 mutant exhibits delayed tapetum degeneration, decreased Ubisch bodies formation and thinner pollen exine, leading to pollen abortion at the mature stage. Furthermore, the expression of several genes involved in tapetal programmed cell death (PCD) and sporopollenin formation is decreased in osgpt1. Our study suggests that OsGPT1 coordinates the development of anther sporophytic tissues and the male gametophyte by integrating carbohydrate and fatty acid metabolism in the plastid.
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- 2021
11. Rice SEPALLATA genes OsMADS5 and OsMADS34 cooperate to limit inflorescence branching by repressing the TERMINAL FLOWER1 ‐like gene RCN4
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Guoqiang Huang, Xiaofei Chen, Di Wu, Jiao Zhang, Ludovico Dreni, Wanqi Liang, Dabing Zhang, Xiao Deng, Liu Yang, Cristina Ferrándiz, Wanwan Zhu, and Qingcai Meng
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0106 biological sciences ,2. Zero hunger ,Meristem determinacy ,0303 health sciences ,Oryza sativa ,Physiology ,Mutant ,Wild type ,food and beverages ,Plant Science ,Meristem ,Biology ,01 natural sciences ,Cell biology ,03 medical and health sciences ,Inflorescence ,MADS-box ,030304 developmental biology ,010606 plant biology & botany ,Panicle - 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 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 ~7× more spikelets than wild type. 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.
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- 2021
12. A small Rho GTPase OsRacB is required for pollen germination in rice
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Wenguo Cai, Mingjiao Chen, Xiaofei Chen, Yangfan Xu, and Wanqi Liang
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rho GTP-Binding Proteins ,Oryza sativa ,Mutant ,Arabidopsis ,Stamen ,food and beverages ,Oryza ,Cell Biology ,GTPase ,Biology ,medicine.disease_cause ,biology.organism_classification ,eye diseases ,Cell biology ,Germination ,Pollen ,otorhinolaryngologic diseases ,medicine ,Pollen tube ,Monomeric GTP-Binding Proteins ,Plant Proteins ,Developmental Biology - Abstract
Plant Rho small GTPases (Rop/Rac) are versatile molecular switches regulating many plant developmental processes. Particularly, their important functions in regulating pollen development have been demonstrated in Arabidopsis. A group of conserved Rop/Rac activators RopGEFs were recently reported to regulate rice (Oryza sativa) pollen tube germination, indicating that rice and Arabidopsis may have a conserved Rop/Rac mediated signaling pathway in regulating pollen tube growth. However, the Rop/Rac activated by the rice pollen specific RopGEFs remains to be identified. Here we demonstrated a Rop/Rac gene, OsRacB, co-expressed with the mature pollen expressed OsRopGEF2/3/6/8. The knockout mutants were normal in anther and pollen development but defective in the pollen grain germination, suggesting a specific and non-redundant role of OsRacB in the mature pollen. We further demonstrated that OsRacB is directly activated by the pollen specific expressing OsRopGEFs in vitro. Together with the previous study, we establish a RopGEF-Rop/Rac regulon which plays essential roles in rice pollen grain germination. Our data encourage further identification of the upstream and downstream players of RopGEF-Rop/Rac signaling in pollen germination and have agricultural implications for breeding robust seed yielding cultivars.
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- 2021
13. Dissection of the Genetic Basis of Rice Panicle Architecture Using a Genome-wide Association Study
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Shaoxing Bai, Su Su, Wensheng Wang, Zhikang Li, Fengli Zhang, Dabing Zhang, Wanqi Liang, Jun Hong, and Ling Li
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Candidate gene ,Genome-wide association study ,Quantitative trait loci ,Population ,Soil Science ,Plant Science ,Quantitative trait locus ,Japonica ,SB1-1110 ,Genetic variation ,education ,Panicle ,Molecular breeding ,Genetics ,education.field_of_study ,biology ,Panicle length ,food and beverages ,Plant culture ,biology.organism_classification ,Panicle architecture ,Hormone ,Original Article ,Rice ,Natural variation ,Agronomy and Crop Science - 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.
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- 2021
14. Carbon Starved Anther modulates sugar and ABA metabolism to protect rice seed germination and seedling fitness
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Sixue Chen, Jingbin Li, Linlin Sun, Yangyang Hu, Jin Shi, Xiaofei Chen, Zheng Yuan, Dabing Zhang, Duoxiang Wang, Jing Yu, and Wanqi Liang
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Regular Issue ,Oryza sativa ,biology ,Physiology ,Abiotic stress ,food and beverages ,Germination ,Oryza ,Plant Science ,biology.organism_classification ,Horticulture ,Seedlings ,Seedling ,Aleurone ,Seeds ,Genetics ,biology.protein ,Imbibition ,MYB ,Genetic Fitness ,Amylase ,Sugars ,Abscisic Acid ,Plant Proteins - Abstract
Seed germination is critical for plant survival and agricultural production, which is affected by both internal seed factors and external environmental conditions. However, the genetic basis and underlying molecular mechanisms of early seed germination in crops remain largely unclear. Here, we report that R2R3 MYB transcription factor Carbon Starved Anther (CSA) is expressed specifically in Oryza sativa embryo and aleurone in response to seed imbibition, peaking at 3–6 h and undetectable by 24-h post-imbibition. CSA seeds germinated more quickly than wild-type rice seeds and had higher levels of amylase activity, glucose, and inactive abscisic acid-glucose ester (ABA-GE), but lower levels of ABA. Through analyzing the CSA-associated transcriptome and CSA binding to downstream target genes, we identified two glycolytic genes as direct CSA targets. CSA inhibits Amylase 3A expression to limit glucose production from starch and activates Os3BGlu6 expression to promote de-conjugation of ABA-GE to ABA; these functions serve to slow germination and improve seedling resilience to abiotic stress in the first 3 weeks of growth. Therefore, this study unveils a protection mechanism conferred by CSA during early seed germination by balancing glucose and ABA metabolism to optimize seed germination and stress response fitness.
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- 2021
15. Integrating GWAS and transcriptomics to identify genes involved in seed dormancy in rice
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Jianxin Shi, Dabing Zhang, Wanqi Liang, and Jin Shi
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Genetics ,Candidate gene ,Oryza sativa ,biology ,Seed dormancy ,food and beverages ,Single-nucleotide polymorphism ,General Medicine ,Quantitative trait locus ,biology.organism_classification ,Japonica ,Germination ,Hordeum vulgare ,Agronomy and Crop Science ,Biotechnology - 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 hampered 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.
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- 2021
16. <scp>HSP70</scp> ‐16 and <scp>VDAC3</scp> jointly inhibit seed germination under cold stress in Arabidopsis
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Jun Hong, Lei Shi, Muhammad Ashraf, Fiza Liaquat, Alisdair R. Fernie, Qionglei Mao, Muhammad Uzair, Wanqi Liang, Xiaoruo Ran, and Jianxin Shi
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Voltage-dependent anion channel ,VDAC3 ,biology ,Arabidopsis Proteins ,Physiology ,Chemistry ,Cold-Shock Response ,fungi ,Arabidopsis ,food and beverages ,Germination ,Plant Science ,biology.organism_classification ,Hsp70 ,Endosperm ,Cell biology ,chemistry.chemical_compound ,Heat shock protein ,Seeds ,biology.protein ,Voltage-Dependent Anion Channels ,HSP70 Heat-Shock Proteins ,Abscisic acid - Abstract
Abscisic acid (ABA) transport plays a crucial role in seed germination under unfavourable conditions such as cold stress. Both heat shock protein 70 (HSP70) and voltage-dependent anion channel (VDAC) protein are involved in cold stress responses in Arabidopsis. However, their roles in seed germination with regard to ABA signaling remain unknown. Here we demonstrated that Arabidopsis HSP70-16 and VDAC3 jointly suppress seed germination under cold stress conditions. At 4°C, both HSP70-16 and VDAC3 facilitated the efflux of ABA from the endosperm to the embryo and thus inhibited seed germination. HSP70-16 interacted with VDAC3 on the plasma membrane and in the nucleus, and the interplay between HSP70-16 and VDAC3 activated the opening of the VDAC3 ion channel. Our work established a novel function of HSP70-16 in seed germination under cold stress and a possible association of VDAC3 activity with ABA transportation from endosperm to embryo under cold stress conditions. This study reveals that HSP70-16 interacts with VDAC3 and facilitates the opening of the VDAC3 ion channel, which influences ABA efflux from endosperm to embryo, thus negatively regulates seed germination under cold stress.
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- 2021
17. MADS1 maintains barley spike morphology at high ambient temperatures
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Natalie S. Betts, Jin Shi, Hendrik N. J. Kuijer, Rachel A. Burton, Chaoqun Shen, Xiujuan Yang, Wanqi Liang, Robbie Waugh, Dabing Zhang, Huiran Liu, Matthew R. Tucker, and Gang Li
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0106 biological sciences ,0301 basic medicine ,Regulation of gene expression ,fungi ,Mutant ,food and beverages ,Promoter ,Plant Science ,Meristem ,Biology ,01 natural sciences ,Phenotype ,Cell biology ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Inflorescence ,chemistry ,Cytokinin ,Gene ,010606 plant biology & botany - Abstract
Temperature stresses affect plant phenotypic diversity. The developmental stability of the inflorescence, required for reproductive success, is tightly regulated by the interplay of genetic and environmental factors. However, the mechanisms underpinning how plant inflorescence architecture responds to temperature are largely unknown. We demonstrate that the barley SEPALLATA MADS-box protein HvMADS1 is responsible for maintaining an unbranched spike architecture at high temperatures, while the loss-of-function mutant forms a branched inflorescence-like structure. HvMADS1 exhibits increased binding to target promoters via A-tract CArG-box motifs, which change conformation with temperature. Target genes for high-temperature-dependent HvMADS1 activation are predominantly associated with inflorescence differentiation and phytohormone signalling. HvMADS1 directly regulates the cytokinin-degrading enzyme HvCKX3 to integrate temperature response and cytokinin homeostasis, which is required to repress meristem cell cycle/division. Our findings reveal a mechanism by which genetic factors direct plant thermomorphogenesis, extending the recognized role of plant MADS-box proteins in floral development.
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- 2021
18. Two rice MYB transcription factors maintain male fertility in response to photoperiod by modulating sugar partitioning
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Wanqi Liang, Jing Yu, Yangyang Hu, Canhua Wang, Duoxiang Wang, Haili Hou, Jingbin Li, Dabing Zhang, Linlin Sun, and Fengli Zhang
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0106 biological sciences ,0301 basic medicine ,Physiology ,Sterility ,Photoperiod ,Mutant ,Regulator ,Flowers ,Plant Science ,Biology ,01 natural sciences ,Transcriptome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,MYB ,Sugar ,Transcription factor ,Plant Proteins ,photoperiodism ,food and beverages ,Oryza ,Cell biology ,Plant Breeding ,030104 developmental biology ,Sugars ,Transcription Factors ,010606 plant biology & botany - 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.
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- 2021
19. Impact of Participation in Groundwater Market on Farmland, Income, and Water Access: Evidence from Pakistan
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Amar Razzaq, Meizhen Xiao, Yewang Zhou, Hancheng Liu, Azhar Abbas, Wanqi Liang, and Muhammad Asad ur Rehman Naseer
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Geography, Planning and Development ,water extraction ,income inequality ,water productivity ,land use ,sustainability ,Aquatic Science ,Biochemistry ,Water Science and Technology - Abstract
Groundwater irrigation has a critical role in the sustainability of arable farming in many developing countries including Pakistan. Groundwater irrigation is generally practiced to supplement surface water supplies in Pakistan. Nevertheless, uninterrupted and extensive use of groundwater irrigation has raised several concerns about its sustainability and resultant environmental implications. Due to the scarcity of groundwater and heterogeneity in farmers’ resources, informal groundwater markets have emerged in Pakistan, where farmers trade water using a contractual system. Yet, the effects of these markets on agricultural productivity and equity remain largely unknown. This paper aims to analyze the impact of participation in the groundwater market on farmland utilization, cropping patterns, water access, and income. We analyze these impacts using primary data collected from 360 farmers in three different zones of the country’s largest province. The farmers were categorized as buyers, sellers, and self-users of water. Results indicate that participation in water markets increased agricultural land utilization, evinced by a higher cropping intensity among participants. A horizontal and vertical equity analysis of water markets shows that although large farmers have better access to groundwater irrigation, water market participation improves equity to water access. Based on income inequality measures such as the Gini coefficient and the Lorenz curve, water market participation also improves farmer incomes regardless of farm size. Propensity score matching revealed that wheat yield and income among water-market participants went up by approximately 150 kg and PKR 4503 per acre compared with non-participants. Groundwater market participants’ higher crop productivity and income level suggest that water markets need a thorough revisit in terms of policy focus and institutional support to ensure sustainable rural development.
- Published
- 2022
- Full Text
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20. Function of the pseudo phosphotransfer proteins has diverged between rice and Arabidopsis
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Kevin Beaver, Samantha Louise Boeshore, Wanqi Liang, Jan Šimura, G. Eric Schaller, Charlie Hodgens, Karin Ljung, Joseph J. Kieber, Kartika Sari, Ian D. Kerr, Emily J. Tallerday, Dawei Xu, Christian A. Burr, Allison Melling, Rahul Bhosale, John Vaughan-Hirsch, and Anthony Bishopp
- Subjects
0106 biological sciences ,0301 basic medicine ,Cytokinins ,component signaling ,Mutant ,Arabidopsis ,Oryza sativa ,Plant Science ,Biology ,01 natural sciences ,Genome ,cytokinin ,03 medical and health sciences ,chemistry.chemical_compound ,Plant Growth Regulators ,Gene Expression Regulation, Plant ,Genetics ,Agricultural Science ,Gene ,Plant Proteins ,Science & Technology ,Arabidopsis Proteins ,Plant Sciences ,fungi ,Histidine kinase ,food and beverages ,Oryza ,Cell Biology ,biology.organism_classification ,030104 developmental biology ,chemistry ,two‐ ,Cytokinin ,plant hormones ,Life Sciences & Biomedicine ,Function (biology) ,010606 plant biology & botany - Abstract
The phytohormone cytokinin plays a significant role in nearly all aspects of plant growth and development. Cytokinin signaling has primarily been studied in the dicot model Arabidopsis, with relatively little work done in monocots, which include rice (Oryza sativa) and other cereals of agronomic importance. The cytokinin signaling pathway is a phosphorelay comprised of the histidine kinase receptors, the authentic histidine phosphotransfer proteins (AHPs) and type-B response regulators (RRs). Two negative regulators of cytokinin signaling have been identified: the type-A RRs, which are cytokinin primary response genes, and the pseudo histidine phosphotransfer proteins (PHPs), which lack the His residue required for phosphorelay. Here, we describe the role of the rice PHP genes. Phylogenic analysis indicates that the PHPs are generally first found in the genomes of gymnosperms and that they arose independently in monocots and dicots. Consistent with this, the three rice PHPs fail to complement an Arabidopsis php mutant (aphp1/ahp6). Disruption of the three rice PHPs results in a molecular phenotype consistent with these elements acting as negative regulators of cytokinin signaling, including the induction of a number of type-A RR and cytokinin oxidase genes. The triple php mutant affects multiple aspects of rice growth and development, including shoot morphology, panicle architecture, and seed fill. In contrast to Arabidopsis, disruption of the rice PHPs does not affect root vascular patterning, suggesting that while many aspects of key signaling networks are conserved between monocots and dicots, the roles of at least some cytokinin signaling elements are distinct. ispartof: PLANT JOURNAL vol:106 issue:1 pages:159-173 ispartof: location:England status: published
- Published
- 2021
21. Impact of internet usage on the subjective well-being of urban and rural households: Evidence from Vietnam
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Wanqi Liang and Wenying Li
- Subjects
Economics and Econometrics ,Communication ,Library and Information Sciences ,Management, Monitoring, Policy and Law ,Information Systems ,Management Information Systems - Published
- 2023
22. Paeoniflorin alleviates endothelial dysfunction caused by overexpression of soluble fms-like tyrosine kinase 1 and soluble endoglin in preeclampsia via VEGFA upregulation
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Wanqi Liang, Wei Hua, Zhao Xinyuan, Fan Yang, Ting Guo, Jin Zhang, Jianhua Zhang, and Xuerong Zheng
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Vascular Endothelial Growth Factor A ,0301 basic medicine ,Applied Microbiology and Biotechnology ,Biochemistry ,Umbilical vein ,Analytical Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Glucosides ,Pre-Eclampsia ,Pregnancy ,Human Umbilical Vein Endothelial Cells ,Humans ,MTT assay ,Viability assay ,Molecular Biology ,Tube formation ,Vascular Endothelial Growth Factor Receptor-1 ,030219 obstetrics & reproductive medicine ,Chemistry ,Organic Chemistry ,Endoglin ,General Medicine ,Paeoniflorin ,Molecular biology ,Vascular endothelial growth factor A ,030104 developmental biology ,embryonic structures ,Monoterpenes ,cardiovascular system ,Female ,Endothelium, Vascular ,Tyrosine kinase ,Soluble fms-like tyrosine kinase-1 ,Biotechnology - Abstract
This study assessed the protective effects of paeoniflorin against preeclampsia-related endothelial damage (ED). Human umbilical vein endothelial cells (HUVECs) isolated from healthy puerperae were identified by immunofluorescence assay. After paeoniflorin treatment, HUVECs were induced by soluble fms-like tyrosine kinase 1 (sFlt-1) and soluble endoglin (sEng) to establish ED. Cell viability, migration, invasion, tube formation, and apoptosis were assessed by (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) tetrazolium MTT assay, Scratch assay, Transwell assay, tube formation assay, and flow cytometry. VEGFA expression in HUVECs was analyzed by Western blot. HUVECs were successfully isolated and identified as Von Willebrand factor (vWF) positive. Individual treatment or cotreatment of sFlt-1 and sEng inhibited migration, invasion and tube formation, enhanced apoptosis, and decreased VEGFA expression in HUVECs. Paeoniflorin pretreatment partially reversed the effects delivered by cotreatment of sFlt-1 and sEng in HUVECs. Paeoniflorin alleviated preeclampsia-related ED caused by overexpression of sFlt-1 and sEng by upregulating VEGFA.
- Published
- 2020
23. Temperature-sensitive male sterility in rice determined by the roles of AGO1d in reproductive phasiRNA biogenesis and function
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Chuanlin Shi, Jie Zhang, Bingjin Wu, Rachel Jouni, Changxiu Yu, Blake C. Meyers, Wanqi Liang, and Qili Fei
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Plant Infertility ,Physiology ,Nucleotides ,Temperature ,Oryza ,Starch ,Plant Science ,MicroRNAs ,Gene Expression Regulation, Plant ,RNA, Plant ,Argonaute Proteins ,RNA, Small Interfering ,Uridine ,Plant Proteins - Abstract
Phased secondary siRNAs (phasiRNAs) are broadly present in the reproductive tissues of flowering plants, with spatial-temporal specificity. However, the ARGONAUTE (AGO) proteins associated with phasiRNAs and their miRNA triggers remain elusive. Here, through histological and high-throughput sequencing analyses, we show that rice AGO1d, which is specifically expressed in anther wall cells before and during meiosis, associates with both miR2118 and miR2275 to mediate phasiRNA biogenesis. AGO1d preferentially binds to miR2118-triggered 21-nucleotide (nt) phasiRNAs with a 5'-terminal uridine, suggesting a dual role in phasiRNA biogenesis and function. Depletion of AGO1d causes a reduction of 21- and 24-nt phasiRNAs and temperature-sensitive male sterility. At lower temperatures, anthers of the ago1d mutant predominantly show excessive tapetal cells with little starch accumulation during pollen formation, possibly caused by the dysregulation of cell metabolism. These results uncover an essential role of AGO1d in rice anther development at lower temperatures and demonstrate coordinative roles of AGO proteins during reproductive phasiRNA biogenesis and function.
- Published
- 2022
24. Genetic Basis Underlying Tiller Angle in Rice (Oryza sativa L.) by Genome-wide Association Study
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Shaoxing Bai, Jun Hong, Su Su, Zhikang Li, Wensheng Wang, Jianxin Shi, Wanqi Liang, and Dabing Zhang
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Plant Breeding ,Quantitative Trait Loci ,Chromosome Mapping ,food and beverages ,Oryza ,Plant Science ,General Medicine ,Agronomy and Crop Science ,Genome-Wide Association Study - Abstract
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 3K Rice Genomes Project (3K RGP). We detected a total of 18 QTLs using 1,135,519 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.
- Published
- 2022
25. Rice pollen aperture formation is regulated by the interplay between OsINP1 and OsDAF1
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Wanqi Liang, Lu Zhu, Hui Yuan, Xu Zhang, Qian Tan, Guochao Zhao, Natalie S. Betts, and Dabing Zhang
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Annulus (mycology) ,Oryza sativa ,biology ,Aperture ,food and beverages ,Plant Science ,medicine.disease_cause ,biology.organism_classification ,Cell biology ,Germination ,Pollen ,Arabidopsis ,medicine ,Pollen tube ,Tetrad - Abstract
The aperture on the pollen surface provides an exit for the emerging pollen tube. Apertures exhibit huge morphological variation across plant species-grasses, including rice, possess a complex aperture consisting of an annulus and an operculum-but little is known about how this species-specific cell-surface pattern forms. Here, we report a lectin receptor-like kinase in Oryza sativa, OsDAF1, which is essential for annulus formation and thus for fertility. OsDAF1 is evenly distributed in early microsporocytes but localizes to the distal pre-aperture site at the tetrad stage. We further reveal that the rice orthologue of a key aperture factor in Arabidopsis, OsINP1, has conserved and diversified roles in rice aperture formation. Disruption of OsINP1 prevents formation of the aperture, precluding pollen-tube germination. Furthermore, our results demonstrate that OsINP1 is required for polarization of OsDAF1 via direct protein interaction, suggesting that OsINP1 has an additional role in the formation of annulus that is absent in Arabidopsis. Our study reveals the importance of the aperture for rice grain yield and reveals mechanisms controlling pollen aperture development in cereal species.
- Published
- 2020
26. Transcriptome profiling reveals phase-specific gene expression in the developing barley inflorescence
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Gang Li, Dabing Zhang, Wanqi Liang, Hendrik N. J. Kuijer, Xiujuan Yang, and Huiran Liu
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2. Zero hunger ,0106 biological sciences ,Genetics ,0303 health sciences ,Candidate gene ,fungi ,lcsh:S ,food and beverages ,Plant Science ,Meristem ,Biology ,lcsh:S1-972 ,01 natural sciences ,lcsh:Agriculture ,Transcriptome ,03 medical and health sciences ,Inflorescence ,Gene expression ,Hordeum vulgare ,lcsh:Agriculture (General) ,Agronomy and Crop Science ,Gene ,030304 developmental biology ,010606 plant biology & botany ,Panicle - Abstract
The shape of an inflorescence varies among cereals, ranging from a highly branched panicle in rice to a much more compact spike in barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). However, little is known about the molecular basis of cereal inflorescence architecture. We profiled transcriptomes at three developmental stages of the barley main shoot apex — spikelet initiation, floral organ differentiation, and floral organ growth — and compared them with those from vegetative seedling tissue. Transcript analyses identified 3688 genes differentially transcribed between the three meristem stages, with a further 1394 genes preferentially expressed in reproductive compared with vegetative tissue. Co-expression assembly and Gene Ontology analysis classified these 4888 genes into 28 clusters, revealing distinct patterns for genes such as transcription factors, histone modification, and cell-cycle progression specific for each stage of inflorescence development. We also compared expression patterns of VRS (SIX-ROWED SPIKE) genes and auxin-, gibberellic acid- and cytokinin-associated genes between two-rowed and six-rowed barley to describe regulators of lateral spikelet fertility. Our findings reveal barley inflorescence phase-specific gene expression, identify new candidate genes that regulate barley meristem activities and flower development, and provide a new genetic resource for further dissection of the molecular mechanisms of spike development. Keywords: Inflorescence meristem, Transcriptome, Gene expression, Hormones, Barley
- Published
- 2020
27. A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems
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Jie Zong, Li Wang, Lu Zhu, Lianle Bian, Bo Zhang, Xiaofei Chen, Guoqiang Huang, Xuelian Zhang, Junyi Fan, Liming Cao, George Coupland, Wanqi Liang, Dabing Zhang, and Zheng Yuan
- Subjects
Gene Expression Regulation, Plant ,Physiology ,Meristem ,Oryza ,Plant Science ,Inflorescence ,Transcriptome ,Plant Proteins - 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.
- Published
- 2022
28. Identification And Functional Analysis of 3-Phosphatidylinositol Kinase FAB1/PIKfyve Gene Family in Rice (Oryza sativa)
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Yichun Xu, Wanqi Liang, Canhua Wang, and Jing Yu
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General Medicine - Published
- 2022
29. Ethylene inhibits rice root elongation in compacted soil via ABA- and auxin-mediated mechanisms
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Guoqiang Huang, Azad Kilic, Michal Karady, Jiao Zhang, Poonam Mehra, Xiaoyun Song, Craig J. Sturrock, Wanwan Zhu, Hua Qin, Sjon Hartman, Hannah M. Schneider, Rahul Bhosale, Ian C. Dodd, Robert E. Sharp, Rongfeng Huang, Sacha J. Mooney, Wanqi Liang, Malcolm J. Bennett, Dabing Zhang, and Bipin K. Pandey
- Subjects
roots ,Multidisciplinary ,Crop Physiology ,Indoleacetic Acids ,Oryza ,Ethylenes ,PE&RC ,Plant Roots ,Mixed Function Oxygenases ,soil compaction ,Soil ,ABA ,Mutation ,Centre for Crop Systems Analysis ,ethylene ,auxin ,Abscisic Acid ,Plant Proteins - Abstract
Soil compaction represents a major agronomic challenge, inhibiting root elongation and impacting crop yields. Roots use ethylene to sense soil compaction as the restricted air space causes this gaseous signal to accumulate around root tips. Ethylene inhibits root elongation and promotes radial expansion in compacted soil, but its mechanistic basis remains unclear. Here, we report that ethylene promotes abscisic acid (ABA) biosynthesis and cortical cell radial expansion. Rice mutants of ABA biosynthetic genes had attenuated cortical cell radial expansion in compacted soil, leading to better penetration. Soil compaction-induced ethylene also up-regulates the auxin biosynthesis gene OsYUC8 . Mutants lacking OsYUC8 are better able to penetrate compacted soil. The auxin influx transporter OsAUX1 is also required to mobilize auxin from the root tip to the elongation zone during a root compaction response. Moreover, osaux1 mutants penetrate compacted soil better than the wild-type roots and do not exhibit cortical cell radial expansion. We conclude that ethylene uses auxin and ABA as downstream signals to modify rice root cell elongation and radial expansion, causing root tips to swell and reducing their ability to penetrate compacted soil.
- Published
- 2022
30. PERSISTENT TAPETAL CELL2 Is Required for Normal Tapetal Programmed Cell Death and Pollen Wall Patterning
- Author
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Zhijing Luo, Muhammad Uzair, Yueya Zhang, Ki-Hong Jung, Wanqi Liang, Dabing Zhang, Lukas Schreiber, Jing Yu, Jianxin Shi, Dawei Xu, and Mingjiao Chen
- Subjects
0106 biological sciences ,Programmed cell death ,Plant Infertility ,Genotype ,Physiology ,Arabidopsis ,Stamen ,Apoptosis ,DNA Fragmentation ,Flowers ,Plant Science ,Biology ,medicine.disease_cause ,01 natural sciences ,Meiosis ,Gene Expression Regulation, Plant ,Pollen ,otorhinolaryngologic diseases ,Genetics ,medicine ,Arabidopsis thaliana ,Gene Regulatory Networks ,RNA-Seq ,Research Articles ,Plant Proteins ,Cell Nucleus ,Tapetum ,Gene Expression Profiling ,Gene Expression Regulation, Developmental ,food and beverages ,Oryza ,Lipid Metabolism ,biology.organism_classification ,Lipids ,Cell biology ,Phenotype ,Mutation ,Microscopy, Electron, Scanning ,AT-Hook Motifs ,Pollen wall ,Transcription Factors ,010606 plant biology & botany - Abstract
The timely programmed cell death (PCD) of the tapetum, the innermost somatic anther cell layer in flowering plants, is critical for pollen development, including the deposition and patterning of the pollen wall. Although several genes involved in tapetal PCD and pollen wall development have been characterized, the underlying regulatory mechanism remains elusive. Here we report that PERSISTENT TAPETAL CELL2 (PTC2), which encodes an AT-hook nuclear localized protein in rice (Oryza sativa), is required for normal tapetal PCD and pollen wall development. The mutant ptc2 showed persistent tapetal cells and abnormal pollen wall patterning including absent nexine, collapsed bacula, and disordered tectum. The defective tapetal PCD phenotype of ptc2 was similar to that of a PCD delayed mutant, ptc1, in rice, while the abnormal pollen wall patterning resembled that of a pollen wall defective mutant, Transposable Element Silencing Via AT-Hook, in Arabidopsis (Arabidopsis thaliana). Levels of anther cutin monomers in ptc2 anthers were significantly reduced, as was expression of a series of lipid biosynthetic genes. PTC2 transcript and protein were shown to be present in the anther after meiosis, consistent with the observed phenotype. Based on these data, we propose a model explaining how PTC2 affects anther and pollen development. The characterization of PTC2 in tapetal PCD and pollen wall patterning expands our understanding of the regulatory network of male reproductive development in rice and will aid future breeding approaches.
- Published
- 2019
31. OsFH3 Encodes a Type II Formin Required for Rice Morphogenesis
- Author
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Shuwei Chang, Zhanhong Ren, Chang Liu, Pingzhou Du, Jingbin Li, Zengyu Liu, Fengli Zhang, Haili Hou, Jianxin Shi, Wanqi Liang, Litao Yang, Haiyun Ren, and Dabing Zhang
- Subjects
QH301-705.5 ,rice ,Organic Chemistry ,fungi ,profilin–actin complex ,food and beverages ,General Medicine ,macromolecular substances ,Catalysis ,Article ,localization ,Computer Science Applications ,morphological defects ,Inorganic Chemistry ,Chemistry ,OsFH3 ,Physical and Theoretical Chemistry ,Biology (General) ,Molecular Biology ,QD1-999 ,Spectroscopy - Abstract
The actin cytoskeleton is crucial for plant morphogenesis, and organization of actin filaments (AF) is dynamically regulated by actin-binding proteins. However, the roles of actin-binding proteins, particularly type II formins, in this process remain poorly understood in plants. Here, we report that a type II formin in rice, Oryza sativa formin homolog 3 (OsFH3), acts as a major player to modulate AF dynamics and contributes to rice morphogenesis. osfh3 mutants were semi-dwarf with reduced size of seeds and unchanged responses to light or gravity compared with mutants of osfh5, another type II formin in rice. osfh3 osfh5 mutants were dwarf with more severe developmental defectiveness. Recombinant OsFH3 could nucleate actin, promote AF bundling, and cap the barbed end of AF to prevent elongation and depolymerization, but in the absence of profilin, OsFH3 could inhibit AF elongation. Different from other reported type II formins, OsFH3 could bind, but not bundle, microtubules directly. Furthermore, its N-terminal phosphatase and tensin homolog domain played a key role in modulating OsFH3 localization at intersections of AF and punctate structures of microtubules, which differed from other reported plant formins. Our results, thus, provide insights into the biological function of type II formins in modulating plant morphology by acting on AF dynamics.
- Published
- 2021
- Full Text
- View/download PDF
32. SMALL REPRODUCTIVE ORGANS, a SUPERMAN-like transcription factor, regulates stamen and pistil growth in rice
- Author
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Wanwan Zhu, Zhijing Luo, Dabing Zhang, Liu Yang, Ludovico Dreni, Hui Li, Li Yang, Wei Xu, Lei Duan, Guoqiang Huang, Wanqi Liang, and Mingjiao Chen
- Subjects
Zinc finger ,Gynoecium ,Cell division ,Physiology ,Meristem ,Stamen ,food and beverages ,Oryza ,Plant Science ,Flowers ,Biology ,biology.organism_classification ,Cell biology ,Floral meristem determinacy ,Gene Expression Regulation, Plant ,Arabidopsis ,Genitalia ,Gene ,Transcription factor ,Plant Proteins ,Transcription Factors - Abstract
Organ size is mainly determined by cell division and cell expansion. Several genetic factors regulating development of plant lateral organs have been characterised, 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-localised C2 H2 zinc finger protein orthologous to Arabidopsis transcription factor SUPERMAN (SUP). Combined developmental, genetic, histological and transcriptomic analyses were used to determine the function of SRO in regulating reproductive organ size. SRO affects genes involved in cell division, cell expansion and phytohormone signalling in the rice flower. SRO is specifically expressed in the first stages of stamen filament development to regulate their correct formation and separation. In addition, SRO non-cell-autonomously regulates the size and functionality of male and female reproductive organs. The B-class MADS-box gene OsMADS16/SPW1 is epistatic to SRO, while SRO regulates reproductive organ specification and floral meristem determinacy synergistically with C-class genes OsMADS3 and OsMADS58. These findings provide insights into how an evolutionarily conserved transcription factor has a pivotal role in reproductive organ development in core eudicots and monocots, through partially conserved expression, function, and regulatory network.
- Published
- 2021
33. RIPs Interact with OsFH5 and Control the Rice Morphology by Affecting Stability of OsFH5
- Author
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Qi Xie, Shuwei Chang, Wanwan Zhu, Guoqiang Huang, Duoxiang Wang, Litao Yang, Wanqi Liang, and Dabing Zhang
- Subjects
Chemistry ,Stability (learning theory) ,Morphology (biology) ,Biological system ,Control (linguistics) - Abstract
E3 ubiquitin ligases have been more widely reported to mediate the degradation of target proteins. In our research, one SIAH type E3 ligase was identified, named RIP1, and there are five genes were found to be highly homologous to it, named RIP2 to RIP6 dividedly. Y2H and BiFC were carried out to prove the interaction between RIPs and OsFH5, moreover, homo- and hetero- oligomers can be formed among RIPs and they all can affect the localization of OsFH5. Degradation experiments showed that RIP1 is able to slow down the degradation rate of OsFH5, and also RIP5, RIP6. There was no obvious phenotype in both RIP1 overexpression and mutant transgenic lines, whereas in rips multi-knock out lines showed up similar defects to osfh5, such as, dwarf height; less smooth and rounder seeds; leaves width became wilder. Otherwise, rips also exhibit some special phenotypes, for instance, the angles between leaves and stems were appreciable enlarged; spiral crimped roots. In addition, microfilaments organization in rips appeared disordered than wild type. All above illustrate that RIPs influence morphology by interacting with OsFH5 and affecting its subcellular localization, stability or maybe involved in other pathways in rice.
- Published
- 2021
34. Gibberellins orchestrate panicle architecture mediated by DELLA-KNOX signalling in rice
- Author
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Qiaoquan Liu, Su Su, Changquan Zhang, Zhijing Luo, Mingjiao Chen, Xiaofei Chen, Jun Hong, Wanqi Liang, Shaoxing Bai, Shuwei Chang, and Dabing Zhang
- Subjects
Mutant ,Meristem ,Plant Science ,Biology ,Quantitative trait locus ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Gibberellin ,Gibberellic acid ,Research Articles ,Panicle ,Plant Proteins ,rice ,food and beverages ,Oryza ,Gibberellins ,Cell biology ,Complementation ,chemistry ,signalling pathway ,panicle architecture ,Homeobox ,SLR1 ,biosynthesis ,Agronomy and Crop Science ,KNOX class 1 ,Biotechnology ,Research Article - Abstract
Summary Panicle architecture is a key determinant of grain yield in cereals, but the mechanisms governing panicle morphogenesis and organ development remain elusive. Here, we have identified a quantitative trait locus (qPA1) associated with panicle architecture using chromosome segment substitution lines from parents Nipponbare and 9311. The panicle length, branch number and grain number of Nipponbare were significantly higher than CSSL‐9. Through map‐based cloning and complementation tests, we confirmed that qPA1 was identical to SD1 (Semi Dwarf1), which encodes a gibberellin 20‐oxidase enzyme participating in gibberellic acid (GA) biosynthesis. Transcript analysis revealed that SD1 was widely expressed during early panicle development. Analysis of sd1/osga20ox2 and gnp1/ osga20ox1 single and double mutants revealed that the two paralogous enzymes have non‐redundant functions during panicle development, likely due to differences in spatiotemporal expression; GNP1 expression under control of the SD1 promoter could rescue the sd1 phenotype. The DELLA protein SLR1, a component of the GA signalling pathway, accumulated more highly in sd1 plants. We have demonstrated that SLR1 physically interacts with the meristem identity class I KNOTTED1‐LIKE HOMEOBOX (KNOX) protein OSH1 to repress OSH1‐mediated activation of downstream genes related to panicle development, providing a mechanistic link between gibberellin and panicle architecture morphogenesis.
- Published
- 2021
35. Rice SEPALLATA genes OsMADS5 and OsMADS34 cooperate to limit inflorescence branching by repressing the TERMINAL FLOWER1-like gene RCN4
- Author
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Wanwan, Zhu, Liu, Yang, Di, Wu, Qingcai, Meng, Xiao, Deng, Guoqiang, Huang, Jiao, Zhang, Xiaofei, Chen, Cristina, Ferrándiz, Wanqi, Liang, Ludovico, Dreni, and Dabing, Zhang
- Subjects
Gene Expression Regulation, Plant ,Meristem ,Oryza ,Inflorescence ,Plant Proteins - 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.
- Published
- 2021
36. Defective Pollen Wall 3 (DPW3), a novel alpha integrin‐like protein, is required for pollen wall formation in rice
- Author
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Jianping Hu, Xiaofei Chen, Palash Chandra Mondol, Lei Duan, Dawei Xu, Dabing Zhang, Wanqi Liang, Mingjiao Chen, Jianxin Shi, and Canhua Wang
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Ubisch body ,Stamen ,Golgi Apparatus ,Plant Science ,Biology ,Endoplasmic Reticulum ,medicine.disease_cause ,01 natural sciences ,Plant Epidermis ,03 medical and health sciences ,chemistry.chemical_compound ,symbols.namesake ,Microspore ,Gene Expression Regulation, Plant ,Pollen ,Tobacco ,medicine ,Conserved Sequence ,Phylogeny ,Plant Proteins ,Gametophyte ,Base Sequence ,Cell Membrane ,Callose ,food and beverages ,Oryza ,Golgi apparatus ,Cell biology ,Phenotype ,030104 developmental biology ,chemistry ,symbols ,Integrin alpha Chains ,Pollen wall ,010606 plant biology & botany - 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.
- Published
- 2019
37. Integrating GWAS and transcriptomics to identify genes involved in seed dormancy in rice
- Author
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Jin Shi, Jianxin Shi, Wanqi Liang, and Dabing Zhang
- Subjects
Quantitative Trait Loci ,Seeds ,food and beverages ,Germination ,Oryza ,Genes, Plant ,Plant Dormancy ,Transcriptome ,Polymorphism, Single Nucleotide ,Genetic Association Studies - 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 hampered 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.
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- 2021
38. AUXIN RESPONSE FACTORS 6 and 17 control the flag leaf angle in rice by regulating secondary cell wall biosynthesis of lamina joints
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Jiao Zhang, Le Dong, Allison M. L. van de Meene, Natalie S. Betts, Heng Hu, Shuai Zheng, Guoqiang Huang, Dabing Zhang, Staffan Persson, Wanqi Liang, Fengli Zhang, and Malcolm J. Bennett
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0106 biological sciences ,Lamina ,AcademicSubjects/SCI01280 ,Mutant ,Plant Science ,Biology ,01 natural sciences ,03 medical and health sciences ,Auxin ,Cell Wall ,Gene ,Research Articles ,030304 developmental biology ,Plant Proteins ,chemistry.chemical_classification ,0303 health sciences ,Oryza sativa ,AcademicSubjects/SCI01270 ,AcademicSubjects/SCI02288 ,AcademicSubjects/SCI02287 ,fungi ,AcademicSubjects/SCI02286 ,food and beverages ,Oryza ,Cell Biology ,Phenotype ,Cell biology ,Plant Leaves ,chemistry ,Secondary cell wall ,010606 plant biology & botany ,Flag (geometry) ,Transcription Factors - Abstract
Flag leaf angle impacts the photosynthetic capacity of densely grown plants and is thus an important agronomic breeding trait for crop architecture and yield. The hormone auxin plays a key role in regulating this trait, yet the underlying molecular and cellular mechanisms remain unclear. Here, we report that two rice (Oryza sativa) auxin response factors (ARFs), OsARF6 and OsARF17, which are highly expressed in lamina joint tissues, control flag leaf angle in response to auxin. Loss-of-function double osarf6 osarf17 mutants displayed reduced secondary cell wall levels of lamina joint sclerenchymatous cells (Scs), resulting in an exaggerated flag leaf angle and decreased grain yield under dense planting conditions. Mechanical measurements indicated that the mutant lamina joint tissues were too weak to support the weight of the flag leaf blade, resembling the phenotype of the rice increased leaf angle1 (ila1) mutant. We demonstrate that OsARF6 and OsARF17 directly bind to the ILA1 promoter independently and synergistically to activate its expression. In addition, auxin-induced ILA1 expression was dependent on OsARF6 and OsARF17. Collectively, our study reveals a mechanism that integrates auxin signaling with the secondary cell wall composition to determine flag leaf angle, providing breeding targets in rice, and potentially other cereals, for this key trait., Two auxin response genes influence the secondary cell wall biosynthesis and the strength of lamina joints, thereby contributing to the adjustment of flag leaf angles.
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- 2021
39. Transcriptome Analysis Reveals Photoperiod-Associated Genes Expressed in Rice Anthers
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Wanqi Liang, Shiyu Sun, Jingbin Li, Xiangxiang Zhao, Dabing Zhang, Wenguo Cai, Duoxiang Wang, Gang Li, and Yaqi Lei
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Genetics ,photoperiodism ,rice anther ,WGCNA ,Period (gene) ,Stamen ,food and beverages ,Plant Science ,Biology ,phytohormone ,lcsh:Plant culture ,medicine.disease_cause ,photoperiod ,Transcriptome ,PGMS ,carbohydrate ,Pollen ,Gene expression ,transport ,medicine ,lcsh:SB1-1110 ,Gene ,transcriptome ,Pollen maturation ,Original Research - Abstract
Environmental conditions, such as photoperiod and temperature, can affect male fertility in plants. While this feature is heavily exploited in rice to generate male-sterile lines for hybrid breeding, the underlying molecular mechanisms remain largely unknown. In this study, we use a transcriptomics approach to identify key genes and regulatory networks affecting pollen maturation in rice anthers in response to different day lengths. A total of 11,726 differentially expressed genes (DEGs) were revealed, of which 177 were differentially expressed at six time points over a 24-h period. GO enrichment analysis revealed that genes at all time points were enriched in transport, carbohydrate, and lipid metabolic processes, and signaling pathways, particularly phytohormone signaling. In addition, co-expression network analysis revealed four modules strongly correlated with photoperiod. Within these four modules, 496 hub genes were identified with a high degree of connectivity to other photoperiod-sensitive DEGs, including two previously reported photoperiod- and temperature-sensitive genes affecting male fertility, Carbon Starved Anther and UDP-glucose pyrophosphorylase, respectively. This work provides a new understanding on photoperiod-sensitive pollen development in rice, and our gene expression data will provide a new, comprehensive resource to identify new environmentally sensitive genes regulating male fertility for use in crop improvement.
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- 2021
40. Automated High-Resolution Structure Analysis of Plant Root with a Morphological Image Filtering Algorithm
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Liang Gong, Xiaofeng Du, Chenhui Lin, Kai Zhu, Chengliang Liu, and Wanqi Liang
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0106 biological sciences ,0301 basic medicine ,Article Subject ,General Mathematics ,General Engineering ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,Engineering (General). Civil engineering (General) ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,QA1-939 ,TA1-2040 ,Mathematics ,010606 plant biology & botany - Abstract
Research on rice (Oryza sativa) roots demands the automatic analysis of root architecture during image processing. It is challenging for a digital filter to identify the roots from the obscure and cluttered background. The original Frangi algorithm, presented by Alejandro F. Frangi in 1998, is a successful low-pass filter dedicated to blood vessel image enhancement. Considering the similarity between vessels and roots, the Frangi filter algorithm is applied to outline the roots. However, the original Frangi only enhances the tube-like primary roots but erases the lateral roots during filtering. In this paper, an improved Frangi filtering algorithm (IFFA), designed for plant roots, is proposed. Firstly, an automatic root phenotyping system is designed to fulfill the high-throughput root image acquisition. Secondly, multilevel image thresholding, connected components labeling, and width correction are used to optimize the output binary image. Thirdly, to enhance the local structure, the Gaussian filtering operator in the original Frangi is redesigned with a truncated Gaussian kernel, resulting in more discernible lateral roots. Compared to the original Frangi filter and commercially available software, IFFA is faster and more accurate, achieving a pixel accuracy of 97.48%. IFFA is an effective morphological filtering approach to enhance the roots of rice for segmentation and further biological research. It is convincing that IFFA is suitable for different 2-D plant root image processing and morphological analysis.
- Published
- 2021
41. Rice OsBRCA2 Is Required for DNA Double-Strand Break Repair in Meiotic Cells
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Hongyu Shen, James D. Higgins, Ruifeng Fu, Chong Wang, Jie Zhang, and Wanqi Liang
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0106 biological sciences ,0301 basic medicine ,DNA repair ,RAD51 ,Synapsis ,homologous recombination ,Plant Science ,lcsh:Plant culture ,Biology ,BRCA2 ,01 natural sciences ,Double Strand Break Repair ,Cell biology ,03 medical and health sciences ,DMC1 ,030104 developmental biology ,Meiosis ,Homologous chromosome ,meiosis ,lcsh:SB1-1110 ,Homologous recombination ,Original Research ,010606 plant biology & botany - Abstract
The mammalian BREAST CANCER 2 (BRCA2) gene is a tumor suppressor that plays a crucial role in DNA repair and homologous recombination (HR). Here, we report the identification and characterization of OsBRCA2, the rice orthologue of human BRCA2. Osbrca2 mutant plants exhibit normal vegetative growth but experience complete male and female sterility as a consequence of severe meiotic defects. Pairing, synapsis and recombination are impaired in osbrca2 male meiocytes, leading to chromosome entanglements and fragmentation. In the absence of OsBRCA2, localization to the meiotic chromosome axes of the strand-invasion proteins OsRAD51 and OsDMC1 is severely reduced and in vitro OsBRCA2 directly interacts with OsRAD51 and OsDMC1. These results indicate that OsBRCA2 is essential for facilitating the loading of OsRAD51 and OsDMC1 onto resected ends of programmed double-strand breaks (DSB) during meiosis to promote single-end invasions of homologous chromosomes and accurate recombination. In addition, treatment of osbrca2-1 seedlings with mitomycin C (MMC) led to hypersensitivity. As MMC is a genotoxic agent that creates DNA lesions in the somatic cells that can only be repaired by HR, these results suggest that OsBRCA2 has a conserved role in DSB repair and HR in rice.
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- 2020
42. MADS1 maintains barley spike morphology at high ambient temperatures
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Gang, Li, Hendrik N J, Kuijer, Xiujuan, Yang, Huiran, Liu, Chaoqun, Shen, Jin, Shi, Natalie, Betts, Matthew R, Tucker, Wanqi, Liang, Robbie, Waugh, Rachel A, Burton, and Dabing, Zhang
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Crops, Agricultural ,Hot Temperature ,Phenotype ,Genotype ,Gene Expression Regulation, Plant ,Australia ,Genetic Variation ,Hordeum ,MADS Domain Proteins ,Inflorescence ,Genes, Plant - Abstract
Temperature stresses affect plant phenotypic diversity. The developmental stability of the inflorescence, required for reproductive success, is tightly regulated by the interplay of genetic and environmental factors. However, the mechanisms underpinning how plant inflorescence architecture responds to temperature are largely unknown. We demonstrate that the barley SEPALLATA MADS-box protein HvMADS1 is responsible for maintaining an unbranched spike architecture at high temperatures, while the loss-of-function mutant forms a branched inflorescence-like structure. HvMADS1 exhibits increased binding to target promoters via A-tract CArG-box motifs, which change conformation with temperature. Target genes for high-temperature-dependent HvMADS1 activation are predominantly associated with inflorescence differentiation and phytohormone signalling. HvMADS1 directly regulates the cytokinin-degrading enzyme HvCKX3 to integrate temperature response and cytokinin homeostasis, which is required to repress meristem cell cycle/division. Our findings reveal a mechanism by which genetic factors direct plant thermomorphogenesis, extending the recognized role of plant MADS-box proteins in floral development.
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- 2020
43. Rice transcription factor MADS32 regulates floral patterning through interactions with multiple floral homeotic genes
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Yu Yu, Jie Xu, Jiayang Xie, Zheng Yuan, Zhijing Luo, Staffan Persson, Ben Xu, Li Wang, Dan Lu, Liming Cao, Yun Hu, Ru Jia, Mingjiao Chen, Xiaofei Chen, Dabing Zhang, Wanqi Liang, and Xuelian Zhang
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Gynoecium ,Subfamily ,Physiology ,fungi ,Stamen ,Genes, Homeobox ,food and beverages ,MADS Domain Proteins ,Oryza ,Plant Science ,Flowers ,Biology ,Meristem ,Orphan gene ,Phenotype ,Evolutionary biology ,Gene Expression Regulation, Plant ,Homeobox ,Homeotic gene ,Transcription factor ,reproductive and urinary physiology ,Plant Proteins ,Transcription Factors - Abstract
Floral patterning is regulated by intricate networks of floral identity genes. The peculiar MADS32 subfamily genes, absent in eudicots but prevalent in monocots, control floral organ identity. However, how the MADS32 family genes interact with other floral homeotic genes during flower development is mostly unknown. We show here that the rice homeotic transcription factor OsMADS32 regulates floral patterning by interacting synergistically with E class protein OsMADS6 in a dosage-dependent manner. Furthermore, our results indicate important roles for OsMADS32 in defining stamen, pistil, and ovule development through physical and genetic interactions with OsMADS1, OsMADS58, and OsMADS13, and in specifying floral meristem identity with OsMADS6, OsMADS3, and OsMADS58, respectively. Our findings suggest that OsMADS32 is an important factor for floral meristem identity maintenance and that it integrates the action of other MADS-box homeotic proteins to sustain floral organ specification and development in rice. Given that OsMADS32 is an orphan gene and absent in eudicots, our data substantially expand our understanding of flower development in plants.
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- 2020
44. NERD1 is required for primexine formation and plasma membrane undulation during microsporogenesis in Arabidopsis thaliana
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Wanqi Liang, Dabing Zhang, Dawei Xu, Sumie Ishiguro, Jianxin Shi, and Palash Chandra Mondol
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Tapetum ,Callose ,Stamen ,food and beverages ,Plant Science ,medicine.disease_cause ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Pollen exine formation ,Cell biology ,chemistry.chemical_compound ,chemistry ,Sporopollenin ,Microspore ,Pollen ,Locule ,Genetics ,medicine ,Agronomy and Crop Science ,Molecular Biology ,Biotechnology ,Research Article - Abstract
The primexine formation and plasma membrane undulation are the crucial steps of pollen wall formation in many angiosperms. However, the molecular mechanism underlining these processes is largely unknown. In Arabidopsis, NEW ENHANCER OF ROOT DWARFISM1 (NERD1), a transmembrane protein, was reported to play pleiotropic roles in plant development including male fertility control; while, how NERD1 disruption impacts male reproduction is yet unclear. Here, we revealed that the male sterility of nerd1 mutants is attributed to defects in early steps of pollen wall formation. We found that nerd1-2 is void of primexine formation and microspore plasma membrane undulation, defective in callose deposition. Consequently, sporopollenin precursors are unable to deposit and assemble on the microspore surface, but instead accumulated in the anther locule and tapetal cells, and ultimately leading to microspore abortion. NERD1 is localized in the Golgi and is expressed in both vegetative and reproductive organs, with the highest expression in reproductive tissues, including the tapetum, male meiocytes, tetrads and mature pollen grains. Our results suggest that NERD1 is required for the primexine deposition and microspore plasma membrane undulation, thus essential for sporopollenin assembly and pollen exine formation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42994-020-00022-1) contains supplementary material, which is available to authorized users.
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- 2020
45. Automated high-resolution structure analysis of plant root with a morphological image filtering algorithm
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Chenhui Lin, Chenliang Liu, Wilson Joe, Jun Hong, Kai Zhu, Liang Gong, and Wanqi Liang
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symbols.namesake ,Pixel ,Computer science ,Binary image ,Gaussian function ,symbols ,Segmentation ,Image processing ,Filter (signal processing) ,Digital filter ,Algorithm ,Thresholding - Abstract
Background: Research on rice (Oryza sativa) roots requires the automatic analysis of root structure using image processing. It is challenging for a digital filter to identify the roots from the obscured and cluttered background, and to separate the primary roots from lateral roots. The original Frangi filter (FF), presented by Alejandro F. Frangi in 1998, is a low-pass filter dedicated to blood vessel image enhancement. Considering the similarity between vessels and roots, the FF is applied to identify the roots. However, the original FF only enhances the tube-like primary roots but erases the lateral roots. Hence, a new method is developed to meet the demands by simultaneously maintaining the primary and lateral morphological structure of roots. Result: In this work, a crucial part of the FF, Gaussian filtering, is redesigned to discriminate against the primary and lateral roots in a 2-D image. Inspired by the structure-awareness of the FF, an Improved Frangi Filtering Algorithm (IFFA) designed for plant roots is proposed. First, Multilevel image thresholding, connected-components labeling and width correction are used to optimize the resultant binary image. Then, to enhance the local structure, the truncated Gaussian kernel is modified resulting in more discernible lateral roots. Compared to the original FF and the Automatic Root Image Analysis (ARIA), a commercial software, IFFA is a faster and more accurate algorithm achieving an identification accuracy of 97.48%. Conclusion: IFFA is an effective 2-D filtering approach to enhance the roots of rice (Oryza sativa) for segmentation and further biological research. IFFA is faster than ARIA and the original FF, and IFFA’s accuracy outperforms its counterparts as per the Intersection Over Union (IOU) and Dice Similarity Coefficient (DSC) criteria.
- Published
- 2020
46. Genome-wide analysis of RopGEF gene family to identify genes contributing to pollen tube growth in rice (Oryza sativa)
- Author
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Eui Jung Kim, Dabing Zhang, Wanqi Liang, Jeniffer Silva, Yu-Jin Kim, Sung Wook Park, Ki-Hong Jung, and Woo Jong Hong
- Subjects
0106 biological sciences ,0301 basic medicine ,Nicotiana benthamiana ,Oryza sativa ,Plant Science ,RopGEF ,Pollen Tube ,medicine.disease_cause ,Genes, Plant ,01 natural sciences ,03 medical and health sciences ,lcsh:Botany ,Arabidopsis ,Pollen ,medicine ,Gene family ,Gene ,Plant Proteins ,Genetics ,biology ,food and beverages ,Promoter ,Oryza ,biology.organism_classification ,lcsh:QK1-989 ,030104 developmental biology ,ROP/Rac ,Multigene Family ,Pollen tube ,010606 plant biology & botany ,Research Article ,Genome-Wide Association Study - Abstract
Background In plants, the key roles played by RopGEF-mediated ROP signaling in diverse processes, including polar tip growth, have been identified. Despite their important roles in reproduction, a comprehensive analysis of RopGEF members has not yet been performed in rice (Oryza sativa). To determine whether RopGEF regulators are involved in rice pollen tube growth, we performed genome-wide analysis of this family in rice. Results Phylogenomic and meta-expression analysis of eleven RopGEFs in rice showed that four genes were preferentially expressed in mature pollen. These four genes contain the plant-specific Rop nucleotide exchanger (PRONE) domain and possible phosphorylated residues, suggesting a conserved role in polar tip growth with Arabidopsis thaliana. In subcellular localization analysis of the four RopGEFs through tobacco (Nicotiana benthamiana) infiltration, four proteins were predominantly identified in plasma membrane. Moreover, double mutants of RopGEF2/8 exhibited reduced pollen germination, causing partial male sterility. These genes possess unique cis-acting elements in their promoters compared with the other RopGEF genes. Conclusions In this study, four RopGEF genes were identified as pollen-specific gene in eleven members of rice, and the expression pattern, promoter analysis, and evolutionary relationship of the RopGEF family were studied compared with Arabidopsis. Our study indicated that four RopGEF genes might function during pollen germination in distinct subcellular localization. Our study could provide valuable information on the functional study of RopGEF in rice.
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- 2020
47. DWT1/DWL2 act together with OsPIP5K1 to regulate plant uniform growth in rice
- Author
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Malcolm J. Bennett, Fang Fang, Jingyao Tang, Shiwei Ye, and Wanqi Liang
- Subjects
Phosphatidylinositol 4,5-Diphosphate ,0106 biological sciences ,0301 basic medicine ,Physiology ,Amino Acid Motifs ,Regulator ,Plant Development ,Dwarfism ,Plant Science ,Biology ,01 natural sciences ,03 medical and health sciences ,Gene Expression Regulation, Plant ,medicine ,Transcription factor ,Plant Proteins ,Cell Nucleus ,food and beverages ,Oryza ,Plants, Genetically Modified ,medicine.disease ,Phenotype ,Hedgehog signaling pathway ,Cell biology ,Protein Transport ,030104 developmental biology ,Mutation ,Second messenger system ,Shoot ,DWT1, DWL2, Nuclear signalling, Phosphatidylinositol-4-phosphate 5-kinase, Phosphoinositide, PIP5K, Plant uniformity, WOX ,Homeobox ,Protein Binding ,010606 plant biology & botany - Abstract
•Uniform growth of the main shoot and tillers significantly influences rice plant architecture and grain yield. The WUSCHEL‐related homeobox transcription factor DWT1 is a key regulator of this important agronomic trait, disruption of which causes enhanced main shoot dominance and tiller dwarfism by an unknown mechanism. •Here, we have used yeast‐two‐hybrid screening to identify OsPIP5K1, a member of the rice phosphatidylinositol‐4‐phosphate 5‐kinase family, as a protein that interacts with DWT1. Cytological analyses confirmed that DWT1 induces accumulation of OsPIP5K1 and its product PI(4,5)P2, a phosphoinositide secondary messenger, in nuclear bodies. •Mutation of OsPIP5K1 compounds the dwarf dwt1 phenotype but abolishes the main shoot dominance. Conversely, overexpression of OsPIP5K1 partially rescues dwt1 developmental defects. Furthermore, we showed that DWL2, the homologue of DWT1, is also able to interact with OsPIP5K1 and shares partial functional redundancy with DWT1 in controlling rice uniformity. •Overall, our data suggest that nuclear localised OsPIP5K1 acts with DWT1 and/or DWL2 to coordinate the uniform growth of rice shoots, likely to be through nuclear phosphoinositide signals, and provides insights into the regulation of rice uniformity via a largely unexplored plant nuclear signalling pathway.
- Published
- 2020
48. Additional file 9 of Genome-wide analysis of RopGEF gene family to identify genes contributing to pollen tube growth in rice (Oryza sativa)
- Author
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Kim, Eui-Jung, Park, Sung-Wook, Woo-Jong Hong, Silva, Jeniffer, Wanqi Liang, Dabing Zhang, Jung, Ki-Hong, and Kim, Yu-Jin
- Abstract
Additional file 9: Table S2. OsRopGEF isogene-specific primers for qPCR and cloning.
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- 2020
- Full Text
- View/download PDF
49. Additional file 2 of Genome-wide analysis of RopGEF gene family to identify genes contributing to pollen tube growth in rice (Oryza sativa)
- Author
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Kim, Eui-Jung, Park, Sung-Wook, Woo-Jong Hong, Silva, Jeniffer, Wanqi Liang, Dabing Zhang, Jung, Ki-Hong, and Kim, Yu-Jin
- Subjects
genetic structures - Abstract
Additional file 2: Figure S2. Meta-expression analysis of entire AtRopGEF genes. The heatmap was prepared using the Genevestigator. We chose five representative tissues, including pollen. It revealed that five Arabidopsis RopGEFs were highly expressed in pollen. The dark red color of the heatmap indicated the highest expression; white color, lowest expression.
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- 2020
- Full Text
- View/download PDF
50. Additional file 3 of Genome-wide analysis of RopGEF gene family to identify genes contributing to pollen tube growth in rice (Oryza sativa)
- Author
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Kim, Eui-Jung, Park, Sung-Wook, Woo-Jong Hong, Silva, Jeniffer, Wanqi Liang, Dabing Zhang, Jung, Ki-Hong, and Kim, Yu-Jin
- Abstract
Additional file 3: Figure S3. Protein sequence alignment domain analysis and conserved phosphorylated amino acid residues of C-termini of RopGEF genes. Every OsRopGEF and AtRopGEF protein sequence was collected and aligned, followed by the PRONE domain (C1, C2, C3) and the WW-motif. At the end part of the sequence, we found some conserved regions. According to previous studies, S510 in the C-terminus of AtRopGEF12 is involved in the C-terminal inhibition of GEF activity. As in AtRopGEF12, the serine residue is conserved in each of the OsRopGEF2, OsRopGEF3, and OsRopGEF8 genes but not in OsRopGEF6. However, K (Lysine) can also be phosphorylated.
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- 2020
- Full Text
- View/download PDF
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