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| 1 | Control of Leaf Senescence by an MeOH- Jasmonates Cascade that Is Epigenetically Regulated by OsSRT1 in Rice显示文摘 | ChuanYing Fang Hua Zhang Jian Wan YangYang Wu Kang Li Cheng Jin Wei Chen ShouChuang Wang WenSheng Wang HaiWei Zhang Pan Zhang Fei Zhang LiangHuan Qu Xianqing Liu Dao-Xiu Zhou Jie Luo | 2016 | Molecular Plant2016，9，10： | 14 |
| 2 | The Structure and Function of Major Plant Metabolite Modifications显示文摘Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality. | Shouchuang Wang Saleh Alseekh Alisdair R.Fernie Jie Luo | 2019 | Molecular Plant2019，12，7： | 13 |
| 3 | Manipulation of SlMXl for enhanced carotenoids accumulation and drought resistance in tomato显示文摘Plants are the ultimate source of nutrients in the human diet. To ensure adequate availability of high quality food for an increasing world population, traits including improved tolerance of stresses and nutrient levels need to be selected in crops, both individually and in combination. Here we report the identification of Sl MX1 encoding a MIXTA-like MYB transcription factor in tomato that simultaneously modulates drought resistance and metabolic processes through regulating key structural and regulatory genes of the corresponding pathways. Over-expression of Sl MX1 results in substantially increased drought tolerance and improved fruit quality, while knocking down Sl MX1 resulted in the opposite phenotypes. Our study indicates an effective way with multiple beneficial traits by genetic engineering of a single regulatory gene and can be a novel approach to breeding crops. | Mohamed Ewas Yanqiang Gao Shouchuang Wang Xianqing Liu Hongyan Zhang Elsayed M. E. Nishawy Farhan Aii Raheel Shahzad Khurram Ziaf Hizar Subthain Cathie Martin Jie Luo | 2016 | Science Bulletin2016，61，18： | 9 |
| 4 | Rice metabolic regulatory network spanning the entire life cycle显示文摘As one of the most important crops in the world,rice(Oryza sativa)is a model plant for metabolome research.Although many studies have focused on the analysis of specific tissues,the changes in metab-olite abundance across the entire life cycle have not yet been determined.In this study,combining both tar-geted and nontargeted metabolite profiling methods,a total of 825 annotated metabolites were quantified in rice samples from different tissues covering the entire life cycle.The contents of metabolites in different tissues of rice were significantly different,with various metabolites accumulating in the plumule and radicle during seed germination.Combining these data with transcriptome data obtained from the same time period,we constructed the Rice Metabolic Regulation Network.The metabolites and co-expressed genes were further divided into 12 clusters according to their accumulation patterns,with members within each cluster displaying a uniform and clear pattern of abundance across development.Using this dataset,we established a comprehensive metabolic profile of the rice life cycle and used two independent strategies to identify novel transcription factors-namely the use of known regulatory genes as bait to screen for new networks underlying lignin metabolism and the unbiased identification of new glycerophospholipid metabolism regulators on the basis of tissue specificity.This study thus demonstrates how guilt-by-association analysis of metabolome and transcriptome data spanning the entire life cycle in cereal crops provides novel resources and tools to aid in understanding the mechanisms underlying important agro-nomic traits. | Chenkun Yang Shuangqian Shen Shen Zhou Yufei Li Yuyuan Mao Junjie Zhou Yuheng Shi Longxu An Qianqian Zhou Wenju Peng Yuanyuan Lyu Xuemei Liu Wei Chen Shouchuang Wang Lianghuan Qu Xianqing Liu Alisdair R.Fernie Jie Luo | 2022 | Molecular Plant2022，15，2： | 3 |
| 5 | OsRLCK160 contributes to flavonoid accumulation and UV-B tolerance by regulating OsbZIP48 in rice显示文摘Plants produce specialized metabolites to adapt to the ever-changing environments.Flavonoids are antioxidants essential for growth,development,and breeding with increased stress resistance in crops.However,the mechanism of the involvement of flavonoids in ultraviolet-B(UV-B)stress in rice(Oryza sativa)is largely unknown.In this study,we cloned and functionally identified a receptor-like kinase(OsRLCK160)and a bZIP transcription factor(OsbZIP48)positively regulating flavonoid accumulation through metabolite-based genome-wide association study of the flavonoid content in rice.Meanwhile,OsRLCK160 interacted with and phosphorylated OsbZIP48 to regulate the flavonoid accumulation and participate in UV-B tolerance in rice.Our study indicates the importance of applying OsRLCK160 and OsbZIP48 to advance the fundamental understanding of stable rice production and breed UV-B-tolerant rice varieties,which may contribute to breeding high-yield rice varieties. | Feng Zhang Jiacheng Huang Hao Guo Chenkun Yang Yufei Li Shuangqian Shen Chuansong Zhan Lianghuan Qu Xianqing Liu Shouchuang Wang Wei Chen Jie Luo | 2022 | Science China(Life Sciences)2022，65，7： | 2 |
| 6 | Hybrid Optimization-Based GRU Neural Network for Software Reliability Prediction显示文摘Aiming at the problems of low prediction accuracy and weak generalization ability of current reliability prediction models,this paper proposes a hybrid multi-layer heterogeneous particle swarm optimization algorithm(HMHPSO)that can simultaneously optimize the structure and parameters of the GRU neural network.It first introduced a multi-layer heteromass particle swarm optimization(MHPSO)algorithm,which sets the population topology as a hierarchical structure and introduces the concept of attractors,so as to improve the update formula of particle speed,and enhance the information interaction ability between particles,increase the diversity of the groups,thereby improving the optimization ability of the algorithm.Then the HMHPSO used the quantum particle swarm optimization(QPSO)algorithm to determine the structure of the GRU,that is,the number of hidden nodes.Experimental results show that the algorithm can generate GRU neural networks with high generalization performance and low architecture complexity,and has better prediction accuracy in software reliability prediction. | Maochuan Wu Junyu Lin Shouchuang Shi Long Ren Zhiwen Wang | 2020 | 国际计算机前沿大会会议论文集2020，，2： | 0 |
| 7 | Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity显示文摘DNA methylation is an important epigenetic marker,yet its diversity and consequences in tomato breeding at the population level are largely unknown.We performed whole-genome bisulfite sequencing(WGBS),RNA sequencing,and metabolic profiling on a population comprising wild tomatoes,landraces,and cultivars.A total of 8,375 differentially methylated regions(DMRs)were identified,with methylation levels progressively decreasing from domestication to improvement.We found that over 20%of DMRs overlapped with selective sweeps.Moreover,more than 80%of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms(SNPs),and DMRs had strong linkages with adjacent SNPs.We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs.We detected 971 and 711 large-effect loci via SNP and DMR markers,respectively.Combined with multi-omics,we identified 13 candidate genes and updated the polyphenol biosynthetic pathway.Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity.Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants. | Hao Guo Peng Cao Chao Wang Jun Lai Yuan Deng Chun Li Yingchen Hao Zeyong Wu Ridong Chen Qi Qiang Alisdair RFernie Jun Yang Shouchuang Wang | 2023 | Science China(Life Sciences)2023，66，8： | 0 |
| 8 | Targeted approaches to improve tomato fruit taste显示文摘Tomato(Solanum lycopersicum)is the most valuable fruit and horticultural crop species worldwide.Compared with the fruits of their progenitors,those of modern tomato cultivars are,however,often described as having unsatisfactory taste or lacking f lavor.The f lavor of a tomato fruit arises from a complex mix of tastes and volatile metabolites,including sugars,acids,amino acids,and various volatiles.However,considerable differences in fruit f lavor occur among tomato varieties,resulting in mixed consumer experiences.While tomato breeding has traditionally been driven by the desire for continual increases in yield and the introduction of traits that provide a long shelf-life,consumers are prepared to pay a reasonable premium for taste.Therefore,it is necessary to characterize preferences of tomato f lavor and to define its underlying genetic basis.Here,we review recent conceptual and technological advances that have rendered this more feasible,including multi-omics-based QTL and association analyses,along with the use of trained testing panels,and machine learning approaches.This review proposes how the comprehensive datasets compiled to date could allow a precise rational design of tomato germplasm resources with improved organoleptic quality for the future. | Shouchuang Wang Qi Qiang Lijun Xiang Alisdair R.Fernie Jun Yang | 2023 | Horticulture Research2023，10，1： | 0 |
| 9 | Elucidation of the melitidin biosynthesis pathway in pummelo显示文摘Specialized plant metabolism is a rich resource of compounds for drug discovery.The acylated flavonoid glycoside melitidin is being developed as an anti-cholesterol statin drug candidate,but its biosynthetic route in plants has not yet been fully characterized.Here,we describe the gene discovery and functional characterization of a new flavonoid gene cluster(UDP-glucuronosyltransferases(Cg UGTs),1,2rhamnosyltransferase(Cg1,2Rha T),acyltransferases(Cg ATs))that is responsible for melitidin biosynthesis in pummelo(Citrus grandis(L.)Osbeck).Population variation analysis indicated that the tailoring of acyltransferases,specific for bitter substrates,mainly determine the natural abundance of melitidin.Moreover,3-hydroxy-3-methylglutaryl-Co A reductase enzyme inhibition assays showed that the product from this metabolic gene cluster,melitidin,may be an effective anti-cholesterol statin drug candidate.Co-expression of these clustered genes in Nicotiana benthamiana resulted in the formation of melitidin,demonstrating the potential for metabolic engineering of melitidin in a heterologous plant system.This study establishes a biosynthetic pathway for melitidin,which provides genetic resources for the breeding and genetic improvement of pummelo aimed at fortifying the content of biologically active metabolites. | Shuangqian Shen Shouchuang Wang Chenkun Yang Chao Wang Qianqian Zhou Shen Zhou Ran Zhang Yufei Li Zixuan Wang Liupan Dai Wenjv Peng Yingchen Hao Hao Guo Guangping Cao Xianqing Liu Fan Yao Qiang Xu Alisdair RFernie Jie Luo | 2023 | Journal of Integrative Plant Biology2023，65，11： | 0 |
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