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Chinese Journal of Chemistry 2014年第7期32卷 650-653页

作者： yong-qing yang Zheng Lu School of Pharmacy Jiangsu UniversityZhenjiangJiangsu 212013China

Poor solubility of Hantzsch ester is used as indicator in the reduction of methylidene *** Knoevenagel reaction is integrated to develop a reductive alkylation of malononitrile with aryl and aliphatic aldehyde as the ... 详细信息

关键词： heterogeneous reduction Hantzsch ester Knoevenagel condensation reductive alkylation

PCMD:A multilevel comparison database of intraand cross-species metabolic profiling in 530 plant species

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Plant Communications 2024年第10期5卷 33-44页

作者： Yue Hu Yao Ruan Xin-Le Zhao Feng Jiang Dongxu Liu Qiang Zhu qing-Ye Zhang qing-yong yang National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070HubeiChina Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Yazhouwan National Laboratory Sanya 572024China

Comparative metabolomics plays a crucial role in investigating gene function,exploring metabolite evolution,and accelerating crop genetic ***,a systematic platform for intra-and crossspecies comparison of metabolites is currently ***,we report the Plant Comparative Metabolome Database(PCMD;http://***/PCMD),a multilevel comparison database based on predicted metabolic profiles of 530 plant *** PCMD serves as a platform for comparing metabolite characteristics at various levels,including species,metabolites,pathways,and biological *** database also provides a number of user-friendly online tools,such as species comparison,metabolite enrichment,and ID conversion,enabling users to perform comparisons and enrichment analyses of metabolites across different *** addition,the PCMD establishes a unified system based on existing metabolite-related databases by standardizing metabolite *** PCMD is the most speciesrich comparative plant metabolomics database currently available,and a case study demonstrates its ability to provide new insights into plant metabolic diversity.

关键词： comparative metabolomics plant database multilevel comparison metabolite characteristics

BnVIR:bridging the genotype-phenotype gap to accelerate mining of candidate variations underlying agronomic traits in Brassica napus

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Molecular Plant 2022年第5期15卷 779-782页

作者： Zhiquan yang Congyuan Liang LuLu Wei Shengbo Wang Feifan Yin Dongxu Liu Liang Guo yongming Zhou qing-yong yang National Key Laboratory of Crop Genetic Improvement College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070China

Dear Editor,Genetic variations,which range from single nucleotide polymor-phisms(SNPs)and short insertion/deletions(InDels)to large-scale structural variations(SVs),are the basis of phenotypic *** the effect of geneti... 详细信息

关键词： agronomic traits InDel

BnlR:A multi-omics database with various tools for Brassica napus research and breeding

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Molecular Plant 2023年第4期16卷 775-789页

作者： Zhiquan yang Shengbo Wang Lulu Wei Yiming Huang Dongxu Liu Yupeng Jia Chengfang Luo Yuchen Lin Congyuan Liang Yue Hu Cheng Dai Liang Guo yongming Zhou qing-yong yang National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Innovative Center of Molecular Genetics and Evolution School of Life SciencesGuangzhou UniversityGuangzhou 510405China

In the post-genome-wide association study era,multi-omics techniques have shown great power and poten-tial for candidate gene mining and functional genomics ***,due to the lack of effective data integration and multi-omics analysis platforms,such techniques have not still been applied widely in rape-seed,an important oil crop ***,we report a rapeseed multi-omics database(BnlR;http:/l ***/BnlR),which provides datasets of six omics including genomics,transcriptomics,variomics,epigenetics,phenomics,and metabolomics,as well as numerous"variation-gene expression-phenotype"associations by using multiple statistical *** addition,a series of multi-omics search and analysis tools are integrated to facilitate the browsing and application of these *** is the most comprehensive multi-omics database for rapeseed so far,and two case studies demonstrated its power to mine candidate genes associated with specific traits and analyze their potential regulatory mechanisms.

关键词： Brassica napus multi-omics database candidate gene mining functional genomics

Genome-and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus

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Molecular Plant 2021年第3期14卷 470-487页

作者： Shan Tang Hu Zhao Shaoping Lu Liangqian Yu Guofang Zhang Yuting Zhang qing-yong yang yongming Zhou Xuemin Wang Wei Ma Weibo Xie Liang Guo National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhanChina Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhanChina Department of Biology University of Missouri-St.LouisSt.LouisMO 63121USA Donald Danforth Plant Science Center St.LouisMO 63132USA School of Biological Sciences Nanyang Technological UniversitySingapore 637551Singapore

Seed oil content(SOC)is a highly important and complex trait in oil ***,we decipher the genetic basis of natural variation in SOC of Brassica napus by genome-and transcriptome-wide association studies using 505 inbred *** mapped reliable quantitative trait loci(QTLs)that control SOC in eight environments,evaluated the effect of each QTL on SOC,and analyzed selection in QTL regions during ***-hundred and ninety-two genes and four gene modules significantly associated with SOC were identified by analyzing population transcriptomes from seeds.A gene prioritization framework,POCKET(prioritizing the candidate genes by incorporating information on knowledge-based gene sets,effects of variants,genome-wide association studies,and transcriptome-wide association studies),was implemented to determine the causal genes in the QTL regions based on multi-omic datasets.A pair of homologous genes,BnPMT6s,in two QTLs were identified and experimentally demonstrated to negatively regulate *** study provides rich genetic resources for improving SOC and valuable insights toward understanding the complex machinery that directs oil accumulation in the seeds of *** and other oil crops.

关键词： Brassica napus seed oil content QTL GWAS TWAS gene module

BjuIR:A multi-omics database with various tools for accelerating functional genomics research in Brassica juncea

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Plant Communications 2024年第8期5卷 96-99页

作者： Linna Zhang Jinyuan Xiao Congyuan Liang Yifan Chen Changchun Yu Xinle Zhao Jiawei Li Mingli Yan Qian yang Hao Chen Zhongsong Liu Zhengjie Wan Zhiquan yang qing-yong yang National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data College of InformaticsHuazhong Agricultural UniversityWuhan 430070China National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Yazhouwan National Laboratory Sanya 572025China National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan 430070China Crop Research Institute Hunan Academy of Agricultural SciencesChangsha 410125China College of Agronomy Hunan Agricultural UniversityChangsha 410128China

Dear Editor,Advances in high-throughput omics technologies,along with methodologies for integrating multi-omics datasets,have substantially enhanced the efficiency of identifying candidate genes in breeding(Gusev et al.,2018;Gupta et al.,2019).However,this process is often complex and *** address this challenge,databases that integrate extensive data and enable convenient and efficient functional genomics studies are being developed(Ma et al.,2021;yang et al.,2023).

关键词： functional integrating convenient

PlantCFG:A comprehensive database with web tools for analyzing candidate flowering genes in multiple plants

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Plant Communications 2024年第2期5卷 11-14页

作者： Dongxu Liu Jiawei Li Shengbo Wang Tingting Huang Fangting Tao Yuchen Lin Wei Lin Xinle Zhao Yiming Huang Yupeng Jia Zhiquan yang Chengfang Luo Qiang Zhu Wing-Kin Sung Jian Wu qing-yong yang National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Hong Kong Genome Institute Hong Kong Science ParkShatinHong KongChina State Key Laboratory of Biocontrol School of Life SciencesSun Yat-Sen UniversityGuangzhou 510275China School of Life Sciences University of Science and Technology of ChinaHefei 230026China Key Laboratory of Plant Functional Genomics of the Ministry of Education Yangzhou UniversityYangzhou 225009China

Dear Editor,The transition from the vegetative to the reproductive phase of plant development,known as the floral transition,plays important roles in the plant life *** is a vulnerable but crucial phase for building crop yield,and proper timing of this period is therefore vital for obtaining optimal yields(Jung and Muller,2009).Analysis of flowering time is currently an important research topic in several fields,including plant molecular genetics,evolutionary biology,ecology,and crop breeding(Huang et al.,2011).

关键词： database web breeding

Functional genomics of Brassica napus:Progresses,challenges,and perspectives

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Journal of Integrative Plant Biology 2024年第3期66卷 484-509页

作者： Zengdong Tan Xu Han Cheng Dai Shaoping Lu Hanzi He Xuan Yao Peng Chen Chao yang Lun Zhao qing-yong yang Jun Zou Jing Wen Dengfeng Hong Chao Liu Xianhong Ge Chuchuan Fan Bing Yi Chunyu Zhang Chaozhi Ma Kede Liu Jinxiong Shen Jinxing Tu Guangsheng yang Tingdong Fu Liang Guo Hu Zhao National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Yazhouwan National Laboratory Sanya 572025China

Brassica napus,commonly known as rapeseed or canola,is a major oil crop contributing over 13%to the stable supply of edible vegetable oil *** and understanding the gene functions in the *** genome is crucial for genomic breeding.A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in *** this review,we present an overview of the progress made in the functional genomics of ***,including the availability of germplasm resources,omics databases and cloned functional *** on the current progress,we also highlight the main challenges and perspectives in this *** advances in the functional genomics of *** contribute to a better understanding of the genetic basis underlying the complex agronomic traits in *** and will expedite the breeding of high quality,high resistance and high yield in *** varieties.

关键词： accelerate breeding Brassica napus functional genomics high resistance high yield

过表达丹参GGPPS研究丹参酮类的生物合成途径

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中国科学：生命科学 2017年第5期47卷 586-594页

作者：杨悦杨长青王勇杨蕾上海辰山植物园中国科学院上海辰山植物科学研究中心上海市资源植物功能基因组学重点实验室上海201602 中国科学院上海生命科学研究院植物生理生态研究所中国科学院合成生物学重点实验室上海200032 东北林业大学森林植物生态学教育部重点实验室哈尔滨150040

丹参酮是药用植物丹参(Salvia miltiorrhiza)中具有较强生物活性的脂溶性二萜醌类化合物,是目前国际上广泛认可的有效治疗心脑血管疾病的天然药物之一.本研究通过分析过表达萜类生物合成途径中的牻牛儿基牻牛儿基焦磷酸合酶(GGPPS)的转... 详细信息

丹参酮是药用植物丹参(Salvia miltiorrhiza)中具有较强生物活性的脂溶性二萜醌类化合物,是目前国际上广泛认可的有效治疗心脑血管疾病的天然药物之一.本研究通过分析过表达萜类生物合成途径中的牻牛儿基牻牛儿基焦磷酸合酶(GGPPS)的转基因丹参,发现丹参酮类化合物与叶绿素具有共同的上游生物合成途径,而下游途径因组织的特异化而不同,从而生成不同的代谢产物.通过对丹参毛状根外施两个萜类生物合成途径的抑制剂Lovastatin和Fosmidomycin,在处理6周丹参酮积累达到稳定时测定丹参酮的含量,探明了丹参酮类的生物合成主要是通过质体中的MEP途径来完成,而非胞质中的MVA途径.本研究为丹参酮类的代谢生物学及合成生物学研究提供了证据和基础.

关键词：丹参酮 MEP途径 MVA途径抑制剂过表达

Xiaoyun,a model accession for functional genomics research in Brassica napus

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Plant Communications 2024年第1期5卷 16-19页

作者： Pengfei Wang Yixian Song Zhaoqi Xie Ming Wan Rui Xia Yushun Jiao Hui Zhang Guangsheng yang Zhixiong Fan qing-yong yang Dengfeng Hong National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Hubei Hongshan Laboratory Wuhan 430070China Crop Institute Anhui Academy of Agricultural ScienceHefei 230031China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070China

Dear Editor,Rapeseed(Brassica napus)provides quality edible plant oil and industrial raw materials,as well as protein-rich animal feed;however,molecular characterization of functional genes in rapeseed remains challenging,largely owing to its complex polyploid genome,relatively long generation time,and environmentally sensitive *** accelerate functional genomics research on rapeseed,especially in an artificially controlled,stable environment like that of comprehensive speed breeding(CSB;Song et al.,2022),we screened out the representative *** accession Xiaoyun(小芸),with a rapid cycling time and scaleddown but normal plant architecture.

关键词： traits functional cycling