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Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Horticultural Plant Journal 2024年第4期10卷 971-982页

作者： Wei Sun Zhicheng Zhang guusje bonnema Xiaowu Wang Aalt Dirk Jan van Dijk State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Sino-Dutch Joint Lab of Vegetable Genomics Beijing 100081China Bioinformatics Group Wageningen University and Research6708 PB Wageningenthe Netherlands Plant Breeding Wageningen University and Research6708 PB Wageningenthe Netherlands Biosystems Data Analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam1090 GE Amsterdamthe Netherlands

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains *** uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground *** expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription *** to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial *** on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial *** explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell *** results demonstrated the utility of our computational approach for predicting candidate genes in crop *** findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

关键词： Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa Transcription factor

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Expression changes of mi RNA-regulated genes associated with the formation of the leafy head in cabbage

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Horticultural Plant Journal 2024年第4期10卷 1007-1019页

作者： Jorge Aleman-Baez Jose Fernando Acevedo-Zamora Johan Bucher Chengcheng Cai Roeland E.Voorrips guusje bonnema Plant Breeding Wageningen University and ResearchWageningenThe Netherlands

The vegetative development of cabbage(Brassica oleracea ***)passes through seedling,rosette,folding and heading *** that form the rosette are large and mostly *** the following developmental stages,the plants produce leaves that curve inward to produce the leafy *** microRNAs and their target genes have been described participating in leaf development and leaf *** aim of this study is to investigate the role of miRNA-regulated genes in the transition from the rosette to the heading *** compared the mi RNA and gene abundances between emerging rosette and heading *** remove transcripts(miRNAs and genes)whose regulation was most likely associated with plant age rather than the change from rosette to heading stage,we utilized a non-heading collard green(*** ***)morphotype as *** resulted in 33 DEMs and 1998 DEGs with likely roles in the transition from rosette to heading stage in *** these 1998 DEGs,we found enriched GO terms related to DNA-binding transcription factor activity,transcription regulator activity,iron ion binding,and *** predicted the target genes of these 33 DEMs and focused on the subset that was differentially expressed(1998DEGs)between rosette and heading stage leaves to construct mi RNA-target gene interaction *** main finding is a role for miR396b-5p targeting two Arabidopsis thaliana orthologues of GROWTH REGULATING FACTORs 3(GRF3)and 4(GRF4)in pointed cabbage head formation.

关键词： Brassica oleracea var.capitata RNA sequencing miRNA-target gene network leafy head formation

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利用cDNA-AFLP技术鉴定甘蓝显性核不育基因相关表达序列

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园艺学报 2003年第6期30卷 668-672页

作者：娄平王晓武 guusje.bonnema 方智远中国农业科学院蔬菜花卉研究所北京100081 Laboratory of Plant Breeding Wageningen UniversityWageningen 6700AJNetherlards

利用cDNA-AFLP技术,比较分析了一个甘蓝与两个青花菜自交系回交转育的显性核基因雄性不育材料与对应可育亲本植株花蕾发育过程中基因表达的差异。将花蕾混合提取RNA合成cDNA建立6个cDNA池,分析128个引物组合获得了26000个片段,共鉴定24... 详细信息

利用cDNA-AFLP技术,比较分析了一个甘蓝与两个青花菜自交系回交转育的显性核基因雄性不育材料与对应可育亲本植株花蕾发育过程中基因表达的差异。将花蕾混合提取RNA合成cDNA建立6个cDNA池,分析128个引物组合获得了26000个片段,共鉴定24个片段与雄性不育相关,其中13条表现为质的差异,11条表现为量的差异;将其中引物组合A16T15产生的300 bp左右的差异片段进行克隆测序,BLAST结果表明,该序列与花粉特异性相关的硫氧还蛋白氨基酸序列同源性达89％。

关键词： cDNA-AFLP 技术鉴定甘蓝显性核不育基因基因表达基因序列

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番茄植株与白粉病菌互作过程中叶片胞间蛋白变化的初步分析

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中国蔬菜 2003年第3期 8-10页

作者：李成伟王晓武 guusje bonnema 商丘师范学院生物系商丘476000 中国农业科学院蔬菜花卉研究所中荷联合园艺作物基因组分析实验室 Wageningen大学植物科学系

利用SDS -PAGE方法分析番茄抗白粉病过程中番茄叶片胞间蛋白 (IntercellularProtein)的变化趋势 ,比较了含有Ol 1的抗病品种和感病品种间的差异 ,从分泌蛋白的角度研究了番茄抗白粉病的机理。

关键词：番茄植株白粉病菌互作叶片胞间蛋白变化趋势 SDS-PAGE方法抗病机理白粉病

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Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage(Brassica rapa)

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Horticulture Research 2019年第1期6卷 95-107页

作者： XiaoXue Sun Ram Kumar Basnet Zhichun Yan Johan Bucher Chengcheng Cai Jianjun Zhao guusje bonnema Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei Collaborative Innovation Center of Vegetable Industry in HebeiDepartment of HorticultureHebei Agricultural UniversityBaoding 071001China Plant Breeding Wageningen University and ResearchWageningen 6708PBThe Netherlands Quantitative genetics department Rijk Zwaan Breeding B.V.Eerste Kruisweg 9Fijnaart 4793 RSThe Netherlands

Chinese cabbage plants go through seedling and rosette stages before forming their leafy *** cabbage plants resemble pak-choi plants at their seedling stage,but in their rosette stage the leaves of Chinese cabbage differentiate,as they increase in size with shorter *** order to understand the molecular pathways that play a role in leafy head formation,transcript abundance of young emerging leaves was profiled during development of two Chinese cabbage genotypes and a single pak-choi *** two Chinese cabbages differed in many aspects,among others earliness,leaf size and shape,leaf numbers,and leafy head ***-wide transcriptome analysis clearly separated the seedling stages of all three genotypes together with the later stages from pak-choi,from the later developmental stages of both Chinese cabbages(rosette,folding,and heading).Weighted correlation network analysis and hierarchical clustering using Euclidean distances resulted in gene clusters with transcript abundance patterns distinguishing the two Chinese cabbages from *** clusters included genes with transcript abundance affected by both genotype and developmental stage,whereas two clusters showed only genotype *** included a genotype by developmental stage cluster highly enriched with the MapMan category photosynthesis,with high expression during rosette and folding in Chinese cabbages and low expression in the heading inner leaves that are not exposed to *** other clusters contained many genes in the MapMan categories Cell,showing again differences between pak-choi and both Chinese *** discuss how this relates to the differences in leaf blade growth between Chinese cabbage and pak-choi,especially at the rosette ***,comparison of the transcriptome between leaves of two very different Chinese cabbages with pak-choi during plant development allowed the identification of specific gene categories associated with leafy head formation.

关键词： seedling heading analysis

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What makes turnips:anatomy,physiology and transcriptome during early stages of its hypocotyl-tuber development

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Horticulture Research 2019年第1期6卷 1364-1377页

作者： Mengyang Liu Niccolo Bassetti Stefan Petrasch Ningwen Zhang Johan Bucher Shuxing Shen Jianjun Zhao guusje bonnema Plant Breeding Wageningen University and ResearchWageningenthe Netherlands Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei Collaborative Innovation Center of Vegetable Industry in HebeiCollege of HorticultureHebei Agricultural UniversityBaodingChina Biosystematics Group Wageningen University and ResearchWageningenthe Netherlands Department of Plant Science University of CaliforniaDavisCAUSA

Brassica species are characterized by their tremendous intraspecific diversity,exemplified by leafy vegetables,oilseeds,and crops with enlarged inflorescences or above ground storage *** contrast to potato tubers that are edible storage organs storing energy as starch and are the vegetative propagation modules,the storage organs of turnips,grown from true seed,are swollen hypocotyls with varying degrees of root and stem that mainly store glucose and *** highlight their anatomical origin,we use the term“hypocotyl-tuber”for these turnip vegetative storage *** combined cytological,physiological,genetic and transcriptomic approaches,aiming to identify the initial stages,molecular pathways and regulatory genes for hypocotyl-tuber induction in turnips(*** ***).We first studied the development of the hypocotyl zone of turnip and Pak choi and found that 16 days after sowing(DAS)morphological changes occurred in the xylem which indicated the early tuberization *** culture experiments showed a clear effect of auxin on hypocotyl-tuber *** expressed genes between 1 and 6 weeks after sowing in turnip hypocotyls,located in genomic regions involved in tuber initiation and/or tuber growth defined by QTL and selective sweeps for tuber formation,were identified as candidate genes that were studied in more detail for their role in hypocotyl-tuber *** included a Bra-FLOR1 paralogue with increased expression 16 DAS,when the hypocotyl starts swelling,suggesting dual roles for duplicated flowering time genes in flowering and hypocotyltuber ***-CYP735A2 was identified for its possible role in tuber growth via *** Coexpression Network Analysis(WGCNA)identified 59 modules of co-expressed ***-FLOR1 and Bra-CYP735A2 were grouped in a module that included several genes involved in carbohydrate transport and metabolism,cell-wall growth,auxin regulation and secondary metabolism that serve as star

关键词： organs metabolism anatomy

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Genetic analysis of the “head top shape” quality trait of Chinese cabbage and its association with rosette leaf variation

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Horticulture Research 2021年第1期8卷 1374-1385页

作者： Xiaoxue Sun Ying Gao Yin Lu Xiaomeng Zhang Shuangxia Luo Xing Li Mengyang Liu Daling Feng Aixia Gu Xueping Chen Shuxin Xuan Yanhua Wang Shuxing Shen guusje bonnema Jianjun Zhao State Key Laboratory of North China Crop Improvement and Regulation Key Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiCollaborative Innovation Center of Vegetable Industry in HebeiCollege of HorticultureHebei Agricultural University071000 BaodingChina Plant Breeding Wageningen University and ResearchWageningenThe Netherlands

The agricultural and consumer quality of Chinese cabbage is determined by its *** shape is defined by the folding of the heading leaves,which defines the head top shape(HTS).The overlapping HTS,in which the heading leaves curve inward and overlap at the top,is the shape preferred by *** understand the genetic regulation of HTS,we generated a large segregating F 2 population from a cross between pak choi and Chinese cabbage,with phenotypes ranging from nonheading to heading with either outward curving or inward curving overlapping heading *** was correlated with plant height,outer/rosette leaf length,and petiole length.A high-density genetic map was *** trait locus(QTL)analysis resulted in the identification of 22 QTLs for leafy head-related traits,which included five HTS *** segregant analysis(BSA)was used to confirm HTS QTLs and identify candidate genes based on informative single-nucleotide ***,the HTS QTLs colocalized with QTLs for plant height,outer/rosette leaf,and petiole length,consistent with the observed phenotypic *** QTL analysis and BSA laid a foundation for molecular marker-assisted breeding of Chinese cabbage HTS and directions for further research on the genetic regulation of this trait.

关键词： heading trait breeding

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白菜类作物(***)遗传多样性的AFLP分析

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蔬菜分子育种研讨会

作者：赵建军王晓武 guusje.bonnema Dick.Vreugdenhil Maarten.Koornneef 许泽永孙日飞中国农业科学院蔬菜花卉研究所油料所 Laboratory of Plant Genetics and Breeding Wageningen UniversityThe Netherlands

利用荧光AFLP技术,采用4对AFLP引物组合对国内外161份白菜类作物(***)和2份甘蓝型油菜(***)进行了总基因组DNA水平上的多态性检测,获得了524个标记,其中多态性标记为476个,平均每对引物组合可以扩增出119个多态性带。UPGMA聚类分析结果... 详细信息

利用荧光AFLP技术,采用4对AFLP引物组合对国内外161份白菜类作物(***)和2份甘蓝型油菜(***)进行了总基因组DNA水平上的多态性检测,获得了524个标记,其中多态性标记为476个,平均每对引物组合可以扩增出119个多态性带。UPGMA聚类分析结果表明,白菜类作物分为由不同亚类群聚类组成的两大类群—类群Ⅰ、类群Ⅱ。低的bootstrap值说明各个亚类群内与亚类群间的遗传变异幅度相当。材料起源与聚合分类结果基本一致,亚洲和欧洲来源材料分别归属于类群Ⅰ和类群Ⅱ。Ⅰ类群包括中国结球白菜(CC1,CC2)和中国不结球白菜(PC1,PC2)两个亚类群。中国菜心和白菜型油菜均聚类于PC亚类群,揭示出二者的起源与不结球白菜相关;Ⅱ类群包括芜菁(T1,T2)、意大利菜心Broccolleto(Bro)、油用欧洲类型和印度Sarson(Oil1,Oil2)以及日本水菜Mizuna(Miz)。

关键词：白菜类作物遗传多样性 AFLP

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国外制冷系统及压缩机技术的新动向

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家电科技 2007年第10期 12-13页

作者： Lisa bonnema 陈

无论是提高系统的效率，还是使周围的环境更健康，制冷业一直都致力于设计出更好的制冷产品。

关键词：制冷系统压缩机技术国外制冷业

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北荷兰省电力公司总部,荷兰

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世界建筑 1984年第1期 36-38页

作者： A·邦尼玛

北荷兰省电力公司总部的总建筑面积达2.4万平方米,如设计成一栋办公大楼则体量庞大。因而建筑师在这里结合环境特点,采取了分散式平面布局,化整为零,围绕着一个平面不规则的水池布置了五栋四层高的坡顶建筑,每栋楼都设有绿化内院和绿化... 详细信息

北荷兰省电力公司总部的总建筑面积达2.4万平方米,如设计成一栋办公大楼则体量庞大。因而建筑师在这里结合环境特点,采取了分散式平面布局,化整为零,围绕着一个平面不规则的水池布置了五栋四层高的坡顶建筑,每栋楼都设有绿化内院和绿化屋顶平台;每两栋楼间或以平桥、廊榭相连,或以高架桥沟通。四条水道穿绕其间,使

关键词：荷兰电力办公楼

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