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Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple(Malus×domestica)

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Horticulture Research 2019年第1期6卷 1116-1128页

作者： Katchen Julliany Pereira Silva Jugpreet Singh Ryland Bednarek zhangjun fei Awais Khan Plant Pathology and Plant-Microbe Biology Section Cornell UniversityGenevaNY 14456USA Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA

Apple cultivars with durable resistance are needed for sustainable management of fire blight,the most destructive bacterial disease of *** studies have identified genetic resistance to fire blight in both wild species and cultivated apples,more research is needed to understand the molecular mechanisms underlying host–pathogen interaction and differential genotypic responses to fire blight *** have analyzed phenotypic and transcriptional responses of‘Empire’and‘Gala’apple cultivars to fire blight by infecting them with a highly aggressive *** *** progress,based on the percentage of visual shoot necrosis,started showing significant(p<0.001)differences between‘Empire’and‘Gala’4 days after infection(dai).‘Empire’seems to slow down bacterial progress more rapidly after this *** further compared transcriptome profiles of‘Empire’and‘Gala’at three different time points after fire blight *** genes showed differential expression in‘Gala’at earlier stages,but the number of differentially expressed genes increased in‘Empire’at 3 *** classes related to defense,cell cycle,response to stress,and biotic stress were identified and a few co-expression gene networks showed particular enrichment for plant defense and abiotic stress response *** of these genes also co-localized in previously identified quantitative trait locus regions for fire blight resistance on linkage groups 7 and 12,and can serve as functional candidates for future *** results highlight different molecular mechanisms for pathogen perception and control in two apple cultivars and will contribute toward better understanding of ***-Malus pathosystem.

关键词： blight cultivar networks

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Plant Genome Editing Database (PGED): A Call for Submission of Information about Genome-Edited Plant Mutants

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Molecular Plant 2019年第2期12卷 127-129页

作者： Yi Zheng Ning Zhang Gregory B. Martin zhangjun fei Boyce Thompson Institute for Plant Research Ithaca NY 14853 USA Plant Pathology and Plant-Microbe Biology Section School of Integrative 2Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca NY 14853 USA USDA-ARS Robert W. Holley Center for Agriculture and Health Ithaca NY 14853 USA These authors contributed equally to this article

Recent advances in genome editing technologies, particularly CRISPR/Cas, enable the alteration of DNA sequences to produce deletions, insertions, and substitutions in genes (Jaganathan et al., 2018), as well as large ... 详细信息

关键词： Plant Genome Editing Database (PGED) Genome-Edited Plant Mutants

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Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency

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Journal of Integrative Plant Biology 2019年第4期61卷 492-508页

作者： Zhaoliang Zhang Yi Zheng Byung-Kook Ham Shupei Zhang zhangjun fei William J.Lucas State Key Laboratory of Tea Biology and Utilization Anhui Agricultural University Boyce Thompson Institute for Plant Research Cornell University Global Institute for Food Security Department of Biology University of Saskatchewan Department of Plant Biology College of Biological Sciences University of California

In response to phosphate(Pi) deficiency, it has been shown that micro-RNAs(miRNAs) and mRNAs are transported through the phloem for delivery to sink tissues. Growing evidence also indicates that long noncoding RNAs(lncRNAs) are critical regulators of Pi homeostasis in plants. However, whether lncRNAs are present in and move through the phloem, in response to Pi deficiency, remains to be established. Here, using cucumber as a model plant, we show that lncRNAs are enriched in the phloem translocation stream and respond,systemically, to an imposed Pi-stress. A well-known lncRNA, IPS1, the target mimic(TM) of miRNA399,accumulates to a high level in the phloem, but is not responsive to early Pi deficiency. An additional 24 miRNA TMs were also detected in the phloem translocation stream; among them miRNA171 TMs and miR166 TMs were induced in response to an imposed Pi *** studies identified 22 lncRNAs which move systemically into developing leaves and root tips. A CU-rich PTB motif was further identified in these mobile lncRNAs. Our findings revealed that lncRNAs respond to Pi deficiency, non-cell-autonomously, and may act as systemic signaling agents to coordinate early Pi deficiency signaling, at the whole-plant level.

关键词： Plant lncRNAs enriched phloem phosphate deficiency

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Transcriptome analysis provides insights into the regulation of metabolic processes during postharvest cold storage of loquat(Eriobotrya japonica)fruit

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Horticulture Research 2019年第1期6卷 1142-1152页

作者： Wenli Liu Jing Zhang Chen Jiao Xueren Yin zhangjun fei Qingbiao Wu Kunsong Chen School of Mathematical Science Zhejiang UniversityYuquan Campus310027 HangzhouP.R.China Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Zhejiang UniversityZijingang Campus310058 HangzhouP.R.China USDA-ARS Robert W.Holley Center for Agriculture and Health IthacaNY 14853USA

Loquat(Eriobotrya japonica)fruit accumulates lignin during postharvest storage under chilling conditions(0℃),while low-temperature conditioning(LTC;5℃for 6 days followed by transfer to 0℃)or heat treatment(HT;40℃for 4 h followed by transfer to 0℃)can alleviate *** we compared transcriptome profiles of loquat fruit samples under LTC or HT to those stored at 0℃at five time points from day 1 to day 8 after ***-throughput transcriptome sequences were de novo assembled into 53,319 unique transcripts with an N50 length of 1306 bp.A total of 2235 differentially expressed genes were identified in LTC,and 1020 were identified in HT compared to 0℃.Key genes in the lignin biosynthetic pathway,including EjPAL2,EjCAD1,EjCAD3,4CL,COMT,and HCT,were responsive to LTC or HT treatment,but they showed different expression patterns during the treatments,indicating that different structural genes could regulate lignification at different treatment *** network analysis showed that these candidate biosynthetic genes were associated with a number of transcription factors,including those belonging to the AP2,MYB,and NAC *** ontology(GO)enrichment analysis of differentially expressed genes indicated that biological processes such as stress responses,cell wall and lignin metabolism,hormone metabolism,and metal ion transport were significantly affected under LTC or HT treatment when compared to 0℃.Our analyses provide insights into transcriptome responses to postharvest treatments in loquat fruit.

关键词： insight analysis treatment

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An R2R3-type myeloblastosis transcription factor MYB103 is involved in phosphorus remobilization

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Food Production, Processing and Nutrition 2020年第1期2卷 241-248页

作者： Fangwei Yu Shenyun Wang Wei Zhang Hong Wang Li Yu zhangjun fei Jianbin Li Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Institute of Vegetable CropsJiangsu Academy of Agricultural SciencesNanjing 210014China Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA

The members of myeloblastosis transcription factor(MYB TF)family are involved in the regulation of biotic and abiotic stresses in ***,the role of MYB TF in phosphorus remobilization remains largely *** the present study,we show that an R2R3 type MYB transcription factor,MYB103,is involved in phosphorus(P)***103 was remarkably induced by P deficiency in cabbage(Brassica oleracea *** L.).As cabbage lacks the proper mutant for elucidating the mechanism of MYB103 in P deficiency,another member of the crucifer family,Arabidopsis thaliana was chosen for further *** transcript of its homologue AtMYB103 was also elevated in response to P deficiency in ***,while disruption of AtMYB103(myb103)exhibited increased sensitivity to P deficiency,accompanied with decreased tissue biomass and soluble P ***,AtMYB103 was involved in the P reutilization from cell wall,as less P was released from the cell wall in myb103 than in wildtype,coinciding with the reduction of ethylene *** together,our results uncover an important role of MYB103 in the P remobilization,presumably through ethylene signaling.

关键词： Brassica oleracea var.capitata L. Arabidopsis thaliana Cell wall Ethylene Phosphorus MYB103

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The tomato HIGH PIGMENT1/DAMAGED DNA BINDING PROTEIN 1 gene contributes to regulation of fruit ripening

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Horticulture Research 2019年第1期6卷 1438-1447页

作者： Anquan Wang Danyang Chen Qiyue Ma Jocelyn K.C.Rose zhangjun fei Yongsheng Liu James J.Giovannoni School of Biotechnology and Food Engineering Hefei University of TechnologyHefei 230009China Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA Plant Biology Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA United States Department of Agriculture Robert W.Holley CenterCornell UniversityIthacaNY 14853USA

Fleshy fruit ripening is governed by multiple external and internal cues and accompanied by changes in color,texture,volatiles,and nutritional quality *** extended shelf-life and increased phytonutrients are desired,delaying ripening via genetic or postharvest means can be accompanied by reduced nutritional *** we report that the high pigment 1(hp1)mutation at the UV-DAMAGED DNA BINDING PROTEIN 1(DDB1)locus,previously shown to influence carotenoid and additional phytonutrient accumulation via altered light signal transduction,also results in delayed ripening and firmer texture,resulting at least in part from decreased ethylene *** analysis revealed multiple ethylene biosynthesis and signaling-associated genes downregulated in ***,the hp1 mutation impedes softening of the pericarp,placenta,columella as well as the whole fruit,in addition to reduced expression of the FRUITFUL2(FUL2)MADS-box transcription factor and xyloglucan endotransglucosylase/hydrolase 5(XTH5).These results indicate that DDB1 influences a broader range of fruit development and ripening processes than previously thought and present an additional genetic target for increasing fruit quality and shelf-life.

关键词： shelf desired governed

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Tecia solanivora infestation increases tuber starch accumulation in Pastusa Suprema potatoes

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Journal of Integrative Plant Biology 2018年第11期60卷 1083-1096页

作者： Pavan Kumar Etzel Garrido Kun Zhao Yi Zheng Saleh Alseekh Erandi Vargas-Ortiz Alisdair R.Fernie zhangjun fei Katja Poveda Georg Jander Boyce Thompson Institute for Plant Research 533 Tower RoadIthacaNY 14853USA Department of Entomology Cornell UniversityIthacaNY 14853USA Max Planck Institute of Molecular Plant Physiology Wissenschaftspark GolmAm Muhlenberg 114476 PotsdamGermany department of entomology and nematology university of floridaGainesvilleFL 32611USA unidad de microbiologia basica y aplicada facultad de ciencias naturalesuniversidad autonoma de queretaroAv.de las Ciencias SINJuriquillaquerdtaroMdxico department of molecular biology institute for scientific and technological research of san luis potosiMexico

In response to infestation with larvae of the Guatemalan tuber moth （Tecia solanivora）, some Solanum tuberosum （potato） varieties exhibit an overcompensa- tion response, whereby the total dry mass of uninfested tubers is increased. Here, we describe early responses, within the first few days, of T. solanivora feeding, in the Colombian potato variety Pastusa Suprema. Non- targeted metabolite profiling showed significant second- ary metabolism changes in T. solanivora-infested tubers, but not in uninfested systemic tubers. In contrast, changes in primary metabolism were greater in unin- fested systemic tubers than in the infested tubers, with a notable 80% decline in systemic tuber sucrose levels within 1 d of T. solanivora infestation. This suggested either decreased sucrose transport from the leaves or increased sink strength, i.e., more rapid sucrose to starch conversion in the tubers. Increased sucrose synthesis was indicated by higher rubisco activase and lower starch synthase gene expression in the leaves of infested plants. Elevated sink strength was demonstrated by 45% more total starch deposition in systemic tubers of T. solanivord- infested plants compared to uninfested control plants. Thus, rather than investing in increased defense of uninfested tubers, Pastusa Suprema promotes deposition of photoassimilates in the form of starch as a response to T. solanivora infestation.

关键词： Tecia solanivora infestation increases tuber starch accumulation in Pastusa Suprema potatoes Figure

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Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection

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Molecular Horticulture 2021年第1期1卷 72-84页

作者： Xin Wang Kaori Ando Shan Wu Umesh K.Reddy Prabin Tamang Kan Bao Sue A.Hammar Rebecca Grumet James D.McCreight zhangjun fei Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA U.S.Department of Agriculture-Agricultural Research Service Crop Improvement and Protection Research UnitSalinasCA 93905USA Nunhems USA IncAcampoCA 95220USA Gus R.Douglass Institute and Department of Biology West Virginia State UniversityInstituteWV 25112USA U.S.Department of Agriculture-Agricultural Research Service Natural Products Utilization Research UnitThad Cochran Research CenterP.O.Box 1848OxfordMS 38677USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA U.S.Department of Agriculture-Agricultural Research Service Robert W.Holley Center for Agriculture and HealthIthacaNY 14853USA.

Melon(*** L.)is an economically important vegetable crop cultivated *** melon collection in the *** Plant Germplasm System(NPGS)is a valuable resource to conserve natural genetic diversity and provide novel traits for melon *** we use the genotyping-by-sequencing(GBS)technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons *** structure and genetic diversity analyses suggested that *** *** was firstly introduced from the centers of origin,Indian and Pakistan,to Central and West Asia,and then brought to Europe and *** *** from East Asia was likely derived from *** *** in India and Pakistan and displayed a distinct genetic background compared to the rest of *** accessions from other geographic *** developed a core collection of 383 accessions capturing more than 98%of genetic variation in the germplasm,providing a publicly accessible collection for future research and genomics-assisted breeding of ***-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the ***-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural *** study provides insights into melon origin and domestication,and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.

关键词： Melon C.melo Germplasm Genetic characterization Core collection Genome-wide association study

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Transcriptomes of developing fruit of cultivated and wild tomato species

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Molecular Horticulture 2023年第1期3卷 230-233页

作者： Adi Doron‑Faigenboim Michal Moy‑Komemi Marina Petreikov Yelena Eselson Prashant Sonawane Pablo Cardenas zhangjun fei Asaph Aharoni Arthur A.Schaffer Plant Sciences Institute Agricultural Research Organization-Volcani CenterRishon LeZionIsrael Department of Plant and Environmental Sciences Weizmann Institute of ScienceRehovotIsrael Boyce Thompson Institute IthacaNYUSA

Tomato(Solanum lycopersicum)is one of the world’s most extensively cultivated crops,and has been the subject of hundreds of years of breeding and ***,the genetic variability available for the breeding and improvement of tomato within the confines of the species is *** has been described as a“genetic bottleneck”(Miller and Tanksley 1990)and is due to the domestication history of the crop,particularly the transfer of select germplasm from South America to Europe in the 1500 s,followed by selections and return to the New World,again of limited germplasm(Knapp and Peralta 2016).

关键词： breeding germplasm crops

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Kiwifruit Genome Database(KGD):a comprehensive resource for kiwifruit genomics

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Horticulture Research 2020年第1期7卷 1076-1083页

作者： Junyang Yue Jiacheng Liu Wei Tang Ya Qing Wu Xiaofeng Tang Wei Li Ying Yang Lihuan Wang Shengxiong Huang Congbing Fang Kun Zhao zhangjun fei Yongsheng Liu Yi Zheng School of Horticulture Anhui Agricultural UniversityHefei 230036China School of Food and Biological Engineering Hefei University of TechnologyHefei 230009China Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA USDA-Agricultural Research Service Robert W.Holley Center for Agriculture and HealthIthacaNY 14853USA Ministry of Education Key Laboratory for Bio-resource and Eco-environment College of Life ScienceState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu 610064China Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing University of AgricultureBeijing 102206China Plant Science and Technology College Beijing University of AgricultureBeijing 102206China

Kiwifruit(Actinidia spp.)plants produce economically important fruits containing abundant,balanced phytonutrients with extraordinarily high vitamin C *** the release of the first kiwifruit reference genome sequence in 2013,large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit *** efficiently store,analyze,integrate,and disseminate these large-scale datasets to the research community,we constructed the Kiwifruit Genome Database(KGD;http://***/).The database currently contains all publicly available genome and gene sequences,gene annotations,biochemical pathways,transcriptome profiles derived from public RNA-Seq datasets,and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies.A set of user-friendly query interfaces,analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit,which include JBrowse,a popular genome browser,and the NCBI BLAST sequence search *** notable tools developed within KGD include a genome synteny viewer and tools for differential gene expression analysis as well as gene ontology(GO)term and pathway enrichment analysis.

关键词： comprehensive fruit

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