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Horticulture Research 2021年第1期8卷 790-805页

作者： Jinfang Zheng lyndel w.meinhardt Ricardo Goenaga Dapeng Zhang Yanbin Yin Nebraska Food for Health Center Department of Food Science and TechnologyUniversity of NebraskaLincolnNE 68588USA Sustainable Perennial Crops Lab USDA-ARSBeltsvilleMDUSA Tropical Agriculture Research Station USDA-ARSPuerto RicoPRUSA

Dragon fruits are tropical fruits economically important for agricultural *** members of the family of Cactaceae,they have evolved to adapt to the arid *** we report the draft genome of Hylocereus undatus,commercially known as the white-fleshed dragon *** chromosomal level genome assembly contains 11 longest scaffolds corresponding to the 11 chromosomes of *** annotation of *** found~29,000 protein-coding genes,similar to Carnegiea gigantea(saguaro).whole-genome duplication(wGD)analysis revealed a wGD event in the last common ancestor of Cactaceae followed by extensive genome *** divergence time between *** and *** was estimated to be 9.18 *** enrichment analysis of orthologous gene clusters(OGCs)in six Cactaceae plants found significantly enriched OGCs in drought *** flavor-related functions were overrepresented in OGCs that are significantly expanded in *** *** draft genome also enabled the discovery of carbohydrate and plant cell wall-related functional enrichment in dragon fruits treated with trypsin for a longer storage ***,genes of the betacyanin(a red-violet pigment and antioxidant with a very high concentration in dragon fruits)biosynthetic pathway were found to be co-localized on a 12 Mb region of one *** consequence may be a higher efficiency of betacyanin biosynthesis,which will need experimental validation in the *** *** draft genome will be a great resource to study various cactus plants.

关键词： dragon drought whole

Identification of the varietal origin of processed loose-leaf tea based on analysis of a single leaf by SNP nanofluidic array

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The Crop Journal 2016年第4期4卷 304-312页

作者： wanping Fang lyndel w.meinhardt Huawei Tan Lin Zhou Sue Mischke Xinghua wang Dapeng Zhang College of Horticulture Nanjing Agricultural UniversityNanjing 210095JiangsuChina Sustainable Perennial Crops Laboratory USDA-ARS10300 Baltimore AvenueBldg.001Rm.223BARC-WBeltsvilleMD 20705USA Yunnan Pu'er Tea Seeds Propagation and Extension Unit Pu'er 665000YunnanChina

Tea is an important cash crop, representing a $40 billion-a-year global market. Differentiation of the tea market has resulted in increasing demand for tea products that are sustainably and responsibly produced. Tea authentication is important because of growing concerns about fraud involving premium tea products. Analytical technologies are needed for protection and value enhancement of high-quality brands. For loose-leaf teas, the challenge is that the authentication needs to be established on the basis of a single leaf, so that the products can be traced back to the original varieties. A new generation of molecular markers offers an ideal solution for authentication of processed agricultural products. Using a nanofluidic array to identify variant SNP sequences, we tested genetic identities using DNA extracted from single leaves of 14 processed commercial tea products. Based on the profiles of 60 SNP markers, the genetic identity of each tea sample was unambiguously identified by multilocus matching and ordination analysis. Results for repeated samples of multiple tea leaves from the same products(using three independent DNA extractions) showed 100% concordance, showing that the nanofluidic system is a reliable platform for generating tea DNA fingerprints with high accuracy. The method worked well on green, oolong, and black teas, and can handle a large number of samples in a short period of time. It is robust and cost-effective, thus showing high potential for practical application in the value chain of the tea industry.

关键词： Authentication Camellia sinensis Conservation Food adulteration Molecular markers

Traditional varieties of cacao(Theobroma cacao)in Madagascar:their origin and dispersal revealed by SNP markers

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Beverage Plant Research 2021年第1期1卷 23-29页

作者： Yanmei Li Dapeng Zhang Lambert A.Motilal Philippe Lachenaud Sue Mischke lyndel w.meinhardt USDA/ARS NEABeltsville Agricultural Research CenterSPCL10300 Baltimore AvenueBldg.001Rm.223BARC-WBeltsvilleMD 20705USA Southwest University No.2 Tiansheng RoadBeibei DistrictChongqing 400715China Cocoa Research Unit The University of the West IndiesSt.AugustineTrinidadRep.Trinidad and TobagoWest Indies Centre de Coopération Internationale en Recherche Agronomique pour le Développement UPR Bioagresseurs de PérennesTA 80/0234398 Montpellier Cedex 5France

Cacao(Theobroma cacao L.)is an important Neotropical crop originating in South America and dispersed by European explorers,arriving in Madagascar in the late 19th *** Madagascar is an important producer of cocoa for the premium chocolate market,the varietal composition and genetic diversity in cacao germplasm from Madagascar,especially in traditional cacao farms,remains unknown.A total of 190 cacao accessions,including 40 farmer accessions collected from traditional cacao farms in Madagascar,and 150 accessions representing seven reference cacao populations,were analyzed using Single Nucleotide Polymorphism(SNP)*** analysis and Bayesian stratification resulted in the clustering of the 40 farmer accessions into three groups:Criollo,Amelonado and *** three traditional varieties were commonly cultivated in tropical America in the 18th century,but most of them have been replaced by improved *** present study demonstrated that Madagascar is distinctive in that all three traditional cacao varieties,Criollo,Amelonado and Trinitario,are still maintained on-farm for cocoa production,as in Mesoamerica and the Caribbean several hundred years *** from the present study are significant in terms of understanding the early dispersal of cacao from tropical America and Asia to Africa,in addition to the well-documented route from Brazil to São Tomé&Prí*** results also provide new information for planning future conservation and utilization of cacao germplasm in Madagascar.

关键词： Madagascar varieties origin

Varietal identification of tea(Camellia sinensis)using nanofluidic array of single nucleotide polymorphism(SNP)markers

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Horticulture Research 2014年第1期1卷 142-149页

作者： wan-Ping Fang lyndel w.meinhardt Hua-wei Tan Lin Zhou Sue Mischke Dapeng Zhang College of Horticulture Nanjing Agricultural UniversityNanjing 210095China Sustainable Perennial Crops Laboratory USDA-ARSBeltsville Agricultural Research CenterBeltsvilleMD 20705USA

Apart from water,tea is the world’s most widely consumed *** is produced in more than 50 countries with an annual production of approximately 4.7 million *** market segment for specialty tea has been expanding rapidly owing to increased demand,resulting in higher revenues and profits for tea growers and the *** varietal identification is critically important to ensure traceability and authentication of premium tea products,which in turn contribute to on-farm conservation of tea genetic *** a set of single nucleotide polymorphism(SNP)markers developed from the expressed sequence tag(EST)database of Camilla senensis,we genotyped deoxyribonucleic acid(DNA)samples extracted from a diverse group of tea varieties,including both fresh and processed commercial loose-leaf *** validation led to the designation of 60 SNPs that unambiguously identified all 40 tested tea varieties with high statistical rigor(pwere further characterized by ordination and Bayesian clustering *** SNP markers,in combination with a high-throughput genotyping protocol,effectively established and verified specific DNA fingerprints for all tested tea *** method provides a powerful tool for variety authentication and quality control for the tea *** is also highly useful for the management of tea genetic resources and breeding,where accurate and efficient genotype identification is essential.

关键词： revenue breeding expanding

Developing single nucleotide polymorphism markers for the identification of pineapple(Ananas comosus)germplasm

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Horticulture Research 2015年第1期2卷 35-46页

作者： Lin Zhou Tracie Matsumoto Hua-wei Tan lyndel w.meinhardt Sue Mischke Boyi wang Dapeng Zhang Sustainable Perennial Crops Laboratory USDA-ARSBeltsville Agricultural Research CenterBeltsville20705MDUSA Daniel K.Inouye Pacific Basin Agricultural Research Center USDA-ARSHilo96720HIUSA College of Horticulture Nanjing Agricultural UniversityNanjing210095JiangsuChina Yunnan Forestry Technological College Kunming650224YunnanChina

Pineapple(Ananas comosus[L.]Merr.)is the third most important tropical fruit in the world after banana and *** a crop with vegetative propagation,genetic redundancy is a major challenge for efficient genebank management and in *** expressed sequence tag and nucleotide sequences from public databases,we developed 213 single nucleotide polymorphism(SNP)markers and validated 96 SNPs by genotyping the United States Department of Agriculture-Agricultural Research Service pineapple germplasm collection,maintained in Hilo,*** validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple ***-four groups of duplicates were detected,encompassing 130 of the total 170 A cosmos *** results show that somatic mutation has been the main source of intra-cultivar variations in *** clustering and a model-based population stratification suggest that the modern pineapple cultivars are comprised of progenies that are derived from different wild Ananas botanical *** analysis further revealed that both *** *** and *** *** are likely progenitors of pineapple ***,the traditional classification of cultivated pineapple into horticultural groups(e.g.‘Cayenne’,‘Spanish’,‘Queen’)was not well supported by the present *** SNP markers provide robust and universally comparable DNA fingerprints;thus,they can serve as an efficient genotyping tool to assist pineapple germplasm management,propagation of planting material,and pineapple cultivar *** high rate of genetic redundancy detected in this pineapple collection suggests the potential impact of applying this technology on other clonally propagated perennial crops.

关键词： cultivar maintained collection

Developing single nucleotide polymorphism(SNP)markers from transcriptome sequences for identification of longan(Dimocarpus longan)germplasm

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Horticulture Research 2015年第1期2卷 325-334页

作者： Boyi wang Hua-wei Tan wanping Fang lyndel w.meinhardt Sue Mischke Tracie Matsumoto Dapeng Zhang Yunnan Forestry Technological College Kunming650224YunnanChina Sustainable Perennial Crops Laboratory USDA-ARSBeltsville Agricultural Research CenterBeltsville20705MDUSA College of Horticulture Nanjing Agricultural UniversityNanjing210095JiangsuChina Tropical Plant Genetic Resources and Disease Research USDA-ARSHilo96720HIUSA

Longan(Dimocarpus longan Lour.)is an important tropical fruit tree *** varietal identification is essential for germplasm management and *** longan transcriptome sequences from public databases,we developed single nucleotide polymorphism(SNP)markers;validated 60 SNPs in 50 longan germplasm accessions,including cultivated varieties and wild germplasm;and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor(Pwere verified and off-type trees were *** analysis revealed genetic relationships among analyzed *** varieties differed significantly from wild populations(Fst=0.300;Pween varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic *** SNP markers provide a powerful tool to manage longan genetic resources and breeding,with accurate and efficient genotype identification.

关键词： germplasm cultivated breeding

Exogenous abscisic acid significantly affects proteome in teaplant (Camellia sinensis) exposed to drought stress

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Horticulture Research 2014年第1期1卷 167-175页

作者： Lin Zhou Hui Xu Sue Mischke lyndel w.meinhardt Dapeng Zhang Xujun Zhu Xinghui Li wanping Fang College of Horticulture Nanjing Agricultural UniversityNanjing 210095China USDA/ARS Beltsville Agricultural Research CenterSPCLBeltsvilleMD 20705USA

Tea[Camellia sinensis(L.)***]is an important economic crop,and drought is the most important abiotic stress affecting yield and *** acid(ABA)is an important phytohormone responsible for activating drought *** understanding of ABA effects on tea plant under drought stress is essential to develop drought-tolerant tea genotypes,along with crop management practices that can mitigate drought *** objective of the present investigation is evaluation of effects of exogenous ABA on the leaf proteome in tea plant exposed to drought *** protein patterns of tea plants under simulated drought stress[(polyethylene glycol(PEG)-treated]and exogenous ABA treatment were analyzed in a time-course experiment using two-dimensional electrophoresis(2-DE),followed by matrix-assisted laser desorption/ionization time-of-flight(MALDI-TOF)mass spectrometry(MS).Among the 72 protein spots identified by MALDI-TOF MS,16 proteins were downregulated and two were upregulated by exogenous *** upregulated proteins have roles in glycolysis and photosystem II ***-one protein spots were responsive to drought stress and most participate in carbohydrate and nitrogen metabolism,control of reactive oxygen species(ROS),defense,signaling or nucleic acid *** combined treatments of exogenous ABA and drought showed upregulation of 10 protein spots at 12 h and upregulation of 11 proteins at 72 h after initiation of drought *** results support the importance of the role that ABA plays in the tea plant during drought stress,by improving protein transport,carbon metabolism and expression of resistance proteins.

关键词： plant drought stress

A novel method for clustering cellular data to improve classification

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Neural Regeneration Research 2025年第9期20卷 2697-2705页

作者： Diek w.wheeler Giorgio A.Ascoli Center for Neural Informatics Structures&PlasticityKrasnow Institute for Advanced Study Bioengineering Department Volgenau School of Engineering George Mason University FairfaxVAUSA

Many fields,such as neuroscience,are experiencing the vast prolife ration of cellular data,underscoring the need fo r organizing and interpreting large datasets.A popular approach partitions data into manageable subsets via hierarchical clustering,but objective methods to determine the appropriate classification granularity are *** recently introduced a technique to systematically identify when to stop subdividing clusters based on the fundamental principle that cells must differ more between than within *** we present the corresponding protocol to classify cellular datasets by combining datadriven unsupervised hierarchical clustering with statistical *** general-purpose functions are applicable to any cellular dataset that can be organized as two-dimensional matrices of numerical values,including molecula r,physiological,and anatomical *** demonstrate the protocol using cellular data from the Janelia MouseLight project to chara cterize morphological aspects of neurons.

关键词： cellular data clustering dendrogram data classification Levene's one-tailed statistical test unsupervised hierarchical clustering

Genistein:a possible solution for the treatment of Alzheimer’s disease

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Neural Regeneration Research 2025年第10期20卷 2903-2905页

作者： Karolina Pierzynowska Bartosz Karaszewski Grzegorz węgrzyn Department of Molecular Biology University of GdanskGdanskPoland Gdansk Polandand Department of Adult NeurologyFaculty of MedicineMedical University of GdanskGdanskPoland

Neurodegenerative diseases are defined as disorders resulting from the slow and progressive loss of function and eventual death of neural cells that result from the primary pathology of nervous *** can lead to severe nervous system dysfunction,eventually affecting multiple organs and *** hundred neurodegenerative diseases have been described,and owing to their prevalence,severity.

关键词： organs Alzheimer death

Glia-to-neuron reprogramming to the rescue?

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Neural Regeneration Research 2025年第5期20卷 1395-1396页

作者： Jack w.Hickmott Cindi M.Morshead Department of Surgery University of TorontoTorontoONCanada Donnelly Centre for Cellular and Biomolecular Research TorontoONCanada Institute of Biomedical Engineering University of TorontoTorontoONCanada The KITE Research Institute Toronto Rehabilitation InstituteUniversity Health NetworkTorontoONCanada

Over the last two decades,the dogma that cell fate is immutable has been increasingly challenged,with important implications for regenerative *** brea kth rough discovery that induced pluripotent stem cells could be generated from adult mouse fibroblasts is powerful proof that cell fate can be *** exciting extension of the discovery of cell fate impermanence is the direct cellular reprogram ming hypothesis-that terminally differentiated cells can be reprogrammed into other adult cell fates without first passing through a stem cell state.

关键词： programming passing proof