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Patterns of genomic and phenomic diversity in wine and table grapes

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Horticulture Research 2017年第1期4卷 181-191页

作者： zoëmigicovsky Jason Sawler Kyle M Gardner Mallikarjuna K Aradhya Bernard H Prins Heidi R Schwaninger Carlos D Bustamante Edward S Buckler Gan-Yuan Zhong Patrick J Brown Sean Myles Department of Plant Food and Environmental SciencesFaculty of AgricultureDalhousie UniversityTruroB2N 5E3NSCanada Anandia Labs VancouverV6T 1Z4BCCanada Agriculture and Agri-Food Canada Fredericton Research and Development CentreFrederictonE3B 4Z7NBCanada United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm RepositoryUniversity of CaliforniaDavis95616CAUSA United States Department of Agriculture Agricultural Research ServiceGrape Genetics Research UnitNew York State Agricultural Experiment StationCornell UniversityGeneva14456NYUSA Department of Genetics Stanford UniversityStanfordCA 94305USA Department of Plant Breeding and Genetics Cornell UniversityIthaca14853NYUSA United States Department of Agriculture Agricultural Research ServicePlant Genetic Resources UnitNew York State Agricultural Experiment StationCornell UniversityGeneva14456NYUSA Department of Crop Science University of IllinoisUrbana61801ILUSA

Grapes are one of the most economically and culturally important crops worldwide,and they have been bred for both winemaking and fresh *** we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world’s largest grape gene banks,the grape germplasm collection of the United States Department of *** find that phenological events throughout the growing season are correlated,and quantify the marked difference in size between table and wine *** pairing publicly available historical phenotype data with genome-wide polymorphism data,we identify large effect loci controlling traits that have been targeted during domestication and breeding,including hermaphroditism,lighter skin pigmentation and muscat *** for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited,whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian *** uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger *** results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes.

关键词： harbor religious crops

Rootstock effects on scion phenotypes in a‘Chambourcin’experimental vineyard

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Horticulture Research 2019年第1期6卷 992-1004页

作者： zoëmigicovsky Zachary N.Harris Laura LKlein Mao Li Adam McDermaid Daniel H.Chitwood Anne Fennell Laszlo G.Kovacs Misha Kwasniewski Jason P.Londo Qin Ma Allison J.Miller Department of Plant and Animal Sciences Faculty of AgricultureDalhousie UniversityTruroNS B2N 5E3Canada Department of Biology Saint Louis University3507 Laclede AvenueSt.LouisMO 63103-2010USA Donald Danforth Plant Science Center 975 North Warson RoadSt.LouisMO 63132-2918USA Department of Math&Statistics BioSNTRSouth Dakota State UniversityBrookingsSD 57006USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Department of Computational Mathematics Science and EngineeringMichigan State UniversityEast LansingMI 48824USA Department of Agronomy Horticulture&Plant ScienceBioSNTRSouth Dakota State UniversityBrookingsSD 57006USA Department of Biology Missouri State University901S.National AvenueSpringfieldMO 65897USA Department of Food Science University of Missouri221 Eckles HallColumbiaMO 65211USA United States Department of Agriculture Agricultural Research Service:Grape Genetics Research Unit630 West North StreetGenevaNY 14456-1371USA

Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural *** is a common horticultural practice that joins the roots(rootstock)of one plant to the shoot(scion)of another,providing an excellent method for investigating how these two organ systems affect each *** this study,we used the French-American hybrid grapevine‘Chambourcin’(Vitis L.)as a model to explore the rootstock–scion *** examined leaf shape,ion concentrations,and gene expression in‘Chambourcin’grown ungrafted as well as grafted to three different rootstocks(‘SO4’,‘1103P’and‘3309C’)across 2 years and three different irrigation *** found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and *** ion concentrations,the primary source of variation identified was the position of a leaf in a shoot,although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ***,we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted ***,our work reveals the subtle and complex effect of grafting on‘Chambourcin’leaf morphology,ionomics,and gene expression.

关键词： Root grafted irrigation

Genomic consequences of apple improvement

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Horticulture Research 2021年第1期8卷 97-109页

作者： zoe migicovsky Kyle M.Gardner Christopher Richards C.Thomas Chao Heidi R.Schwaninger Gennaro Fazio Gan-Yuan Zhong Sean Myles Department of Plant Foodand Environmental SciencesFaculty of AgricultureDalhousie UniversityTruroNSCanada USDA-ARS Plant Germplasm Preservation Research UnitFort CollinsCOUSA USDA-ARS Grape Genetics Research UnitGen evaNYUSA Present address:Agriculture and Agri-Food Canada Fredericton Research and Development CentreFrederictonNBCanada

The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of ***,we genetically characterise over 1000 apple accessions from the United States Department of Agriculture(USDA)germplasm collection using over 30,000 singlenucleotide polymorphisms(SNPs).We con fi rm the close genetic relationship between modern apple cultivars and their primary progenitor species,Malus sieversii from Central Asia,and fi nd that cider apples derive more of their ancestry from the European crabapple,Malus sylvestris,than do dessert *** determine that most of the USDA collection is a large complex pedigree:over half of the collection is interconnected by a series of fi rst-degree *** addition,15%of the accessions have a fi rst-degree relationship with one of the top 8 cultivars produced in the *** the exception of‘Honeycrisp',the top 8 cultivars are interconnected to each other via pedigree *** cultivars‘Golden Delicious'and‘Red Delicious'were found to have over 60 fi rst-degree relatives,consistent with their repeated use by apple *** detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased fi *** results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will bene fi t from increased exploitation of its tremendous natural genetic diversity.

关键词： cultivar crops consequences

X-ray imaging of 30 year old wine grape wood reveals cumulative impacts of rootstocks on scion secondary growth and Ravaz index

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Horticulture Research 2023年第1期10卷 31-44页

作者： zoëmigicovsky Michelle Y.Quigley Joey Mullins Tahira Ali Joel F.Swift Anita Rose Agasaveeran Joseph D.Dougherty Brendan Michael Grant Ilayda Korkmaz Maneesh Reddy Malpeddi Emily L.McNichol Andrew W.Sharp Jackie L.Harris Danielle R.Hopkins Lindsay M.Jordan Misha T.Kwasniewski R.Keith Striegler Asia L.Dowtin Stephanie Stotts Peter Cousins Daniel H.Chitwood Plant Foodand Environmental SciencesFaculty of AgricultureDalhousie UniversityTruroNova ScotiaB2N 5E3Canada Department of Horticulture Michigan State UniversityEast LansingMI48823USA College of Natural Science Michigan State UniversityEast LansingMI48823USA Department of Neuroscience Michigan State UniversityEast LansingMI48823USA Department of Biology Saint Louis UniversitySt.LouisMO63103USA Department of Physics and Astronomy Michigan State UniversityEast LansingMI48823USA Department of Computational Mathematics Science&EngineeringMichigan State UniversityEast LansingMI48823USA College of Engineering Michigan State UniversityEast LansingMI48823USA College of Social Science Michigan State UniversityEast LansingMI48823USA Department of Economics Michigan State UniversityEast LansingMI48823USA Department of Biochemistry and Molecular Biology Michigan State UniversityEast LansingMI48823USA College of Arts and Letters Michigan State UniversityEast LansingMI48823USA E.&J.Gallo Winery AcampoCA95220USA Current affiliation:Constellation Brands SoledadCA93960USA Department of Food Science The Pennsylvania State UniversityState CollegePA16803USA Department of Forestry Michigan State UniversityEast LansingMI48823USA Department of Agriculture Foodand Resource SciencesUniversity of Maryland Eastern ShorePrincess AnneMD21853USA Department of Natural Sciences University of Maryland Eastern ShorePrincess AnneMD21853USA E.&J.Gallo Winery ModestoCA95354USA Department of Biology Acadia UniversityWolfvilleNova ScotiaB4P 2R6Canada

Annual rings from 30 year old vines in a California rootstock trial were measured to determine the effects of 15 different rootstocks on Chardonnay and Cabernet Sauvignon *** traits measuring vegetative growth,yield,berry quality,and nutrient uptake were collected at the beginning(1995 to 1999)and end(2017 to 2020)of the lifetime of a vineyard initially planted in 1991 and removed in 2021.X-ray Computed Tomography(CT)was used to measure ring widths in 103 *** width was modeled as a function of ring number using a negative exponential *** and late wood ring widths,cambium width,and scion trunk radius were correlated with 27 *** of annual ring width shows that scions alter the width of the first rings but that rootstocks alter the decay of later rings,consistently shortening ring width throughout the lifetime of the *** index,juice pH,photosynthetic assimilation and transpiration rates,and instantaneous water use efficiency are correlated with scion trunk ***,our research indicates that rootstocks modulate secondary growth over years,altering physiology and agronomic *** act in similar but distinct ways from climate to modulate ring width,which borrowing techniques from dendrochronology,can be used to monitor both genetic and environmental effects in woody perennial crop species.

关键词： rings lifetime removed

Apple whole genome sequences:recent advances and new prospects

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Horticulture Research 2019年第1期6卷 1247-1270页

作者： Cameron P.Peace Luca Bianco Michela Troggio Eric van de Weg Nicholas P.Howard Amandine Cornille Charles-Eric Durel Sean Myles zoëmigicovsky Robert J.Schaffer Evelyne Costes Gennaro Fazio Hisayo Yamane Steve van Nocker Chris Gottschalk Fabrizio Costa David Chagné Xinzhong Zhang Andrea Patocchi Susan E.Gardiner Craig Hardner Satish Kumar Francois Laurens Etienne Bucher Dorrie Main Sook Jung Stijn Vanderzande Department of Horticulture Washington State UniversityPullmanWA 99164USA Computational Biology Fondazione Edmund MachSan Michele all’AdigeTN 38010Italy Department of Genomics and Biology of Fruit Crops Fondazione Edmund MachSan Michele all’AdigeTN 38010Italy Plant Breeding Wageningen University and ResearchWageningen 6708PBThe Netherlands Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Institut für Biologie und Umweltwissenschaften Carl von Ossietzky Universität26129 OldenburgGermany GQE-Le Moulon Institut National de la Recherche AgronomiqueUniversity of Paris-SudCNRSAgroParisTechUniversitéParis-Saclay91190 Gif-sur-YvetteFrance Institut National de la Recherche Agronomique Institut de Recherche en Horticulture et SemencesUMR 134549071 BeaucouzéFrance Department of Plant Food and Environmental SciencesFaculty of AgricultureDalhousie UniversityTruroNS B2N 5E3Canada The New Zealand Institute for Plant and Food Research Ltd Motueka 7198New Zealand School of Biological Sciences University of AucklandAuckland 1142New Zealand AGAP INRACIRADMontpellier SupAgroUniversity of MontpellierMontpellierFrance Plant Genetic Resources Unit USDA ARSGenevaNY 14456USA Laboratory of Pomology Graduate School of AgricultureKyoto UniversityKyoto 606-8502Japan Department of Horticulture Michigan State UniversityEast LansingMI 48824USA The New Zealand Institute for Plant and Food Research Ltd(Plant&Food Research) Palmerston North Research CentrePalmerston North 4474New Zealand College of Horticulture China Agricultural University100193 BeijingChina Agroscope 8820 WädenswilSwitzerland Queensland Alliance of Agriculture and Food Innovation University of QueenslandSt Lucia 4072Australia New Cultivar Innovation Plant and Food ResearchHavelock North 4130New Zealand Agroscope 1260 ChanginsSwitzerland

In 2010,a major scientific milestone was achieved for tree fruit crops:publication of the first draft whole genome sequence(WGS)for apple(Malus domestica).This WGS,v1.0,was valuable as the initial reference for sequence information,fine mapping,gene discovery,variant discovery,and tool development.A new,high quality apple WGS,GDDH13 v1.1,was released in 2017 and now serves as the reference genome for *** the past decade,these apple WGSs have had an enormous impact on our understanding of apple biological functioning,trait physiology and inheritance,leading to practical applications for improving this highly valued *** gene identities for phenotypes of fundamental and practical interest can today be discovered much more ***-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and ***-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for *** understand the species,geographical,and genomic origins of domesticated apple more precisely,as well as its relationship to wild *** WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable,environmentally sound,productive,and consumer-desirable apple *** review includes examples of basic and practical breakthroughs and challenges in using the apple *** for“what’s next”focus on necessary upgrades to the genome sequence data pool,as well as for use of the data,to reach new frontiers in genomics-based scientific understanding of apple.

关键词： breakthrough hundreds frontier

Small extrachromosomal circular DNA in amyotrophic lateral sclerosis matter

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Neural Regeneration Research 2025年第5期20卷 1411-1413页

作者： Marcos J.Arauzo-Bravo Daniela Gerovska Matthias Schwab Alexandra Kretz Computational Biology and Systems Biomedicine Biodonostia Health Research InstituteSan SebastianSpain Basque Foundation for Science IKERBASQUEBilbaoSpainMax Planck Institute for Molecular BiomedicineComputational Biology and Bioinformatics GroupMünsterNorth Rhine-WestphaliaGermany Department of Cell Biology and Histology Faculty of Medicine and NursingUniversity of Basque Country(UPV/EHU)LeioaSpain Department of Neurology Jena University HospitalJenaThuringiaGermany

Comprehensive studies identify motor neuron spectrum disorders including amyotrophic lateral sclerosis(ALS)as globally rising fatal disorders with the highest prevalence in aging populations,influenced by ethnicity and ancestry(GBD 2016 Motor Neuron Disease Colla borators,2018).While~10% of diagnoses involve a family history(fALS),most cases are considered sporadic(sALS).However,population-based studies suggest that even cases without a common index mutation impart heritability(Ryan et al.,2019),indicating a crucial role of rare and as yet unknown genetic denominators.

关键词： amyotrophic sclerosis

Inequalities for the Extended Best Polynomial Approximation Operator in Orlicz Spaces

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Acta Mathematica Sinica,English Series 2019年第2期35卷 185-203页

作者： Sonia ACINAS Sergio FAVIER Felipe zo Departamento de Matemática Facultad de Ciencias y Exactas NaturalesUniversidad Nacional de La Pampa Instituto de Matemática Aplicada San Luis IMASLUniversidad Nacional de San Luis and CONICET Departamento de Matemática Universidad Nacional de San Luis

In this paper we pursue the study of the best approximation operator extended from L~Φ to L~φ, where φ denotes the derivative of the function Φ. We get pointwise convergence for the coefficients of the extended best approximation polynomials for a wide class of function f, closely related to the Calder′on–Zygmund class t_m^p(x) which had been introduced in 1961. We also obtain weak and strong type inequalities for a maximal operator related to the extended best polynomial approximation and a norm convergence result for the coefficients is derived. In most of these results, we have to consider Matuszewska–Orlicz indices for the function φ.

关键词： Orlicz spaces extended best polynomial approximation pointwise and norm convergence weak and strong type inequalities Orlicz indices

Science serving justice:opportunities for enhancing integrity in forensic science in Africa

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Forensic Sciences Research 2021年第3期6卷 295-302页

作者： Antonel Olckers zoëHammatt DNAbiotec(Pty)Ltd PretoriaSouth Africa University of Hawaii and Z Consulting HonoluluHawaiiUSA

If the law has made you a witness,remain a man[practitioner1]of *** have no victim to avenge,no guilty or innocent person to convict or save-you must bear testimony within the limits of science.

关键词： limits witness science.

The COVID-19 pandemic:some thoughts on integrity in research and communication

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Forensic Sciences Research 2021年第3期6卷 310-315页

作者： David Morens zoëHammatt National Institute of Allergy and Infectious Diseases National Institutes of HealthBethesdaMarylandUSA University of Hawaii and Z Consulting HonoluluHawaiiUSA

Principles of integrity and ethical practice in research have been reinforced and honed over *** medical and biomedical fields,they have been shaped by challenges that include endemic,emerg-ing,and re-emerging diseases[1],as well as the scientific responses to each disease as it *** responses include clinical and community prevention trials,vaccine and drug trials for persons with life-threatening diseases,applied and basic research with dangerous microbial agents,and many *** fatal pandemics caused by novel agents-for which neither drugs nor vaccines exist-present additional urgent challenges for scientists,defined here to mean biomedical,medical,and pub-lic health scientists and *** addition to conducting research,scientists are also often tasked with communicating research findings,not only to those who make policy decisions,but also to the media and the public.

关键词： prevention shaped policy