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Genomic consequences of apple improvement

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

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Search for microglia-specific peptides:advances in the discovery toolbox

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Neural Regeneration Research 2025年第2期20卷 471-472页

作者： Ivan Sarabia kyle m.Koss Department of Surgery University of ArizonaTucsonAZUSA

Uncontrolled and chronic inflammatory states in the central nervous system(CNS)are the hallmark of neurodegenerative pathology and every injury or stroke-related *** key mediators of these neuroinflammatory states are glial cells known as microglia,the resident immune cell at the core of the inflammatory event,and astroglia,which encapsulate inflammatory insults in proteoglycan-rich scar *** gliotic scar blocks significant portions of healthy axonal networking,preventing *** most neuroinflammation is exclusively based on the responses of said microglia,their phenotypes are suggested to follow those of macrophages;m1 and m2 are opposites of pro-and ***,microglial phenotypes have been identified to be on an inflammatory spectrum encompassing developmental,homeostatic,and reparative behaviors as opposed to their ability to affect devastating cell death cascades and scar tissue formation.

关键词： inflammation pathology death

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Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity

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molecular Plant 2022年第3期15卷 520-536页

作者： Genevieve Hoopes Xiaoxi meng John P.Hamilton Sai Reddy Achakkagari Fernanda de Alves Freitas Guesdes marie E.Bolger Joseph J.Coombs Danny Esselink Natalie R.Kaiser Linda Kodde maria Kyriakidou Brian Lavrijssen Natascha van Lieshout Rachel Shereda Heather K.Tuttle Brieanne Vaillancourt Joshua C.Wood Jan mde Boer Nolan Bornowski Peter Bourke David Douches Herman Jvan Eck Dave Ellis max J.Feldman kyle m.gardner Johannes C.P.Hopman Jiming Jiang Walter S.De Jong Joseph C.Kuhl Richard G.Novy Stan Oome Vidyasagar Sathuvalli Ek Han Tan Remco A.Ursum m.Isabel Vales Kelly Vining Richard G.F.Visser Jack Vossen G.Craig Yencho Noelle L.Anglin Christian W.B.Bachem Jeffrey B.Endelman Laura m.Shannon martina V.Stromvik Helen H.Tai Bjorn Usadel C.Robin Buell Richard Finkers Department of Plant Biology Michigan State UniversityEast LansingMI 48824USA Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Department of Plant Science McGill UniversitySainte-Anne-de-BellevueQC H9X 3V9Canada Plant Breeding Wageningen University&ResearchPlant Breeding6708 PB Wageningenthe Netherlands IBG-4 Bioinformatics Forschungszentrum JülichWilhelm Johnen Str52428 JülichGermany Department of Plant Soiland Microbial SciencesMichigan State UniversityEast LansingMI 48824USA Bayer Crop Science WoodlandCA 95695USA Averis Seeds B.V. 9640 AA Veendamthe Netherlands International Potato Center 1895 Avenida La MolinaLimaPeru USDA-ARS ProsserWA 99350USA Agriculture and Agri-Food Canada Fredericton Research and Development Centre FrederictonNB E3B 4Z7Canada School of Integrative Plant Science Cornell UniversityIthacaNY 14853-1901USA Department of Plant Sciences University of IdahoMoscowID 83844USA USDA-ARS Small Grains and Potato Germplasm ResearchAberdeenID 83210USA HZPC Research B.V. Edisonweg 58501 XG Jourethe Netherlands Department of Crop and Soil Science Oregon State UniversityHermistonOR 97838USA School of Biology and Ecology University of Maine5735 Hitchner Hall OronoME 04469USA Department of Horticultural Sciences Texas A&M UniversityCollege StationTX 77843-2133USA Department of Horticulture Oregon State UniversityCorvallisOR 97331USA Department of Horticultural Science North Carolina State UniversityRaleighNC 27695-7609USA Department of Horticulture University of Wisconsin-MadisonMadisonWI 53706USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Institute for Biological Data Science Heinrich Heine UniversityDusseldorf40225 DusseldorfGermany Plant Resilience Institute Michigan State UniversityEast LansingMI 48824USA Present address:GenNovation B.V. Wageningenthe Netherlands

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous *** assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity,including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively result in a highly complex transcriptome and predicted proteome,which are distributed across the homologous *** species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding *** a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid *** a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic *** StCDF1 locus controls maturity,and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent *** of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

关键词： potato allele diversity phased assembly polyploid pan-genome wild introgressions

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A crosslinked polymer as dopant-free hole-transport material for efficient n-i-p type perovskite solar cells

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Journal of Energy Chemistry 2021年第4期30卷 211-218页

作者： Linqin Wang Fuguo Zhang Tianqi Liu Wei Zhang Yuanyuan Li Bin Cai Lanlan He Yu Guo Xichuan Yang Bo Xu James m.gardner Lars Kloo Licheng Sun Organic Chemistry Centre of Molecular DevicesDepartment of ChemistryKTH Royal Institute of TechnologySE-10044 StockholmSweden Applied Physical Chemistry Centre of Molecular DevicesDepartment of ChemistryKTH Royal Institute of TechnologySE-10044 StockholmSweden Wallenberg Wood Science Centre Department of Fibre and Polymer TechnologyKTH Royal Institute of TechnologySE-10044 StockholmSweden State Key Laboratory of Fine Chemicals Institute of Artificial PhotosynthesisDUT-KTH Joint Education and Research Centre on Molecular DevicesDalian University of TechnologyDalian 116024LiaoningChina

A new crosslinked polymer,called P65,with appropriate photo-electrochemical,opto-electronic,and thermal properties,has been designed and synthesized as an efficient,dopant-free,hole-transport material(HTm)for n-i-p type planar perovskite solar cells(PSCs).P65 is obtained from a low-cost and easily synthesized spiro[fluorene-9,90-xanthene]-30,60-diol(SFX-OH)-based monomer X65 through a freeradical polymerization *** combination of a three-dimensional(3 D)SFX core unit,holetransport methoxydiphenylamine group,and crosslinked polyvinyl network provides P65 with good solubility and excellent film-forming *** employing P65 as a dopant-free hole-transport layer in conventional n-i-p type PSCs,a power conversion efficiency(PCE)of up to 17.7%is *** the best of our knowledge,this is the first time a 3 D,crosslinked,polymeric dopant-free HTm has been reported for use in conventional n-i-p type *** study provides a new strategy for the future development of a 3 D crosslinked polymeric dopant-free HTm with a simple synthetic route and low-cost for commercial,large-scale applications in future PSCs.

关键词： Perovskite solar cell Hole-transport material Dopant-free Crosslinked polymer Spiro[fluorene-9,9’-xanthene](SFX)

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QTL analysis of soft scald in two apple populations

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Horticulture Research 2016年第1期3卷 117-123页

作者： Kendra A mcClure kyle m.gardner Peter mA Toivonen Cheryl R Hampson Jun Song Charles F Forney John DeLong Istvan Rajcan Sean myles Department of Plant and Animal Sciences Faculty of AgricultureDalhousie UniversityTruroB2N 5E3Nova ScotiaCanada Department of Plant Agriculture Crop Science BuildingUniversity of GuelphGuelphN1G 2W1OntarioCanada Agriculture and Agri-Food Canada Fredericton Research and Development CentreFrederictonE3B 4Z7New BrunswickCanada Agriculture and Agri-Food Canada Summerland Research and Development CentreSummerlandV0H 1Z0British ColumbiaCanada Agriculture and Agri-Food Canada Kentville Research and Development CentreKentvilleB4N 1J5Nova ScotiaCanada

The apple(malus×domestica Borkh.)is one of the world’s most widely grown and valuable fruit *** demand for apples year round,storability has emerged as an important consideration for apple breeding *** scald is a cold storage-related disorder that results in sunken,darkened tissue on the fruit *** breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year *** breeding approaches are protracted and labor intensive,and therefore marker-assisted selection(mAS)is a valuable tool for *** advance mAS for storage disorders in apple,we used genotyping-by-sequencing(GBS)to generate high-density genetic maps in two F1 apple populations,which were then used for quantitative trait locus(QTL)mapping of soft *** total,900 million DNA sequence reads were generated,but after several data filtering steps,only 2%of reads were ultimately used to create two genetic maps that included 1918 and 2818 single-nucleotide *** QTL associated with soft scald were identified in one of the bi-parental populations originating from parent 11W-12-11,an advanced breeding *** study demonstrates the utility of next-generation DNA sequencing technologies for QTL mapping in F1 populations,and provides a basis for the advancement of mAS to improve storability of apples.

关键词： breeding cultivar apple

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Curcurbita pepo subspecies delineates striped cucumber beetle (Acalymma vittatum) preference

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Horticulture Research 2016年第1期3卷 182-189页

作者： L Brzozowski B m Leckie J gardner m P Hoffmann m mazourek Section of Plant Breeding and Genetics School of Integrative Plant ScienceCornell UniversityIthacaNYUSA School of Agriculture Tennessee Tech UniversityCookevilleTNUSA Department of Entomology Cornell UniversityIthacaNYUSA

The striped cucumber beetle(Acalymma vittatum(F.))is a destructive pest of cucurbit crops,and management could be improved by host plant resistance,especially in organic farming ***,despite the variation in striped cucumber beetle preference observed within the economically important species,Cucurbita pepo L.,plant breeders and entomologists lacked a simple framework to classify and exploit these *** study used recent phylogenetic evidence and bioassays to organize striped cucumber beetle preference within *** results indicate preference contrasts between the two agriculturally relevant subspecies:*** *** and *** *** of *** *** were more strongly preferred than *** *** *** structure of beetle preference in *** will allow plant breeders and entomologists to better focus research efforts on host plant non-preference to control striped cucumber beetles.

关键词： beet crops breed

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Guest editorial–special issue on ground control in mining in 2020

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International Journal of mining Science and Technology 2021年第1期31卷 1-2页

作者： michael m.murphy Ted Klemetti Heather Lawson Brijes mishra kyle Perry CDC NIOSH PittsburghPA 15236USA CDC NIOSH SpokaneWA 99207USA Department of mining Engineering West Virginia UniversityMorgantown 26501USA Department of mining Engineering Missouri University of Science and TechnologyRollaMO 65409USA

Ground control is the science of studying and controlling the behavior of rock strata in response to mining ***-control-related research has seen significant advancements over the last 40 years,and these accomplishments are well documented in the proceedings of the annual International Conference on Ground Control in mining(ICGCm)[1].The ICGCm is a forum to promote closer communication among researchers,consultants,regulators,manufacturers,and mine operators to expedite solutions to ground control problems in mining[2–7].Fundamental research and advancements in ground control science define the central core of the conference *** information to mine operators is a priority,as the conference goal is to offer solutions-oriented *** addition,the conference has included innovative technologies and ideas in miningrelated fields such as exploration,geology,and surface and underground mining in all *** new ground control technologies and design standards adopted by the mining industry were first discussed at *** conference is recognized as the leading international forum for introducing new ground-control-related research and products.

关键词： operators closer accomplishment

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Role of ion channels in gastrointestinal cancer

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World Journal of Gastroenterology 2019年第38期25卷 5732-5772页

作者： kyle J Anderson Robert T Cormier Patricia m Scott Department of Biomedical Sciences University of Minnesota Medical School

In their seminal papers Hanahan and Weinberg described oncogenic processes a normal cell undergoes to be transformed into a cancer *** functions of ion channels in the gastrointestinal(GI)tract influence a variety of cellular processes,many of which overlap with these hallmarks of *** this review we focus on the roles of the calcium(Ca^2+),sodium(Na^+),potassium(K^+),chloride(Cl^-)and zinc(Zn^2+)transporters in GI cancer,with a special emphasis on the roles of the KCNQ1 K+channel and CFTR Cl-channel in colorectal cancer(CRC).Ca^2+is a ubiquitous second messenger,serving as a signaling molecule for a variety of cellular processes such as control of the cell cycle,apoptosis,and *** members of the TRP superfamily,including TRPm8,TRPm7,TRPm6 and TRPm2,have been implicated in GI cancers,especially through overexpression in pancreatic adenocarcinomas and down-regulation in colon ***-gated sodium channels(VGSCs)are classically associated with the initiation and conduction of action potentials in electrically excitable cells such as neurons and muscle *** VGSC NaV1.5 is abundantly expressed in human colorectal CRC cell lines as well as being highly expressed in primary CRC *** have demonstrated that conductance through NaV1.5 contributes significantly to CRC cell invasiveness and cancer ***2+transporters of the ZIP/SLC39A and ZnT/SLC30A families are dysregulated in all major GI organ cancers,in particular,ZIP4 up-regulation in pancreatic cancer(PC).more than 70 K+channel genes,clustered in four families,are found expressed in the GI tract,where they regulate a range of cellular processes,including gastrin secretion in the stomach and anion secretion and fluid balance in the intestinal *** distinct types of K+channels are found dysregulated in the GI *** are hERG1 upregulation in PC,gastric cancer(GC)and CRC,leading to enhanced cancer angiogenesis and invasion,and KCNQ1 down-regulation in CR

关键词： Ion channels Gastrointestinal cancer Colorectal cancer Gastric cancer Pancreatic cancer Esophageal cancer Hepatocellular carcinoma Prognostic biomarker Novel therapies Clinical targets

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Guest editorial–Special issue on ground control in mining in 2017

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International Journal of mining Science and Technology 2018年第1期28卷 1-2页

作者： michael m.murphy Brijes mishra kyle Perry Heather Lawson Pittsburgh mining Research Division NIOSH mining Engineering West Virginia University mining&Nuclear Engineering Missouri S&T Spokane mining Research Division NIOSH

Ground control is the science of studying and controlling the behavior of rock strata in response to mining *** control-related research has seen significant advancements over the last 36 years,and these accomplishments are well documented in the proceedings of the annual International Conference on Ground Control in mining(ICGCm)[1].The ICGCm is a forum to promote closer communication among researchers,consultants,regulators,manufacturers,and mine operators to expedite solutions to ground control problems in mining[2–8].Fundamental research and advancements in ground control science define the central core of the conference *** information to mine operators is a priority,as the conference goal is to offer solution-oriented *** addition,the conference has included innovative technologies and ideas in mining-related fields such as exploration,geology,and surface and underground *** new ground control technologies and design standards adopted by the mining industry were first discussed at ***,this conference is recognized as the best forum for introducing new ground control-related research and products.

关键词： Guest controlling exploration response surface forum strata ideas

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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

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