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Discovery and genome-guided mapping of REN12 from Vitis amurensis, conferring strong, rapid resistance to grapevine powdery mildew

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Horticulture Research 2023年第5期10卷 139-149页

作者： Surya Sapkota Cheng Zou Craig Ledbetter Anna Underhill Qi Sun David Gadoury lance cadle-davidson School of Integrative Plant Science Cornell AgriTechCornell UniversityGenevaNY14456USA BRC Bioinformatics Facility Institute of BiotechnologyCornell UniversityIthacaNY14853USA United States Department of Agriculture(USDA)-Agricultural Research Service(ARS) Crop DiseasesPests and Genetics Research UnitSan Joaquin Valley Agricultural Sciences CenterParlierCA93648USA USDA-ARS Grape Genetics Research UnitGenevaNY14456USA

Powdery mildew resistance genes restrict infection attempts at different stages of ***,a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis‘PI 588631’that rapidly stopped over 97%of Erysiphe necator conidia,before or immediately after emergence of a secondary hypha from *** resistance was effective across multiple years of vineyard evaluation on leaves,stems,rachises,and fruit and against a diverse array of *** laboratory *** core genome rhAmpSeq markers,resistance mapped to a single dominant locus(here named REN12)on chromosome 13 near 22.8–27.0 Mb,irrespective of tissue type,explaining up to 86.9%of the phenotypic variation observed on *** sequencing of recombinant vines using skim-seq technology enabled the locus to be further resolved to a 780 kb region,from 25.15 to 25.93 *** analysis indicated the allele-specific expression of four resistance genes(NLRs)from the resistant ***12 is one of the strongest powdery mildew resistance loci in grapevine yet documented,and the rhAmpSeq sequences presented here can be directly used for marker-assisted selection or converted to other genotyping *** no virulent isolates were identified among the genetically diverse isolates and wild populations of *** tested here,NLR loci like REN12 are often ***,stacking of multiple resistance genes and minimal use of fungicides should enhance the durability of resistance and could enable a 90%reduction in fungicides in low-rainfall climates where few other pathogens attack the foliage or fruit.

关键词： Vitis resistance durability

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A High-Throughput Phenotyping System Using Machine Vision to Quantify Severity of Grapevine Powdery Mildew

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Plant Phenomics 2019年第1期1卷 210-222页

作者： Andrew Bierman Tim LaPlumm lance cadle-davidson David Gadoury Dani Martinez Surya Sapkota Mark Rea Lighting Research Center Rensselaer Polytechnic InstituteTroyNY 12180USA United States Department of Agriculture-Agricultural Research Service Grape Genetics Research UnitGenevaNY 14456USA Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant ScienceCornell UniversityGenevaNY 14456USA

Powdery mildews present specific challenges to phenotyping systems that are based on *** previously developed lowthroughput,quantitative microscopy approaches for phenotyping resistance to Erysiphe necator on thousands of grape leaf disk samples for genetic analysis,here we developed automated imaging and analysis methods for *** severity on leaf *** pairing a 46-megapixel CMOS sensor camera,a long-working distance lens providing 3.5×magnification,X-Y sample positioning,and Z-axis focusing movement,the system captured 78%of the area of a 1-cm diameter leaf disk in 3 to 10 focus-stacked images within 13.5 to 26 *** image pixel represented 1.44 m2 of the leaf disk.A convolutional neural network(CNN)based on GoogLeNet determined the presence or absence of *** hyphae in approximately 800 subimages per leaf disk as an assessment of severity,with a training validation accuracy of 94.3%.For an independent image set the CNN was in agreement with human experts for 89.3%to 91.7%of *** live-imaging approach was nondestructive,and a repeated measures time course of infection showed differentiation among susceptible,moderate,and resistant *** over one thousand samples per day with good accuracy,the system can assess host resistance,chemical or biological efficacy,or other phenotypic responses of grapevine to *** addition,new CNNs could be readily developed for phenotyping within diverse pathosystems or for diverse traits amenable to leaf disk assays.

关键词： pairing image enable

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Identification of QTLs for berry acid and tannin in a Vitis aestivalisderived‘Norton'-based population

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Fruit Research 2021年第1期1卷 68-78页

作者： Karlene L.Negus Li-Ling Chen Jonathan Fresnedo-Ramírez Heather A.Scott Gavin L.Sacks lance cadle-davidson Chin-Feng Hwang Department of Environmental Plant Science and Natural Resources and State Fruit Experiment Station at Mountain Grove Campus Missouri State UniversitySpringfieldMO 65897USA Department of Horticulture and Crop Science Ohio State UniversityWoosterOH 44691USA Department of Food Science Cornell UniversityIthacaNY 14853USA USDA-ARS Grape Genetics Research Unit GenevaNY 14456USA

Acidity and tannins are among the grape berry quality traits that influence wine *** advantageous environmental tolerances of Vitis aestivalis-derived‘Norton',its acidity and tannin concentrations often deviate from expectations set for *** of the genetic determinants of malic acid,tartaric acid,pH,and tannin can assist in the improvement of new hybrid *** this purpose,a‘Norton'and ***‘Cabernet Sauvignon'hybrid population containing 223 individuals was used to construct a linkage map containing 384 simple sequence repeat(SSR)and 2,084 genotyping-by-sequencing(GBS)-derived single nucleotide polymorphism(SNP)*** resulting map was 1,441.9 cM in length with an average inter-marker distance of 0.75 cM and spanned 19 linkage groups(LGs).Quantitative trait loci(QTLs)were detected for malic acid,tartaric acid,pH,and *** for malic acid(LG 8)and pH(LG 6)were observed across multiple years and explained approximately 17.7%and 18.5%of the phenotypic variation,***,QTLs for tartaric acid were identified on linkage groups 1,6,7,9,and 17 and tannin on LG 2 in single-year *** QTLs for tartaric acid explained between 8.8−14.3%and tannin explained 24.7%of the phenotypic *** markers linked to these QTLs can be used to improve hybrid cultivar breeding through marker-assisted selection.

关键词： linkage explained approximate

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A next-generation marker genotyping platform(AmpSeq)in heterozygous crops:a case study for marker-assisted selection in grapevine

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Horticulture Research 2016年第1期3卷 302-313页

作者： Shanshan Yang Jonathan Fresnedo-Ramíre Minghui Wang Linda Cote Peter Schweitzer Paola Barba Elizabeth M Takacs Matthew Clark James Luby David C Manns Gavin Sacks Anna Katharine Mansfield Jason Londo Anne Fennell David Gadoury Bruce Reisch lance cadle-davidson Qi Sun Horticulture Section School of Integrative Plant ScienceCornell UniversityGenevaNY 14456USA Bioinformatics Facility Cornell UniversityIthacaNY 14853USA Institute of Biotechnology Cornell UniversityIthacaNY 14853USA Plant Breeding and Genetics Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA Department of Horticultural Science University of MinnesotaSt PaulMN 55108USA Department of Food Science Cornell UniversityGenevaNY 14456USA Department of Food Science Cornell UniversityIthacaNY 14853USA USDA-ARS Grape Genetics Research Unit GenevaNY 14456USA Plant Science Department South Dakota State UniversityBrookingsSD 57007USA Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant ScienceCornell UniversityGenevaNY 14456USA

Marker-assisted selection(MAS)is often employed in crop breeding programs to accelerate and enhance cultivar development,via selection during the juvenile phase and parental selection prior to ***-generation sequencing and its derivative technologies have been used for genome-wide molecular marker *** bridge the gap between marker development and MAS implementation,this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery,low-cost genotyping through amplicon sequencing(AmpSeq)and decision *** results document the development of a MAS package derived from genotyping-by-sequencing using three traits(flower sex,disease resistance and acylated anthocyanins)in grapevine *** vast majority of sequence reads(⩾99%)were from the targeted *** 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data,most amplicons(83 to 87%)had<10%missing data,and read depth had a median of 220–244×.Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy,flexibility,speed,high-throughput,low-cost and easily automated analysis.

关键词： crops breeding cultivar

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Robust genome and RNA editing via CRISPR nucleases in PiggyBac systems

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Bioactive Materials 2022年第8期7卷 313-320页

作者： Yuqian Jiang Rachel Catherine Hoenisch Yun Chang Xiaoping Bao Craig E.Cameron Xiaojun lance Lian Department of Biomedical Engineering Pennsylvania State UniversityUniversity ParkPA16802USA Huck Institutes of the Life Sciences Pennsylvania State UniversityUniversity ParkPA16802USA Department of Biology Pennsylvania State UniversityUniversity ParkPA16802USA davidson School of Chemical Engineering Purdue UniversityWest LafayetteIN47907USA Department of Microbiology and Immunology University of North Carolina School of MedicineChapel HillNC27599USA

CRISPR/Cas-mediated genome editing in human pluripotent stem cells(hPSCs)offers unprecedented opportunities for developing in vitro disease modeling,drug screening and cell-based *** efficiently deliver the CRISPR components,here we developed two all-in-one vectors containing Cas9/gRNA and inducible Cas13d/gRNA cassettes for robust genome editing and RNA interference *** vectors utilized the PiggyBac transposon system,which allows stable expression of CRISPR components in *** Cas9 vector PB-CRISPR exhibited high efficiency(up to 99%)of inducing gene knockout in both protein-coding genes and long non-coding *** other inducible Cas13d vector achieved extremely high efficiency in RNA knockdown(98%knockdown for CD90)with optimized gRNA *** together,our PiggyBac CRISPR vectors can serve as powerful toolkits for studying gene functions in hPSCs.

关键词： CRISPR-Cas9 Genome editing Cas13d RNA editing PiggyBac transposon Human pluripotent stem cells

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Engineered human pluripotent stem cell-derived natural killer cells with PD-L1 responsive immunological memory for enhanced immunotherapeutic efficacy

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Bioactive Materials 2023年第9期27卷 168-180页

作者： Yun Chang Gyuhyung Jin Weichuan Luo Qian Luo Juhyung Jung Sydney N.Hummel Sandra Torregrosa-Allen Bennett D.Elzey Philip S.Low Xiaojun lance Lian Xiaoping Bao davidson School of Chemical Engineering Purdue UniversityWest LafayetteIN47907USA Purdue University Institute for Cancer Research West LafayetteIN47907USA Department of Comparative Pathobiology Purdue UniversityWest LafayetteIN 47907USA Department of Chemistry Purdue UniversityWest LafayetteIN47907USA Department of Biomedical Engineering The Huck Institutes of the Life SciencesDepartment of BiologyThe Pennsylvania State UniversityUniversity ParkPA16802USA

Adoptive chimeric antigen receptor(CAR)-engineered natural killer(NK)cells have shown promise in treating various ***,limited immunological memory and access to sufficient numbers of allogenic donor cells have hindered their broader preclinical and clinical ***,we first assess eight different CAR constructs that use an anti-PD-L1 nanobody and/or universal anti-fluorescein(FITC)single-chain variable fragment(scFv)to enhance antigen-specific proliferation and anti-tumor cytotoxicity of NK-92 cells against heterogenous solid *** next genetically engineer human pluripotent stem cells(hPSCs)with optimized CARs and differentiate them into functional dual CAR-NK *** tumor microenvironment responsive anti-PD-L1 CAR effectively promoted hPSC-NK cell proliferation and cytotoxicity through antigen-dependent activation of phosphorylated STAT3(pSTAT3)and pSTAT5 signaling pathways via an intracellular truncated IL-2 receptorβ-chain(ΔIL-2Rβ)and STAT3-binding tyrosine-X-X-glutamine(YXXQ)***-tumor activities of PD-L1-induced memory-like hPSC-NK cells were further boosted by administering a FITC-folate bi-specific adapter that bridges between a programmable anti-FITC CAR and folate receptor alpha-expressing breast tumor ***,our hPSC CAR-NK engineering platform is modular and could constitute a realistic strategy to manufacture off-the-shelf CAR-NK cells with immunological memory-like phenotype for targeted immunotherapy.

关键词： Natural killer cells Human pluripotent stem cells Immunological memory Immunotherapy Chimeric antigen receptor

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