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Uncovering genetic and metabolite markers associated with resistance against anthracnose fruit rot in northern highbush blueberry

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Horticulture Research 2023年第10期10卷 25-36页

作者： MacKenzie Jacobs Samantha Thompson Adrian E.platts Melanie J.A.Body Alexys Kelsey Amanda Saad patrick Abeli Scott J.Teresi Anthony Schilmiller Randolph Beaudry Mitchell J.Feldmann Steven J.Knapp Guo-qing Song Timothy Miles patrick p.edger Department of Biochemistry and Molecular Biology Michigan State UniversityEast LansingMI 48824USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Molecular plant Science program Michigan State UniversityEast LansingMI 48824USA Department of plant Soil and Microbial SciencesMichigan State UniversityEast LansingMI 48824USA Department of Horticulture and Natural Resources Kansas State UniversityOlatheKS 66061USA Genetics and Genome Sciences program Michigan State UniversityEast LansingMI 48824USA Mass Spectrometry&Metabolomics Core Michigan State UniversityEast LansingMI 48824USA Department of plant Sciences University of CaliforniaDavisCA 95616USA

Anthracnose fruit rot(AFR),caused by the fungal pathogen Colletotrichum fioriniae,is among the most destructive and widespread fruit disease of blueberry,impacting both yield and overall fruit *** cultivars have highly variable resistance against *** date,this pathogen is largely controlled by applying various fungicides;thus,a more cost-effective and environmentally conscious solution for AFR is *** we report three quantitative trait loci associated with AFR resistance in northern highbush blueberry(Vaccinium corymbosum).Candidate genes within these genomic regions are associated with the biosynthesis of flavonoids(***)and resistance against ***,we examined gene expression changes in fruits following inoculation with Colletotrichum in a resistant cultivar,which revealed an enrichment of significantly differentially expressed genes associated with certain specialized metabolic pathways(*** biosynthesis)and pathogen *** non-targeted metabolite profiling,we identified a flavonol glycoside with properties consistent with a quercetin rhamnoside as a compound exhibiting significant abundance differences among the most resistant and susceptible individuals from the genetic mapping *** analysis revealed that this compound exhibits significant abundance differences among the most resistant and susceptible individuals when analyzed as two ***,individuals within each group displayed considerable overlapping variation in this compound,suggesting that its abundance may only be partially associated with resistance against *** findings should serve as a powerful resource that will enable breeding programs to more easily develop new cultivars with superior resistance to AFR and as the basis of future research studies.

关键词： applying resistance specialized

VcRR2 regulates chilling-mediated flowering through expression of hormone genes in a transgenic blueberry mutant

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Horticulture Research 2019年第1期6卷 531-546页

作者： Tianyi Lin Aaron Walworth Xiaojuan Zong Gharbia H.Danial Elise M.Tomaszewski pete Callow Xiumei Han L.Irina Zaharia patrick p.edger Gan-yuan Zhong Guo-qing Song plant Biotechnology Resource and Outreach Center Department of HorticultureMichigan State UniversityEast LansingMI 48824USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Aquatic and Crop Resource Development National Research Council of CanadaSaskatoonSK S7N 0W9Canada Grape Genetics Research Unit USDA-ARSGenevaNY 14456USA

The molecular mechanism underlying dormancy release and the induction of flowering remains poorly understood in woody ***-legacy is a valuable blueberry mutant,in which a transgene insertion caused increased expression of a RESpONSE REGULATOR 2-like gene(VcRR2).Mu-legacy plants,compared with nontransgenic‘Legacy’plants,show dwarfing,promotion of flower bud formation,and can flower under nonchilling *** conducted transcriptomic comparisons in leaves,chilled and nonchilled flowering buds,and late-pink buds,and analyzed a total of 41 metabolites of six groups of hormones in leaf tissues of both Mu-legacy and‘Legacy’*** analyses uncovered that increased VcRR2 expression promotes the expression of a homolog of Arabidopsis thaliana ENTCOpALYL DIpHOSpHATE SYNTHETASE 1(VcGA1),which induces new homeostasis of hormones,including increased gibberellin 4(GA4)levels in Mu-legacy ***,increased expression of VcRR2 and VcGA1,which function in cytokinin responses and gibberellin synthesis,respectively,initiated the reduction in plant height and the enhancement of flower bud formation of the Mu-legacy plants through interactions of multiple *** nonchilled flower buds,29 differentially expressed transcripts of 17 genes of five groups of hormones were identified in transcriptome comparisons between Mu-legacy and‘Legacy’plants,of which 22 were chilling ***,these analyses suggest that increased expression of VcRR2 was collectively responsible for promoting flower bud formation in highbush blueberry under nonchilling *** report here for the first time the importance of VcRR2 to induce a suite of downstream hormones that promote flowering in woody plants.

关键词： collective insertion dwarf

A roadmap for research in octoploid strawberry

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Horticulture Research 2020年第1期7卷 2300-2316页

作者： Vance M.Whitaker Steven J.Knapp Michael A.Hardigan patrick p.edger Janet p.Slovin Nahla V.Bassil Timo Hytönen Kathryn K.Mackenzie Seonghee Lee Sook Jung Dorrie Main Christopher R.Barbey Sujeet Verma University of Florida Institute of Food and Agricultural SciencesGulf Coast Research and Education CenterWimaumaFlorida 33598USA Department of plant Sciences University of CaliforniaDavisCA 95616USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA USDAARS Genetic Improvement of Fruits and Vegetables Laboratory BeltsvilleMA 20705USA USDA-ARS National Clonal Germplasm Repository CorvallisOR 97333USA Department of Agricultural Sciences Viikki Plant Science CentreUniversity of HelsinkiHelsinki 00790Finland Organismal and Evolutionary Biology Research programme Faculty of Biological and Environmental SciencesViikki Plant Science CentreUniversity of HelsinkiHelsinki 00790Finland NIAB EMR Kent ME196BJUK Department of Horticulture Washington State UniversityPullmanWA 99164USA

The cultivated strawberry(Fragaria×ananassa)is an allo-octoploid species,originating nearly 300 years ago from wild progenitors from the *** that time the strawberry has become the most widely cultivated fruit crop in the world,universally appealing due to its sensory qualities and health *** recent publication of the first highquality chromosome-scale octoploid strawberry genome(***)is enabling rapid advances in genetics,stimulating scientific debate and provoking new research *** this forward-looking review we propose avenues of research toward new biological insights and applications to *** these are the origins of the genome,characterization of genetic variants,and big data approaches to *** areas of research in molecular biology will include the control of flowering,fruit development,fruit quality,and plant–pathogen *** order to realize this potential as a global community,investments in genome resources must be continually augmented.

关键词： straw cultivated looking

Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

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Horticulture Research 2018年第1期5卷 868-878页

作者： Rubina Jibran Helge Dzierzon Nahla Bassil Jill M.Bushakra patrick p.edger Shawn Sullivan Chad E.Finn Michael Dossett Kelly J.Vining Robert VanBuren Todd C.Mockler Ivan Liachko Kevin M.Davies Toshi M.Foster David Chagné The New Zealand Institute for plant&Food Research Limited Private Bag 11600Palmerston North4474New Zealand USDA-ARS National Clonal Germplasm Repository 33447 Peoria RoadCorvallisOR97333USA Department of Horticulture Michigan State UniversityEast LansingMI48824-2604USA phase Genomics SeattleWA98195USA USDA-ARS Horticultural Crops Research Unit CorvallisOR97330USA B.C.Blueberry Council(in partnership with Agriculture and Agri-Food Canada)Agassiz Food Research Centre AgassizBCV0M 1A0Canada The Donald Danforth plant Science Center St.LouisMO63132USA Department of Genome Sciences University of Washington School of MedicineSeattleWA98195USA

Black raspberry(Rubus occidentalis L.)is a niche fruit crop valued for its flavor and potential health *** improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference *** recently released draft genome for black raspberry(ORUS 4115-3)lacks assembly of scaffolds to chromosome *** used high-throughput chromatin conformation capture(Hi-C)and proximity-Guided Assembly(pGA)to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven *** seven pseudo-chromosomes cover~97.2%of the total contig length(~223.8 Mb).Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic *** regions were inferred from recombination frequencies of genetic markers,alignment of 303 bp centromeric sequence with the pGA,and heat map showing the physical contact matrix over the entire *** demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry(Fragaria vesca L.)assembled using only pacBio long-read *** conclude that pGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.

关键词： breeding black interaction

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

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Horticulture Research 2023年第11期10卷 96-105页

作者： Alan E.Yocca Adrian platts Elizabeth Alger Scott Teresi Molla F.Mengist Juliana Benevenuto Luis Felipe V.Ferrão MacKenzie Jacobs Michal Babinski Maria Magallanes-Lundback philipp Bayer Agnieszka Golicz Jodi L.Humann Dorrie Main Richard V.Espley David Chagné Nick W.Albert Sara Montanari Nicholi Vorsa James polashock Luis Díaz-Garcia Juan Zalapa Nahla V.Bassil patricio R.Munoz Massimo Iorizzo patrick p.edger Department of Horticulture Michigan State UniversityEast LansingMI48824United States Department of plant Biology Michigan State UniversityEast LansingMI48824United States Genetics and Genome Sciences Michigan State UniversityEast LansingMI48824United States plants for Human Health Institute North Carolina State UniversityKannapolisNC United States Horticultural Sciences Department University of FloridaGainesvilleFL 32611United States Department of Biochemistry and Molecular Biology Michigan State UniversityEast LansingMI48824United States University of Western Australia Perth 6009 Australia Justus Liebig University Giessen35390 Germany Department of Horticulture Washington State UniversityPullmanWA99163United States The New Zealand Institute for plant and Food Research Limited(pFR) AucklandNew Zealand The New Zealand Institute for plant and Food Research Limited(pFR) PalmerstonNew Zealand The New Zealand Institute for plant and Food Research Limited(pFR) MotuekaNew Zealand SEBS Plant BiologyRutgers UniversityNew Brunswick NJ 01019 United States Department of Viticulture and Enology University of CaliforniaDavisDavisCA 95616United States National Clonal Germplasm Repository USDA-ARSCorvallisOR 97333United States Department of Horticulture North Carolina State UniversityKannapolisNC United States MSU AgBioResearch Michigan State UniversityEast LansingMI48824United States

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed *** industry continues to face a wide variety of production challenges(*** pressures),as well as a demand for higher-yielding cultivars with improved fruit quality ***,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value ***,we describe the construction and analysis of the first pangenome for both blueberry and *** analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in *** genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality *** discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding *** pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational ***,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

关键词： breeding cultivar crops

Human endogenous retrovirus type-W and multiple sclerosis–related smoldering neuroinflammation

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Neural Regeneration Research 2025年第3期20卷 813-814页

作者： Joel Gruchot Laura Reiche Andrew Chan Robert Hoepner patrick Küry Department of Neurology Medical Faculty and University Hospital DüsseldorfHeinrich Heine University DüsseldorfDüsseldorfGermany Department of Neurology InselspitalBern University Hospital and University of BernBernSwitzerland

Introduction to human endogenous retrovirus type-W(HERV-W): Genomic inheritance from the past includes retroviral sequences that have been stably incorporated into our genomes and account for up to 8% of human DNA.

关键词： endogenous inflammation Human

Implementation and application of pyNE sub-voxel R2S for shutdown dose rate analysis

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plasma Science and Technology 2022年第9期24卷 145-151页

作者： Xiaokang ZHANG patrick C SHRIWISE Songlin LIU paul p H WILSON Institute of plasma physics Hefei Institutes of Physical ScienceChinese Academy of SciencesHefei 230031People’s Republic of China Argonne National Laboratory 9700 S.Cass Ave.IL 60439United States of America University of Wisconsin-Madison 1500 Engineering DrMadisonWI 53706United States of America

pyNE R2S is a mesh-based R2S implementation with the capability of performing shutdown dose rate(SDR)analysis directly on CAD geometry with Cartesian or tetrahedral *** supports advanced variance reduction for fusion energy ***,the assumption of homogenized materials of pyNE R2S with a Cartesian mesh throughout a mesh voxel introduces an approximation in the case where a voxel covers multiple non-void *** work implements a sub-voxel method to add fldelity to pyNE R2S with a Cartesian mesh during the process of activation and photon source sampling by performing independent inventory calculations for each cell within a mesh voxel and using the results of those independent calculations to sample the photon source more *** sub-voxel R2S has been verifled with the Frascati Neutron Generator(FNG)-ITER and ITER computational shutdown dose rate benchmark *** results for sub-voxel R2S show satisfactory agreement with the experimental values or reference *** sub-voxel R2S has been applied to the shutdown dose rate calculation of the Chinese Fusion Engineering Testing Reactor(CFETR).In conclusion,sub-voxel R2S is a reliable tool for SDR calculation and obtains more accurate results with the same voxel size than voxel R2S.

关键词： shutdown dose rate R2S sub-voxel pyNE

Reinforcement learning and A^(*)search for the unit commitment problem patrick de Mars^(∗),Aidan O’Sullivan

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Energy and AI 2022年第3期9卷 172-181页

作者： patrick de Mars Aidan O’Sullivan UCL Energy Institute United Kingdom

previous research has combined model-free reinforcement learning with model-based tree search methodsto solve the unit commitment problem with stochastic demand and renewables generation. This approachwas limited to shallow search depths and suffered from significant variability in run time across probleminstances with varying complexity. To mitigate these issues, we extend this methodology to more advancedsearch algorithms based on A^(*) search. First, we develop a problem-specific heuristic based on priority list unitcommitment methods and apply this in Guided A^(*) search, reducing run time by up to 94% with negligibleimpact on operating costs. In addition, we address the run time variability issue by employing a novel anytimealgorithm, Guided IDA^(*), replacing the fixed search depth parameter with a time budget constraint. We showthat Guided IDA^(*) mitigates the run time variability of previous guided tree search algorithms and enablesfurther operating cost reductions of up to 1%.

关键词： Unit commitment Reinforcement learning Tree search power systems

Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies

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National Science Review 2017年第4期4卷 533-542页

作者： Guangdun peng patrick p.L.Tam Naihe Jing State Key Laboratory of Cell Biology CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of SciencesUniversity of Chinese Academy of Sciences Embryology Unit Children’s Medical Research Institute School of Medical SciencesSydney Medical School University of Sydney School of Life Science and Technology Shanghai Tech University

Establishment of progenitor cell populations and lineage diversity during embryogenesis and the differentiation of pluripotent stem cells is a fascinating and intricate biological process. Conceptually, an understanding of this developmental process provides a framework to integrate stem-cell pluripotency, cell competence and differentiating potential with the activity of extrinsic and intrinsic molecular *** recent advent of enabling technologies of high-resolution transcriptome analysis at the cellular,population and spatial levels proffers the capability of gaining deeper insights into the attributes of the gene regulatory network and molecular signaling in lineage specification and differentiation. In this review, we provide a snapshot of the emerging enabling genomic technologies that contribute to the study of development and stem-cell biology.

关键词： early development cell lineage cell identity scRNA-seq spatial transcriptome