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Fire blight QTL analysis in a multi-family apple population identifies a reduced-susceptibility allele in ‘Honeycrisp’

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Horticulture Research 2021年第1期8卷 355-367页

作者： Sarah A.Kostick Soon Li Teh John L.Norelli stijn vanderzande Cameron Peace Kate M.Evans Tree Fruit Research and Extension Center Department of HorticultureWashington State UniversityWenatcheeWA 98801USA United States Department of Agriculture Agricultural Research ServiceAppalachian Fruit Research LaboratoryKearneysvilleWV 25430USA Department of Horticulture Washington State UniversityPullmanWA 99164USA

Breeding apple cultivars with resistance offers a potential solution to fire blight,a damaging bacterial disease caused by Erwinia *** resistance alleles at quantitative trait loci(QTLs)were previously characterized in diverse Malus germplasm with poor fruit quality,which reduces breeding *** study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to *** breeding ***-seven important breeding parents(IBPs)were represented by 314 offspring from 32 full-sib families,with‘Honeycrisp’being the most highly represented *** resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data,QTLs were consistently mapped on chromosomes(Chrs.)6,7,and *** QTLs together explained~28% of phenotypic *** Chr.6 and Chr.15 QTLs colocalized with previously reported QTLs,while the Chr.7 QTL is possibly novel.‘Honeycrisp’inherited a rare reduced-susceptibility allele at the Chr.6 QTL from its grandparent‘Frostbite’.The highly resistant IBP‘Enterprise’had at least one putative reduced-susceptibility allele at all three *** general,lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across *** study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding *** gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.

关键词： blight breeding cultivar

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RosBREED:bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

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Horticulture Research 2020年第1期7卷 527-549页

作者： Amy F.Iezzoni Jim McFerson James Luby Ksenija Gasic Vance Whitaker Nahla Bassil Chengyan Yue Karina Gallardo Vicki McCracken Michael Coe Craig Hardner Jason D.Zurn Stan Hokanson Eric van de Weg Sook Jung Dorrie Main Cassia da Silva Linge stijn vanderzande Thomas M.Davis Lise L.Mahoney Chad Finn Cameron Peace Michigan State University East LansingMI 48824USA Washington State University WenatcheeWA 98801USA University of Minnesota St.PaulMN 55108USA Clemson University ClemsonSC 29634USA University of Florida WimaumaFL 33598USA USDA-ARS CorvallisOR 97333USA Washington State University PuyallupWA 98371USA Washington State University PullmanWA 99164USA Cedar Lake Research Group PortlandOR 97215USA University Queensland BrisbaneQLDAustralia Wageningen University and Research 6700 AA WageningenThe Netherlands University of New Hampshire DurhamNH 03824USA

The Rosaceae crop family(including almond,apple,apricot,blackberry,peach,pear,plum,raspberry,rose,strawberry,sweet cherry,and sour cherry)provides vital contributions to human well-being and is economically significant across the *** 2003,industry stakeholder initiatives prioritized the utilization of genomics,genetics,and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural ***,rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding—a“chasm”existed between existing genomics and genetic information and the application of this knowledge in *** RosBREED project(“Ros”signifying a Rosaceae genomics,genetics,and breeding community initiative,and“BREED”,indicating the core focus on breeding programs),addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research *** was designed to enable the routine application of modern genomics and genetics technologies in *** crop breeding programs,thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural *** review presents a synopsis of the approach,deliverables,and impacts of RosBREED,highlighting synergistic global collaborations and future *** technologies and tools developed are described,including genome-wide scanning platforms and DNA diagnostic *** of DNA-informed breeding use by project participants are presented for all breeding stages,including pre-breeding for disease resistance,parental and seedling selection,and elite selection *** chasm is now bridged,accelerating rosaceous crop genetic improvement.

关键词： breeding cultivar crops

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Elucidation of the ‘Honeycrisp’ pedigree through haplotype analysis with a multi-family integrated SNP linkage map and a large apple (Malus×domestica) pedigree-connected SNP data set

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Horticulture Research 2017年第1期4卷 358-364页

作者： Nicholas P Howard Eric van de Weg David S Bedford Cameron P Peace stijn vanderzande Matthew D Clark Soon Li Teh Lichun Cai James J Luby Department of Horticultural Science University of MinnesotaSt Paul55104MNUSA Department of Plant Breeding Wageningen University and ResearchWageningen6700AJThe Netherlands Department of Horticulture and Landscape Architecture Washington State UniversityPullman99164WAUSA Department of Horticulture Michigan State UniversityEast Lansing48824MIUSA

The apple(Malus×domestica)cultivar Honeycrisp has become important economically and as a breeding *** earlier study with SSR markers indicated the original recorded pedigree of‘Honeycrisp’was incorrect and‘Keepsake’was identified as one putative parent,the other being *** objective of this study was to verify‘Keepsake’as a parent and identify and genetically describe the unknown parent and its grandparents.A multi-family based dense and high-quality integrated SNP map was created using the apple 8 K Illumina Infinium SNP *** map was used alongside a large pedigree-connected data set from the RosBREED project to build extended SNP haplotypes and to identify pedigree relationships.‘Keepsake’was verified as one parent of‘Honeycrisp’and‘Duchess of Oldenburg’and‘Golden Delicious’were identified as grandparents through the unknown *** this finding,siblings of‘Honeycrisp’were identified using the SNP *** records from several of these siblings suggested that the previously unreported parent is a University of Minnesota selection,*** selection is no longer available,but now is genetically described through imputed SNP *** also present the mosaic grandparental composition of‘Honeycrisp’for each of its 17 chromosome *** new pedigree and genetic information will be useful in future pedigree-based genetic studies to connect‘Honeycrisp’with other cultivars used widely in apple breeding *** created SNP linkage map will benefit future research using the data from the Illumina apple 8 and 20 K and Affymetrix 480 K SNP arrays.

关键词： Golden linkage connected

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Validation of SNP markers for fruit quality and disease resistance loci in apple (Malus × domestica Borkh.) using the OpenArray® platform

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Horticulture Research 2019年第1期6卷 1348-1363页

作者： David Chagné stijn vanderzande Chris Kirk Natalie Profitt Rosemary Weskett Susan E.Gardiner Cameron P.Peace Richard K.Volz Nahla V.Bassil The New Zealand Institute for Plant&Food Research Ltd(Plant&Food Research) Palmerston North Research CentrePalmerston NorthNew Zealand Department of Horticulture Washington State UniversityPullmanWAUSA Plant&Food Research Hawke’s Bay Research CentreHavelock NorthNew Zealand USDA-ARS National Clonal Germplasm RepositoryCorvallisORUSA

Genome mapping has promised much to tree fruit breeding during the last 10 ***,one of the greatest challenges remaining to tree fruit geneticists is the translation of trait loci and whole genome sequences into diagnostic genetic markers that are efficient and cost-effective for use by breeders,who must select genetically optimal parents and subsequently select genetically superior individuals among their *** take this translational step,we designed the apple International RosBREED SNP Consortium OpenArray v1.0(IRSCOA v1.0)assay using a set of 128 apple single nucleotide polymorphisms(SNPs)linked to fruit quality and pest and disease resistance trait *** Thermo Fisher Scientific OpenArray®technology enables multiplexed screening of SNP markers using a real-time PCR instrument with fluorescent probe-based Taqman®*** validated the apple IRSCOA v1.0 multitrait assay by screening 240 phenotyped individuals from the Plant&Food Research apple cultivar breeding *** set of individuals comprised commercial and heritage cultivars,elite selections,and families segregating for traits of importance to *** total,33 SNP markers of the IRSCOA v1.0 were validated for use in marker-assisted selection(MAS)for the scab resistances Rvi2/Vh2,Rvi4/Vh4,Rvi6/Vf,fire blight resistance MR5/RLP1,powdery mildew resistance Pl2,fruit firmness,skin colour,flavour intensity,and *** availability of this set of validated trait-associated SNP markers,which can be used individually on multiple genotyping platforms available to various apple breeding programmes or re-designed using the flanking sequences,represents a large translational genetics step from genomics to crop improvement of apple.

关键词： Open resistance breeding

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The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

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Horticulture Research 2021年第1期8卷 2785-2797页

作者： Nicholas P.Howard Cameron Peace Kevin A.T.Silverstein Ana Poets James J.Luby stijn vanderzande Charles-Eric Durel Helene Muranty Caroline Denance Eric van de Weg Institut fur Biologie und Umweltwissenschaften Carl von Ossietzky UniversityOldenburgGermany Department of Horticultural Science University of MinnesotaSt.PaulMNUSA Department of Horticulture and Landscape Architecture Washington State UniversityPullmanWashingtonWAUSA Minnesota Supercomputing Institute University of MinnesotaMinneapolisMNUSA Universited’Angers Institut AgroINRAEIRHSSFR 4207 QuaSaVBeaucouzeFrance Plant Breeding Wageningen University and ResearchWageningenThe Netherlands

Pedigree information is of fundamental importance in breeding programs and related genetics ***,many individuals have unknown *** methods to identify and confirm direct parent–offspring relationships are routine,those for other types of close relationships have yet to be effectively and widely implemented with plants,due to complications such as asexual propagation and extensive *** objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes(referred to in this study as“summed potential lengths of shared haplotypes”,SPLoSH).A custom Python script,HapShared,was developed to generate SPLoSH data in apple and sweet *** was used to establish empirical distributions of SPLoSH data for known relationships in these *** distributions were then used to estimate previously unknown *** studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH *** cherry,a full-sib relationship was deduced for‘Emperor Francis,and‘Schmidt’,a half-sib relationship for‘Van’and‘Windsor’,and the paternal grandparents of‘Stella’were *** apple,29 cultivars were found to share an unknown parent,the pedigree of the unknown parent of‘Cox’s Pomona’was reconstructed,and‘Fameuse’was deduced to be a likely grandparent of‘McIntosh’.Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets,integrated genetic maps,and previously identified pedigree *** with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

关键词： Python breeding crops

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Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array

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Horticulture Research 2019年第1期6卷 1623-1637页

作者： Craig M.Hardner Ben J.Hayes Satish Kumar stijn vanderzande Lichun Cai Julia Piaskowski JoséQuero-Garcia JoséAntonio Campoy Teresa Barreneche Daniela Giovannini Alessandro Liverani Gérard Charlot Miguel Villamil-Castro Nnadozie Oraguzie Cameron P.Peace University of Queensland Queensland Alliance for Agriculture and Food InnovationBrisbaneQLD 4072Australia The New Zealand Institute for Plant and Food Research Limited Hawke’s Bay Research CentreHastings 4130New Zealand Department of Horticulture Washington State UniversityPullmanWA 99164USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA UMR 1332 BFP INRAUniversity of Bordeaux33140 Nouvelle-AquitaineFrance Council for Agricultural Research and Economics(CREA) Fruit Unit of ForlìVia la Canapona1 bis47121 Emilia-RomagnaItaly Centre Technique Interprofessionnel des Fruits et Légumes(CTIFL) 751 Chemin de Balandran30127 BellegardeFrance Department of Horticulture Washington State UniversityIrrigated Agriculture Research and Extension Center24106N Bunn RoadProsserWA 99350USA

The timing of fruit maturity is an important trait in sweet cherry production and *** variation for phenology of fruit maturity in sweet cherry appears to be under strong genetic control,but that control might be complicated by phenotypic instability across *** such genotype-by-environment interaction(G×E)is a common phenomenon in crop plants,knowledge about it is lacking for fruit maturity timing and other sweet cherry *** this study,1673 genome-wide SNP markers were used to estimate genomic relationships among 597 weakly pedigree-connected individuals evaluated over two seasons at three locations in Europe and one location in the USA,thus sampling eight‘environments’.The combined dataset enabled a single meta-analysis to investigate the environmental stability of genomic *** disequilibrium among marker loci declined rapidly with physical distance,and ordination of the relationship matrix suggested no strong structure among *** most parsimonious G×E model allowed heterogeneous genetic variance and pairwise covariances among ***-sense genomic heritability was very high(0.60–0.83),as was accuracy of predicted breeding values(>0.62).Average correlation of additive effects among environments was high(0.96)and breeding values were highly correlated across *** indicated that genomic models can be used in cherry to accurately predict date of fruit maturity for untested individuals in new *** G×E for this trait indicated that phenotypes of individuals will be stable across similar *** analyses for other sweet cherry traits,for which multiple years of data are commonly available among breeders and cultivar testers,would be informative for predicting performance of elite selections and cultivars in new environments.

关键词： maturity environments breeding

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氮碳包封Fe_(3)C纳米颗粒作为高效富氧还原电催化剂

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Science China Materials 2024年第3期67卷 762-770页

作者：汪翠萍李智雷杰李松 stijn F.L.Mertens 胡劲松 School of Chemical Engineering Anhui Province Key Laboratory of Specialty PolymersAnhui University of Science and TechnologyHuainan 232001China Department of Chemistry Energy Lancaster and Materials Science LancasterLancaster UniversityLancaster LA14YBUnited Kingdom Institute of Energy Hefei Comprehensive National Science CenterHefei 230031China

高活性MOF基催化剂的设计和合成为促进动力学不利的氧还原反应(ORR)过程开辟了新的途径.本研究通过在ZIF-8前驱体表面涂覆二茂铁甲酸,然后进行两步炭化工艺,设计和制备了一种具有新型结构的高效电催化剂,以提高ORR性能.两步炭化过程对... 详细信息

高活性MOF基催化剂的设计和合成为促进动力学不利的氧还原反应(ORR)过程开辟了新的途径.本研究通过在ZIF-8前驱体表面涂覆二茂铁甲酸,然后进行两步炭化工艺,设计和制备了一种具有新型结构的高效电催化剂,以提高ORR性能.两步炭化过程对于将热解Fe_(3)C纳米颗粒封装到碳纳米管(CNTs)中以及将Fe单原子隔离到N掺杂碳(NC)基体上至关重要.此外,Fe元素的相对含量对优化催化剂的ORR性能至关重要.所制得Fe_(3)C@CNTs/NC-M催化剂结构先进,在碱性溶液中表现出良好的长期稳定性和电催化ORR性能,其半波电位和极限电流分别达到0.941 V和6.31 mA cm^(-2).此外,该电催化剂在甲醇溶液中具有较强的耐受性和良好的稳定性.Fe_(3)C@CNTs/NC-M锌空气电池(ZAB)具有1.525 V的开路电位,420 mA cm^(-2)时的峰值功率密度为348 mW cm^(-2),10 mA cm^(-2)时的最大容量为843 mA h g_(Zn)^(-1).因此,这种合成策略为构建具有有效和稳定的ORR性能的MOF基电催化材料提供了一条有效途径.

关键词： metal-organic frameworks carbon nanotubes N-doped carbon matrix oxygen reduction reaction Zn-air battery

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Heterogeneous tunable Ⅲ-Ⅴ-on-silicon-nitride mode-locked laser emitting wide optical spectra

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Photonics Research 2024年第3期12卷 I0021-I0027页

作者： MAXIMILIEN BILLET stijn CUYVERS stijn POELMAN ARTUR HERMANS SANDEEP SEEMA SASEENDRA TASUKU NAKAMURA SHINYA OKAMOTO YASUHISA INADA KAZUYA HISADA TAKU HIRASAWA JOAN RAMIREZ DELPHINE NÉEL NICOLAS VAISSIÈRE JEAN DECOBERT PHILIPPE SOUSSAN XAVIER ROTTENBERG GUNTHER ROELKENS JONØ.KJELLMAN BART KUYKEN Photonics Research Group Department of Information TechnologyGhent University-imec9052 GhentBelgium imec 3001 LeuvenBelgium Technology Division Panasonic Holdings CorporationMoriguchi-CityOsakaJapan Ⅲ-Ⅴ Lab F91767 PalaiseauFrance

We demonstrate a Ⅲ-Ⅴ-on-silicon-nitride mode-locked laser through the heterogeneous integration of a semiconductor optical amplifier on a passive silicon-nitride cavity using the technique of micro-transfer printing. In the initial phase of our study, we focus on optimizing the lasing wavelength to be centered at 1550 nm. This optimization is achieved by conducting experiments with 27 mode-locked lasers, each incorporating optical amplifiers featuring distinct multiple-quantum-well photoluminescence values. Subsequently we present a comprehensive study investigating the behavior of the mode-locking regime when the electrical driving parameters are varied. Specifically, we explore the impact of the gain voltage and saturable absorber current on the locking stability of a tunable mode-locked laser. By manipulating these parameters, we demonstrate the precise control of the optical spectrum across a wide range of wavelengths spanning from 1530 to 1580 nm. Furthermore, we implement an optimization approach based on a Monte Carlo analysis aimed at enhancing the mode overlap within the gain region. This adjustment enables the achievement of a laser emitting a 23-nm-wide spectrum while maintaining a defined 10 dB bandwidth for a pulse repetition rate of 3 GHz.

关键词： tunable amplifier mode

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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

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Analogies between Density Functional Theory Response Kernels and Derivatives of Thermodynamic State Functions

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物理化学学报 2018年第6期34卷 699-707页

作者： GEERLINGS Paul DE PROFT Frank FIAS stijn General Chemistry (ALGC). Free University Brussels (VUB) Pleinlaan 2. 1050 Brussel. Belgium.

In view of its use as reactivity theory,Conceptual Density Functional Theory(DFT),introduced by Parr et al.,has mainly concentrated up to now on the E = E[N,v] ***,different ensemble representations can be used involving other variables also,such as ρ and μ.In this study,these different ensemble representations(E,?,F,and R) are briefly *** attention is then given to the corresponding second-order(functional) derivatives,and their analogieswith the second-order derivatives of thermodynamic state functions U,F,H,and G,which are related to each other via Legendre transformations,just as the DFT functionals(Nalewajski and Parr,1982).Starting from an analysis of the convexity/concavity of the DFT functionals,for which explicit proofs are discussed for some cases,the positive/negative definiteness of the associated kernels is derived and a detailed comparison is made with the thermodynamic *** stability conditions in thermodynamics are similar in structure to the convexity/concavity conditions for the DFT ***,the DFT functionals are scrutinized based on the convexity/concavity of their two variables,to yield the possibility of establishing a relationship between the three second-order reactivity descriptors derived from the considered *** two ensemble representations,F and ?,F is eliminated as it has two dependent(extensive)variables,N and ρ.For ?,on the other hand,which is concave for both of its intensive variables(μ and υ),an inequality is derived from its three second-order(functional) derivatives:the global softness,the local softness,and the softness *** with the negative value of the diagonal element of the linear response function,this inequality is shown to be compatible with the Berkowitz-Parr relationship,which relates the functional derivatives of ρ with υ,at constant N and μ.This was recently at stake upon quantifying Kohn's Nearsightedness of Electronic *** analogy

关键词： Conceptual DFT Response kernels Analogy with lhermodynamics Stability-concavity/convexity

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