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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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The apple REFpOp—a reference population for genomics-assisted breeding in apple

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Horticulture Research 2020年第1期7卷 364-379页

作者： Michaela Jung Morgane Roth Maria JoséAranzana Annemarie Auwerkerken Marco Bink Caroline Denancé Christian Dujak Charles-Eric Durel Carolina Font i Forcada Celia M.Cantin Walter Guerra nicholas p.howard Beat Keller Mariusz Lewandowski Matthew Ordidge Marijn Rymenants Nadia Sanin Bruno Studer Edward Zurawicz François Laurens Andrea patocchi Hélène Muranty Molecular plant Breeding Institute of Agricultural SciencesETH Zurich8092 ZurichSwitzerland Breeding Research group Agroscope 8820 WädenswilSwitzerland IRTA(Institut de Recerca i Tecnologia Agroalimentàries) 08140 Caldes de MontbuiBarcelonaSpain Centre for Research in Agricultural Genomics(CRAG)CSIC-IRTA-UAB-UB Campus UAB08193 BellaterraBarcelonaSpain Better3fruit N.V. 3202 RillaarBelgium Biometris Wageningen University and Research6708 PB WageningenThe Netherlands Hendrix Genetics Research Technology and Services B.V.PO Box 1145830AC BoxmeerThe Netherlands IRHS Universitéd’AngersINRAEInstitut AgroSFR 4207 QuaSaV49071 BeaucouzéFrance ARAID(Fundación Aragonesa para la Investigación y el Desarrollo) 50018 ZaragozaSpain Research Centre Laimburg 39040 AuerItaly Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Institute of Biology and Environmental Sciences University of Oldenburg26129 OldenburgGermany Research Institute of Horticulture 96-100 SkierniewicePoland School of Agriculture Policy and DevelopmentUniversity of ReadingWhiteknights RG66AR ReadingUK Laboratory for plant Genetics and Crop Improvement KU Leuven B-3001 LeuvenBelgium GAFL INRAE84140 MontfavetFrance

Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection ***-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs,and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic *** we present an apple reference population:the apple REFpOp,a large collection formed of 534 genotypes planted in six European countries,as a unique tool to accelerate apple *** population consisted of 269 accessions and 265 progeny from 27 parental combinations,representing the diversity in cultivated apple and current European breeding material,respectively.A high-density genome-wide dataset of 303,239 SNps was produced as a combined output of two SNp arrays of different densities using marker imputation with an imputation accuracy of *** on the genotypic data,linkage disequilibrium was low and population structure was *** well-studied phenological traits of horticultural importance were *** found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date,*** decreasing SNp density,the detection of significant marker–trait associations varied depending on trait *** of the trait,10,000 SNps sufficed to maximize genomic prediction *** confirm the suitability of the apple REFpOp design for genomics-assisted breeding,especially for breeding programs using related germplasm,and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.

关键词： breeding planted utilize

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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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Neoadjuvant treatment of esophageal cancer

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World Journal of Gastroenterology 2010年第30期16卷 3793-3803页

作者： nicholas p Campbell Victoria M Villaflor Section of Hematology/Oncology Department of MedicineThe University of Chicago Pritzker School of MedicineChicagoIL 60637United States

The management of esophageal cancer has been evolving over the past 30 years. In the United States, multimodality treatment combining chemotherapy and radiotherapy (RT) prior to surgical resection has come to be accepted by many as the standard of care, although debate about its overall effect on survival still exists, and rightfully so. Despite recent improvements in detection and treatment, the overall survival of patients with esophageal cancer remains lower than most solid tumors, which highlights why further advances are so desperately needed. The aim of this article is to provide a complete review of the history of esophageal cancer treatment with the addition of chemotherapy, RT, and more recently, targeted agents to the surgical management of resectable disease.

关键词： Esophageal cancer Multimodality therapy Neoadjuvant therapy Chemotherapy Radiotherapy Targeted agents Disease management

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Shaping Taste: The Molecular Discovery of Rice Genes Improving Grain Size, Shape and Quality

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Journal of Genetics and Genomics 2015年第11期42卷 597-599页

作者： nicholas p.Harberd Department of plant Sciences University of Oxford

Modern-day human life is absolutely dependent upon the food that we derive from our crop plants. We eat grains, fruits, roots, tubers and other structures, all of which are constructed via coordinated organ growth. Whilst plant organ identity is first established in apical meristems （vegetative and floral shoot meristems and root meristems）, and in other meristematic regions, the final size and shape of organs are defined by subsequent coordination of organ expansion in longitudinal and transverse axes.

关键词： QTLs Shaping Taste The Molecular Discovery of Rice Genes Improving Grain Size Shape and Quality gene

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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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Anthropogenic Influence on Decadal Changes in Concurrent Hot and Dry Events over China around the Mid-1990s

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Advances in Atmospheric Sciences 2024年第2期41卷 233-246页

作者： Qin SU Buwen DONG Fangxing TIAN nicholas p.KLINGAMAN Yunnan Key Laboratory of Meteorological Disasters and Climate Resources in the Great Mekong Subregion Yunnan UniversityKunming 650500China Department of Atmospheric Sciences Yunnan UniversityKunming 650500China National Centre for Atmospheric Science Department of MeteorologyUniversity of ReadingReadingRG66BBUK Geofysisk Institut University of BergenBergen 5007Norway Citadel Investment Group Moor House120 London WallLondonRG66BBUK

The frequency and duration of observed concurrent hot and dry events(HDEs) over China during the growing season(April–September) exhibit significant decadal changes across the mid-1990s. These changes are characterized by increases in HDE frequency and duration over most of China, with relatively large increases over southeastern China(SEC), northern China(NC), and northeastern China(NEC). The frequency of HDEs averaged over China in the present day(pD,1994–2011) is double that in the early period(Ep, 1964–81);the duration of HDEs increases by 60%. Climate experiments with the Met Office Unified Model(MetUM-GOML2) are used to estimate the contributions of anthropogenic forcing to HDE decadal changes over China. Anthropogenic forcing changes can explain 60%–70% of the observed decadal changes,suggesting an important anthropogenic influence on HDE changes over China across the mid-1990s. Single-forcing experiments indicate that the increase in greenhouse gas(GHG) concentrations dominates the simulated decadal changes,increasing the frequency and duration of HDEs throughout China. The change in anthropogenic aerosol(AA) emissions significantly decreases the frequency and duration of HDEs over SEC and NC, but the magnitude of the decrease is much smaller than the increase induced by GHGs. The changes in HDEs in response to anthropogenic forcing are mainly due to the response of climatological mean surface air temperatures. The contributions from changes in variability and changes in climatological mean soil moisture and evapotranspiration are relatively small. The physical processes associated with the response of HDEs to GHG and AA changes are also revealed.

关键词： concurrent hot and dry events decadal variation greenhouse gases aerosol emissions

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On Northern Hemisphere Wave patterns Associated with Winter Rainfall Events in China

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Advances in Atmospheric Sciences 2018年第8期35卷 125-138页

作者： Claudia Christine STEpHAN Yan Ho NG nicholas p. KLINGAMAN National Centre for Atmospheric Science - Climate Department of Meteorology University of Reading Reading RG6 6BB United Kingdom Department of Meteorology University of Reading Reading RG6 6BB United Kingdom

During extended winter （November-April）, 43% of the intraseasonal rainfall variability in China is explained by three spatial patterns of temporally coherent rainfall, These patterns were identified with empirical orthogonal teleconnection （EOT） analysis of observed 1982-2007 pentad rainfall anomalies and connected to midlatitude disturbances. However, ex- amination of individual strong EOT events shows that there is substantial inter-event variability in their dynamical evolution, which implies that precursor patterns found in regressions cannot serve as useful predictors. To understand the physical nature and origins of the extratropical precursors, the EOT technique is applied to six simulations of the Met Office Unified Model at horizontal resolutions of 200-40 km, with and without air-sea coupling. All simulations reproduce the observed precursor patterns in regressions, indicating robust underlying dynamical processes. Further investigation into the dynamics associated with observed patterns shows that Rossby wave dynamics can explain the large inter-event variability. The results suggest that the appaxently slowly evolving or quasi-stationaxy waves in regression analysis are a statistical amalgamation of more rapidly propagating waves with a variety of origins and properties.

关键词： rainfall in China spring flooding Rossby wave dynamics EOT analysis predictability teleconnections

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A polarizing situation： Taking an in-plane perspective for next-generation near-field studies

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Frontiers of physics 2016年第2期11卷 1-17页

作者： p. James Schuck Wel Bao nicholas J. Borys Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA 94720 USA Department of Materials Science and Engineering University of California Berkeley CA 94720-1760 USA

By enabling the probing of light-matter interactions at the functionally relevant length scales of most materials, near-field optical imaging and spectroscopy accesses information that is unobtainable with other methods. The advent of apertureless techniques, which exploit the ultralocalized and enhanced near-fields created by sharp metallic tips or plasmonic nanoparticles, has resulted in rapid adoption of near-field approaches for studying novel materials and phenomena, with spatial resolution approaching sub-molecular levels. However, these approaches are generally limited by the dominant out-of-plane polarization response of apertureless tips, restricting the exploration and discovery of many material properties. This has led to recent design and fabrication breakthroughs in near-field tips engineered specifically for enhancing in-plane interactions with near-field light components. This mini-review provides a perspective on recent progress and emerging directions aimed at utilizing and controlling in-plane optical polarization, highlighting key application spaces where in-plane near-field tip responses have enabled recent advancements in the understanding and development of new nanostructured materials and devices.

关键词： near-field optical microscopy nano-optics TERS plasmonics optical antenna 2D materials

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Green Revolution DELLAs: From translational reinitiation to future sustainable agriculture

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Molecular plant 2021年第4期14卷 547-549页

作者： Qian Liu Kun Wu nicholas p.Harberd Xiangdong Fu State Key Laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China Department of plant Sciences University of OxfordSouth Parks RoadOxford 0X13RBUK College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China

The Green Revolution(GR)of the 1960s saw spectacular increases in cereal crop yields,enabled by widespread adoption of high-yielding semi-dwarf varieties and increased fertilizer ***-dwarfism is caused by mutant wheat Reduced height-1(Rht-1)and rice semi-dwarf1(sd1)alleles,respectively,which confer increased harvest index(grain to straw ratio)and reduced yield loss from“lodging”(flattening of crops by wind or rain).However,despite their obvious global food security benefits,the underlying mechanisms via which GR dwarfing alleles actually work remained *** began to change with the molecular discovery of Rht1(peng et al.,1999).

关键词： dwarf crops cereal

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