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An integrated approach for increasing breeding efficiency in apple and peach in Europe

Horticulture Research 2018年第1期5卷 825-838页

作者： Francois Laurens Maria JoséAranzana Pere Arus Daniele Bassi Marco Bink Joan Bonany Andrea Caprera Luca Corelli-Grappadelli Evelyne Costes charles-eric durel Jehan-Baptiste Mauroux Hélène Muranty Nelson Nazzicari Thierry Pascal Andrea Patocchi Andreas Peil Bénédicte Quilot-Turion Laura Rossini Alessandra Stella Michela Troggio Riccardo Velasco eric van de Weg IRHS INRAAgrocampus-OuestUniversitéd’AngersSFR 4207 QuaSaVUniversitéBretagne Loire42 rue Georges MorelBeaucouzé49071France IRTA(Institut de Recerca i Tecnologia Agroalimentàries) BarcelonaSpain Centre for Research in Agricultural Genomics(CRAG)CSIC-IRTA-UAB-UB Campus UABBellaterraBarcelonaSpain Universitàdegli Studi di Milano-DiSAA Via Celoria 2Milan20133Italy Biometris Wageningen University and ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands IRTA-Mas Badia Mas BadiaLa Tallada17134Spain Parco Tecnologico Padano Via EinsteinLoc.Cascina CodazzaLodi26900Italy Dipartimento di Scienze Agrarie Alma Mater Studiorum-Universitàdi BolognaBolognaItaly UMR AGAP INRAMontpellier34398France GAFL INRAMontfavet84143France Agroscope Research Division Plant BreedingSchloss 1Wädenswil8820Switzerland Julius Kühn-Institute(JKI) Federal Research Centre for Cultivated Plants Institute for Breeding Research on Fruit CropsPillnitzer Platz 3aDresden01326Germany Research and Innovation Center Fondazione Edmund MachSan Michele all’AdigeTrentoItaly CREA-VE Center of Viticulture and Enologyvia XXVIII Aprile 26Conegliano(TV)31015Italy Plant Breeding Wageningen University and ResearchDroevendaalsesteeg 1P.O.Box 386Wageningen6700AJThe Netherlands Hendrix Genetics Research Technology&ServicesBoxmeer5830 ACThe Netherlands

Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and *** bridge the gap,the European Union funded the FruitBreedomics project(March 2011 to August 2015)involving 28 research institutes and private *** complementary approaches were pursued:(i)tool and software development,(ii)deciphering genetic control of main horticultural traits taking into account allelic diversity and(iii)developing plant materials,tools and methodologies for *** breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding,development of new,dense SNP arrays in apple and peach,new phenotypic methods for some complex traits,software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis(PBA).This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies(GWAS)on several European genebank *** also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection *** FruitBreedomics,significant progresses were made in the field of apple and peach breeding,genetics,genomics and bioinformatics of which advantage will be made by breeders,germplasm curators and scientists.A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the *** review covers the scientific discoveries made in this major endeavour,and perspective in the apple and peach breeding and genomics in Europe and beyond.

关键词： breeding germplasm breed

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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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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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Genome mapping of postzygotic hybrid necrosis in an interspecific pear population

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Horticulture Research 2016年第1期3卷 326-337页

作者： Sara Montanari Lester Brewer Robert Lamberts Riccardo Velasco Mickael Malnoy Laure Perchepied Philippe Guérif charles-eric durel Vincent G M Bus Susan E Gardiner David Chagné Research and Innovation Centre Fondazione Edmund MachVia Mach 1San Michele all’Adige38010TNItaly The New Zealand Institute for Plant&Food Research Limited Palmerston North Research CentrePalmerston NorthNew Zealand Institut de Recherche en Horticulture et Semences-UMR1345 Institut National de la Recherche Agronomique(INRA)SFR 4207 Quasav42 rue Georges MorelBeaucouzéF-49071France The New Zealand Institute for Plant&Food Research Limited Motueka Research CentreMotuekaNew Zealand Institut de Recherche en Horticulture et Semences-UMR1345 Universitéd’AngersAngersF-49045France The New Zealand Institute for Plant&Food Research Limited Hawke’s Bay Research CentreHavelock NorthNew Zealand

Deleterious epistatic interactions in plant inter-and intraspecific hybrids can cause a phenomenon known as hybrid necrosis,characterized by a typical seedling phenotype whose main distinguishing features are dwarfism,tissue necrosis and in some cases *** of the chromosome regions associated with this type of incompatibility is important not only to increase our understanding of the evolutionary diversification that led to speciation but also for breeding *** of molecular markers linked to the lethal genes will allow breeders to avoid incompatible inbred combinations that could affect the expression of important agronomic tratis co-segregating with these *** hybrid necrosis has been reported in several plant taxa,including Rosaceae species,this phenomenon has not been described previously in *** the interspecific pear population resulting from a cross between PEAR3(Pyrus bretschneideri×Pyrus communis)and‘Moonglow’(***),we observed two types of hybrid necrosis,expressed at different stages of plant *** a combination of previously mapped and newly developed genetic markers,we identified three chromosome regions associated with these two types of lethality,which were genetically *** type resulted from a negative epistatic interaction between a locus on linkage group 5(LG5)of PEAR3 and a locus on LG1 of‘Moonglow’,while the second type was due to a gene that maps to LG2 of PEAR3 and which either acts alone or more probably interacts with another gene of unknown location inherited from‘Moonglow’.

关键词： breeding seedling dwarf

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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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