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| 1 | An integrated approach for increasing breeding efficiency in apple and peach in Europe显示文摘Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and breeding.To bridge the gap,the European Union funded the FruitBreedomics project(March 2011 to August 2015)involving 28 research institutes and private companies.Three 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 breeders.Decisive 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 collections.FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities.Through 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 public.This review covers the scientific discoveries made in this major endeavour,and perspective in the apple and peach breeding and genomics in Europe and beyond. | 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 | 2018 | Horticulture Research2018，5，1： | 10 |
| 2 | Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple显示文摘Texture is a complex trait and a major component of fruit quality in apple.While the major effect of MdPG1,a gene controlling firmness,has already been exploited in elite cultivars,the genetic basis of crispness remains poorly understood.To further improve fruit texture,harnessing loci with minor effects via genomic selection is therefore necessary.In this study,we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture.Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers.The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance(0.64).Predictions for biparental families using the entire training set varied from low to high accuracy,depending on the family considered.While adding siblings or half-siblings into the training set did not clearly improve predictions,we performed an optimization of the training set size and composition for each validation set.This allowed us to increase prediction accuracies by 0.17 on average,with a maximal accuracy of 0.81 when predicting firmness in the‘Gala’בPink Lady’family.Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple.In particular,we advise to rely on a large training population,with high phenotypic variability from which a‘tailored training population’can be extracted using a priori information on genetic relatedness,in order to predict a specific target population. | Morgane Roth Hélène Muranty Mario Di Guardo Walter Guerra Andrea Patocchi Fabrizio Costa | 2020 | Horticulture Research2020，7，1： | 4 |
| 3 | Apple whole genome sequences:recent advances and new prospects显示文摘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 apple.Over 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 crop.Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly.Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees.High-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 breeders.We understand the species,geographical,and genomic origins of domesticated apple more precisely,as well as its relationship to wild relatives.The 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 production.This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs.Recommendations 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. | 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 | 2019 | Horticulture Research2019，6，1： | 3 |
| 4 | Apple contains receptor-like genes homologous to the Cladosporium fulvum resistance gene family of tomato with a cluster of genes cosegre gating with vf apple scab resistance显示文摘 | Vinatzer B A Patocchi A Gianfranceschi L | 2001 | Mol Plant-Microbe Interact2001，14，： | 1 |
| 5 | Genome mapping of three major resistance genes to woolly apple aphid (Eriosoma lanigerum Hausm.)显示文摘 | V. G. M. Bus D. Chagné H. C. M. Bassett D. Bowatte F. Calenge J.-M. Celton C.-E. Durel M. T. Malone A. Patocchi A. C. Ranatunga E. H. A. Rikkerink D. S. Tustin J. Zhou S. E. Gardiner | 2008 | Tree Genetics & Genomes2008，，2： | 1 |
| 6 | CIoning and inkage mapping of resistance gene homologues in apple显示文摘 | BALDI P PATOCCHI A ZINI E | 2004 | Theor Appl Genet2004，109，： | 1 |
| 7 | Genome mapping of three major resistance genes to woolly apple aphid (Eriosoma lanigerum Hausm.)显示文摘 | V. G. M. Bus D. Chagné H. C. M. Bassett D. Bowatte F. Calenge J.-M. Celton C.-E. Durel M. T. Malone A. Patocchi A. C. Ranatunga E. H. A. Rikkerink D. S. Tustin J. Zhou S. E. Gardiner | 2008 | Tree Genetics & Genomes2008，，2： | 1 |
| 8 | Molecular markers linked to the apple scab resistance gene Vbj derived from Malus baccata jackii显示文摘 | GYGAX M GIANFRANCESCHI L LIEBHARD R KELLERHALS M GESSLER C PATOCCHI A | 2004 | Theor Appl Genet2004，109，： | 1 |
| 9 | Mapping quantita- tive field resistance against apple scab in a ' Fiesta' × 'Discovery' progeny显示文摘 | LIEBHARD R KOLLER B PATOCCHI A KELLERHALS M PFAMMATTER W JERMINI M GESSLER C | 2003 | Phytopathology2003，93，： | 1 |
| 10 | First report of brown rot caused by Monilinia fructicola on apricot in a Swiss orchard显示文摘 | Hilber-Bodmer M Banter M Patocchi A | 2010 | Plant Disease2010，94，5： | 1 |
| 11 | Developnlem of a high- throughput method for quantification of Plasmopara viticola DNA in grapevine leaves by means of quantitative Real-tintc polymerase chain reaction 显示文摘 | Valsesia G Gobbin D Patocchi A | 2005 | Phytopathology2005，95，6： | 1 |
| 12 | Mapping quantitative field resistance against apple scab in a 'Fiesta' × 'Discovery' progeny显示文摘 | LIEBHARD R KOLLER B PATOCCHI A | 2003 | Phytopathology2003，93，： | 1 |
| 13 | QTL mapping of fire blight resistance in apple显示文摘 | Muhammad A. Khan Brion Duffy Cesare Gessler Andrea Patocchi | 2006 | Molecular Breeding2006，，4： | 1 |
| 14 | Apple contains receptor-like gees homologous to theCladosporium fulvumresistance gene family of to-mato with a cluster of genes cosegregating with Vfapple scab resistance显示文摘 | Vinatzer B A Patocchi A Gianfranceschi L | 2001 | Mol Plant Microbe Inter-act2001，14，4： | 1 |
| 15 | Vr2:a new apple seab resistance gene显示文摘 | Patocchi A Bigler B Koller B et a l | 2004 | Theor Appl Genet2004，109，： | 1 |
| 16 | Cloning and linkage mapping of resistance gene homologues in apple 显示文摘 | BALDI P PATOCCHI A ZINI E | 2004 | Theoret Appl Genetics2004，109，1： | 1 |
| 17 | QTL analysis for aphid resistance and growth traits in apple显示文摘 | Sibylle Stoeckli Karsten Mody Cesare Gessler Andrea Patocchi Mauro Jermini Silvia Dorn | 2008 | Tree Genetics & Genomes2008，，4： | 1 |
| 18 | Genome mapping of three major resistance genes to woolly apple aphid (Eriosoma lanigerum Hausm.)显示文摘 | V. G. M. Bus D. Chagné H. C. M. Bassett D. Bowatte F. Calenge J.-M. Celton C.-E. Durel M. T. Malone A. Patocchi A. C. Ranatunga E. H. A. Rikkerink D. S. Tustin J. Zhou S. E. Gardiner | 2008 | Tree Genetics & Genomes2008，，2： | 1 |
| 19 | Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome显示文摘 | E. Silfverberg-Dilworth C. L. Matasci W. E. Weg M. P. W. Kaauwen M. Walser L. P. Kodde V. Soglio L. Gianfranceschi C. E. Durel F. Costa T. Yamamoto B. Koller C. Gessler A. Patocchi | 2006 | Tree Genetics & Genomes2006，，4： | 1 |
| 20 | Ventruia inaequalis resistance in apple显示文摘 | Gessler C Patocchi A Sansavini S | 2006 | Critical Reviews in Plant Sciences2006，25，： | 1 |
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