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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 | 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 |
| 3 | A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species显示文摘Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus domestica Borkh),the genome sequence v1 and v2 could not meet this need;therefore,a novel approach was devised to develop a dense genetic linkage map,providing the most reliable marker-loci order for the highest possible number of markers.The approach was based on four strategies:(i)the use of multiple full-sib families,(ii)the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism(SNP)markers,(iii)the construction of a single backcross-type data set including all families,and(iv)a two-step map generation procedure based on the sequential inclusion of markers.The map comprises 15417 SNP markers,clustered in 3 K HaploBlock markers spanning 1267 cM,with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM.Moreover,chromosome 5 was oriented according to its homoeologous chromosome 10.This map was useful to improve the apple genome sequence,design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies.Its collinearity with the genome sequences v1 and v3 are reported.To our knowledge,this is the shortest published SNP map in apple,while including the largest number of markers,families and individuals.This result validates our methodology,proving its value for the construction of integrated linkage maps for any outbreeding species. | Erica A Di Pierro Luca Gianfranceschi Mario Di Guardo Herma JJ Koehorst-van Putten Johannes W Kruisselbrink Sara Longhi Michela Troggio Luca Bianco Hélène Muranty Giulia Pagliarani Stefano Tartarini Thomas Letschka Lidia Lozano Luis Larisa Garkava-Gustavsson Diego Micheletti Marco CAM Bink Roeland E Voorrips Ebrahimi Aziz Riccardo Velasco François Laurens W Eric van de Weg | 2016 | Horticulture Research2016，3，1： | 3 |
| 4 | Multitask deep-learning-based design of chiral plasmonic metamaterials显示文摘The field of chiral plasmonics has registered considerable progress with machine-learning(ML)-mediated metamaterial prototyping,drawing from the success of ML frameworks in other applications such as pattern and image recognition.Here,we present an end-to-end functional bidirectional deep-learning(DL)model for three-dimensional chiral metamaterial design and optimization.This ML model utilizes multitask joint learning features to recognize,generalize,and explore in detail the nontrivial relationship between the metamaterials’geometry and their chiroptical response,eliminating the need for auxiliary networks or equivalent approaches to stabilize the physically relevant output.Our model efficiently realizes both forward and inverse retrieval tasks with great precision,offering a promising tool for iterative computational design tasks in complex physical systems.Finally,we explore the behavior of a sample ML-optimized structure in a practical application,assisting the sensing of biomolecular enantiomers.Other potential applications of our metastructure include photodetectors,polarization-resolved imaging,and circular dichroism(CD)spectroscopy,with our ML framework being applicable to a wider range of physical problems. | Eric Ashalley Kingsley Acheampong Lucas VBesteiro Peng Yu Arup Neogi Alexander OGovorov Zhiming M.Wang | 2020 | Photonics Research2020，8，7： | 3 |
| 5 | Hyperthermic Intraperitoneal Chemotherapy with Oxaliplatin for Peritoneal Carcinomatosis Arising from Appendix: Preliminary Results of a Survival Analysis显示文摘 | Eric Marcotte MD Lucas Sideris MD FRCSC Pierre Drolet MD FRCPC Andrew Mitchell MD Suzanne Frenette BPharm MSc BCOP Guy Leblanc MD FRCSC Yves E. Leclerc MD FRCSC FACS Pierre Dubé MD MSc FRCSC FACS | 2008 | Annals of Surgical Oncology2008，，10： | 1 |
| 6 | Reaction kinetic modelings of Akardite Ⅱdepletion in single base propellant formulation 显示文摘 | Eric R Bixon Lucas Lopez | 2006 | Propellants Explosives Pyrotechnics2006，31，4： | 1 |
| 7 | Aortic Root Replacement in 372 Marfan Patients: Evolution of Operative Repair Over 30 Years显示文摘 | Duke E. Cameron Diane E. Alejo Nishant D. Patel Lois U. Nwakanma Eric S. Weiss Luca A. Vricella Harry C. Dietz Philip J. Spevak Jason A. Williams Brian T. Bethea Torin P. Fitton Vincent L. Gott | 2009 | The Annals of Thoracic Surgery2009，，5： | 1 |
| 8 | Measurement of Atmospheric Mercury Species with Manual Sampling and Analysis Methods in a Case Study in Indiana显示文摘 | Martin R. Risch Eric M. Prestbo Lucas Hawkins | 2007 | Water Air and Soil Pollution (-)2007，，1： | 1 |
| 9 | Daily spinal mechanical loading as a risk factor for acute non-specific low back pain: a case–control study using the 24-Hour Schedule显示文摘 | Eric W. P. Bakker Arianne P. Verhagen Cees Lucas Hans J. C. M. F. Koning Rob J. Haan Bart W. Koes | 2007 | European Spine Journal2007，，1： | 1 |
| 10 | Enhancing the relevance of Shared Socioeconomic Pathways for climate change impacts, adaptation and vulnerability research显示文摘 | Bas J. Ruijven Marc A. Levy Arun Agrawal Frank Biermann Joern Birkmann Timothy R. Carter Kristie L. Ebi Matthias Garschagen Bryan Jones Roger Jones Eric Kemp-Benedict Marcel Kok Kasper Kok Maria Carmen Lemos Paul L. Lucas Ben Orlove Shonali Pachauri Tom M | 2014 | Climatic Change2014，，3： | 1 |
| 11 | Macrolophus caliginosus (Wagner) as an intraguild prey for the Zoophytophagous Dicyphus taznaninii Wagner (Heteroptera: Miridae)显示文摘 | ERIC LUCAS OSCAR ALOMAR | 2001 | Biological Control2001，20，： | 1 |
| 12 | Analysis of principal gas products during combustion of polyether polyurethane foam at different irradiance levels显示文摘 | Lucas Bustamante Valencia Thomas Rogaume Eric Guillaume | 2009 | Fire Safety Journal2009，44，： | 1 |
| 13 | Comparison among error calculations in differential absorption lidar measurements显示文摘 | Luca FIORANI Eric DURIEUX | 2001 | Optics &Laser Technology2001，33，： | 1 |
| 14 | Pulmonary Macrophage Inhibition and Inhaled Nitric Oxide Attenuate Lung Ischemia-Reperfusion Injury显示文摘 | Leo M. Gazoni Curtis G. Tribble Min Q. Zhao Eric B. Unger Robert A. Farrar Peter I. Ellman Lucas G. Fernandez Victor E. Laubach Irving L. Kron | 2007 | The Annals of Thoracic Surgery2007，，1： | 1 |
| 15 | Comparison among error calculations in differential absorption lidar measurements 显示文摘 | Luca Fiorani Eric Durieux | 2001 | Optics & Laser Technology2001，33，6： | 1 |
| 16 | The effects of proton radiation on UHMWPE material properties for space flight and medical applications 显示文摘 | Chad S Cummings Eric M Lucas Justin A Marro | 2011 | Advances in Space Research2011，48，： | 1 |
| 17 | CDX2 regulates liver intestine–cadherin expression in normal and malignant colon epithelium and intestinal metaplasia显示文摘 | Takao Hinoi Peter C. Lucas Rork Kuick Samir Hanash Kathleen R. Cho Eric R. Fearon | 2002 | Gastroenterology2002，，5： | 1 |
| 18 | Multi- imaging and Bayesian estimation for photon counting with EMOCDs显示文摘 | Eric Lantz Jean-Luc Blanchet Luca Furfaro | 2008 | Monthly Notices of the Royal Astronomical Society2008，，4： | 1 |
| 19 | Analysis of principal gas products during combustion of polyether polyurethane foam at different irradiance levels 显示文摘 | Lucas B V Thomas R Eric G | 2009 | Fire Safety J2009，44，： | 1 |
| 20 | Loss of CDX2 Expression and Microsatellite Instability Are Prominent Features of Large Cell Minimally Differentiated Carcinomas of the Colon显示文摘 | Takao Hinoi Masachika Tani Peter C. Lucas Karel Caca Rodney L. Dunn Ettore Macri Massimo Loda Henry D. Appelman Kathleen R. Cho Eric R. Fearon | 2001 | The American Journal of Pathology2001，，6： | 1 |
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