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| 1 | Accuracy and responses of genomic selection on key traits in apple breeding显示文摘The application of genomic selection in fruit tree crops is expected to enhance breeding eficiency by increasing prediction accuracy,increasing selection intensity and decreasing generation interval.The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits.The training population comprised 977 individuals derived from 20 pedigreed fllsib families.Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an llumina 20K SNP array.From these data,a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application fllsib families.The application families had genotypes at 364 SNPs from a dedicated 512 SNP array,and these genotypic data were extended to the high-density level by imputation.These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values.Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19.The accuracies were strongly affected by the phenotypic distribution and heritability of traits.In the largest family,significant selection response was observed for traits with high heritability and symmetric phenotypic distribution.Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability.Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population.The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs. | Hélène Muranty Michela Troggio Inès Ben Sadok Mehdi Al Rifaï Annemarie Auwerkerken Elisa Banchi Riccardo Velasco Piergiorgio Stevanato W.Eric van de Weg Mario Di Guardo Satish Kumar François Laurens Marco C.A.M.Bink | 2015 | Horticulture Research2015，2，1： | 14 |
| 2 | 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 |
| 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 | Reverse Structural and Gap-Junctional Remodeling After Prolonged Atrial Fibrillation in the Goat显示文摘 | Jannie Ausma Huub M.W. van der Velden Marie-Hélène Lenders Erwin P. van Ankeren Habo J. Jongsma Frans C.S. Ramaekers Marcel Borgers Maurits A. Allessie | 2003 | Circulation: Journal of the American Heart Association2003，，15： | 2 |
| 5 | High-Resolution Spiral Computed Tomography Coronary Angiography in Patients Referred for Diagnostic Conventional Coronary Angiography显示文摘 | Nico R. Mollet Filippo Cademartiri Carlos A.G. van Mieghem Giuseppe Runza Eugène P. McFadden Timo Baks Patrick W. Serruys Gabriel P. Krestin Pim J. de Feyter | 2005 | Circulation2005，，15： | 2 |
| 6 | In vivo matrix production by bone marrow stromal cel s seeded on PLGA scaffolds for ligament tissue engineering显示文摘 | van Eijk F Saris DB Fedorovich NE | | 0，，10： | 1 |
| 7 | PTZ-induced seizures in rats: effects of age and strain显示文摘 | Klioueva IA van Luijtelaar EL Chepurnova NE | 2001 | Physiol Behav2001，72，3： | 1 |
| 8 | A new intraocular lens design to reduce spheri- cal aberration of pseudophakic eyes 显示文摘 | HOLLADAYJT PIERSPA KORANYI G VAN DER MOOREN M NORRBY NE | 2002 | J Refract Surg2002，18，6： | 1 |
| 9 | Normocalcemia is maintained in mice under conditions of calcium malabsorption by vitamin D-induced inhibition of bone mineralization显示文摘 | Lieben Liesbet Masuyama Ritsuko Torrekens Sophie Van Looveren Riet Schrooten Jan Baatsen Pieter Lafage-Proust Marie-Hélène Dresselaers Tom Feng Jian Q Bonewald Lynda F Meyer Mark B Pike J Wesley Bouillon Roger Carmeliet Geert | 2012 | EN2012，，5： | 1 |
| 10 | Changes in cortical thickness during the course of illness in schizophrenia 显示文摘 | van Haren NE Schnack HG Cahn W | 2011 | Arch Gen Psychiatry2011，68，： | 1 |
| 11 | Early postnatal lethality and cardiovascular defects in CXCR7-deficient mice显示文摘 | Gerrits H van Ingen Schenau DS Bakker NE | 2008 | Gen- esis2008，46，5： | 1 |
| 12 | Teaching to inhale: better utilization of powder inhalators after counseling and instruction 显示文摘 | Van't Veer NE Lameijer W De Ley M | 2001 | Ned Tijdschr Geneeskd2001，145，5： | 1 |
| 13 | Case of late-onset corneal decompensation after iris-fixated phakic intraocular lens implantation 显示文摘 | van Eijden R de Vries NE Cruysberg LP Webers CA Beren- schot T Nuijts RM | 2009 | J Cat- aract Refract Surg2009，35，4： | 1 |
| 14 | Risk factors for patellofemoral pain syndrome : A systematic review 显示文摘 | Lankhorst NE Bierma-Zeinstra SM Van Middelkoop M | 2012 | J Orthop Sports Phys Ther2012，42，2： | 1 |
| 15 | Brain volume abnormalities in major depressive disorder: a meta - analy- sis of magnetic resonance imaging studies 显示文摘 | Koolschijn PC van Haren NE Lensvelt - Mulders G J | 2009 | Hum Brain Mapp2009，30，11： | 1 |
| 16 | Brain volume abnormalities in major depressive disorder:A meta-analysis of magnetic resonance imaging studies显示文摘 | Koolschijn PC Van Haren NE Lensvelt-Mulders GJ | | 0，，： | 1 |
| 17 | Aggresome formation in liver cells in response to different toxic mechanisms: role of the ubiquitin-Proteasome pathway and the frameshift mutant of u- biquitin显示文摘 | Freneh BA van Leeuwen F Riley NE | 2001 | ExP Mol Pathol2001，71，3： | 1 |
| 18 | PsychopathoIogy and Psychological Problem in Patients with Bum Scars;Epidemiology and Management显示文摘 | Van Loey NE Van Son MJ | 2003 | Am J Chin Dermatol2003，4，4： | 1 |
| 19 | Plant-induced changes in soil chemistry do not explain differences in uranium transfer显示文摘 | L. Duquène H. Vandenhove F. Tack E. Van der Avoort M. Van Hees J. Wannijn | 2006 | Journal of Environmental Radioactivity2006，，1： | 1 |
| 20 | Enhanced pulmonary leptin expression in patients with severe COPD and asymptomatic smokers显示文摘 | Vernooy JH Drummen NE van Suylen RJ | 2009 | Thorax2009，64，1： | 1 |
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