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| 1 | Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple显示文摘The apple dwarfing rootstock‘Malling9’(‘M9’)has been used worldwide both to reduce scion vigour and as a genetic source for breeding new rootstocks.Progeny of‘M9’segregate for rootstock-induced dwarfing of the scion,indicating that this trait is controlled by one or more genetic factors.A quantitative trait locus(QTL)analysis of a rootstock population derived from the cross between‘M9’בRobusta5’(non-dwarfing)and grafted with‘Braeburn’scions identified a major QTL(Dw1)on linkage group(LG)5,which exhibits a significant influence on dwarfing of the scion.A smaller-effect QTL affecting dwarfing(Dw2)was identified on LG11,and four minor-effect QTLs were found on LG6,LG9,LG10 and LG12.Phenotypic analysis indicates that the combination of Dw1 and Dw2 has the strongest influence on rootstock-induced dwarfing,and that Dw1 has a stronger effect than Dw2.Genetic markers linked to Dw1 and Dw2 were screened over 41 rootstock accessions that confer a range of effects on scion growth.The majority of the dwarfing and semi-dwarfing rootstock accessions screened carried marker alleles linked to Dw1 and Dw2.This suggests that most apple dwarfing rootstocks have been derived from the same genetic source. | Toshi M Foster Jean-Marc Celton David Chagné D Stuart Tustin Susan E Gardiner | 2015 | Horticulture Research2015，2，1： | 10 |
| 2 | 新西兰苹果品种及砧木育种成就与对中国的启示显示文摘20世纪60年代新西兰的Don Mc Kenzie博士从果农J.H.Kidd配置的杂交后代中选出了世界级的苹果品种‘嘎拉’。随后,新西兰植物与食品研究所于80年代初期开始了持续专业的苹果育种研究,先后培育出了一系列优良的世界性品种。苹果育种技术也从常规育种进入了分子育种时代,一跃成为世界苹果育种强国,吸引了世界众多果树科研单位和育种者争相学习其先进技术和科研成果。为了进一步提升中国苹果育种水平,缩小与苹果育种强国的差距,作者系统的介绍了新西兰的苹果品种和砧木选育的发展历程、选育方法,特别是生物技术在新品种选育中的应用,并对比分析目前中国苹果品种及砧木选育的方法,提出中国苹果育种方法的改进建议,希望对中国的苹果育种工作有所启发。 | 张恒涛 BUS Vincent G.M. WHITE Allan G. 阎振立 过国南 张瑞萍 刘珍珍 YAO Jia-long CHAGNE David | 2016 | 果树学报2016，33，4： | 5 |
| 3 | Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data显示文摘Black raspberry(Rubus occidentalis L.)is a niche fruit crop valued for its flavor and potential health benefits.The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome.The recently released draft genome for black raspberry(ORUS 4115-3)lacks assembly of scaffolds to chromosome scale.We used high-throughput chromatin conformation capture(Hi-C)and Proximity-Guided Assembly(PGA)to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven pseudo-chromosomes.The seven pseudo-chromosomes cover~97.2%of the total contig length(~223.8 Mb).Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic map.Centromeric regions were inferred from recombination frequencies of genetic markers,alignment of 303 bp centromeric sequence with the PGA,and heat map showing the physical contact matrix over the entire genome.We demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry(Fragaria vesca L.)assembled using only PacBio long-read sequences.We conclude that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data. | Rubina Jibran Helge Dzierzon Nahla Bassil Jill M.Bushakra Patrick P.Edger Shawn Sullivan Chad E.Finn Michael Dossett Kelly J.Vining Robert VanBuren Todd C.Mockler Ivan Liachko Kevin M.Davies Toshi M.Foster David Chagné | 2018 | Horticulture Research2018，5，1： | 4 |
| 4 | 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 |
| 5 | Validation of SNP markers for fruit quality and disease resistance loci in apple (Malus × domestica Borkh.) using the OpenArray® platform显示文摘Genome mapping has promised much to tree fruit breeding during the last 10 years.Nevertheless,one of the greatest challenges remaining to tree fruit geneticists is the translation of trait loci and whole genome sequences into diagnostic genetic markers that are efficient and cost-effective for use by breeders,who must select genetically optimal parents and subsequently select genetically superior individuals among their progeny.To take this translational step,we designed the apple International RosBREED SNP Consortium OpenArray v1.0(IRSCOA v1.0)assay using a set of 128 apple single nucleotide polymorphisms(SNPs)linked to fruit quality and pest and disease resistance trait loci.The Thermo Fisher Scientific OpenArray®technology enables multiplexed screening of SNP markers using a real-time PCR instrument with fluorescent probe-based Taqman®assays.We validated the apple IRSCOA v1.0 multitrait assay by screening 240 phenotyped individuals from the Plant&Food Research apple cultivar breeding programme.This set of individuals comprised commercial and heritage cultivars,elite selections,and families segregating for traits of importance to breeders.In total,33 SNP markers of the IRSCOA v1.0 were validated for use in marker-assisted selection(MAS)for the scab resistances Rvi2/Vh2,Rvi4/Vh4,Rvi6/Vf,fire blight resistance MR5/RLP1,powdery mildew resistance Pl2,fruit firmness,skin colour,flavour intensity,and acidity.The availability of this set of validated trait-associated SNP markers,which can be used individually on multiple genotyping platforms available to various apple breeding programmes or re-designed using the flanking sequences,represents a large translational genetics step from genomics to crop improvement of apple. | David Chagné Stijn Vanderzande Chris Kirk Natalie Profitt Rosemary Weskett Susan E.Gardiner Cameron P.Peace Richard K.Volz Nahla V.Bassil | 2019 | Horticulture Research2019，6，1： | 3 |
| 6 | QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit ( Prunus avium L.)显示文摘 | Suneth S. Sooriyapathirana Amjad Khan Audrey M. Sebolt Dechun Wang Jill M. Bushakra Kui Lin-Wang Andrew C. Allan Susan E. Gardiner David Chagné Amy F. Iezzoni | 2010 | Tree Genetics & Genomes2010，，6： | 2 |
| 7 | 中国实生和无性系苹果砧木及其杂交后代矮化基因型分子鉴定显示文摘【目的】利用已开发的矮化性状分子标记(Dw1/Dw2)筛选中国实生和自育无性系苹果砧木,探明各个砧木品种的矮化基因型,为苹果砧木育种工作中亲本选择及矮化分子辅助育种提供帮助。【方法】以不同地区采集的24份中国实生和自育的无性系苹果砧木、147份新疆野苹果(李2-3)בM9’和345份山荆子(野1-2)בM9’杂交后代单株的叶片DNA为模板,以矮化砧木‘M9’‘M116’和‘MM106’为对照,利用已经开发的Dw1和Dw2矮化标记的SSR引物进行PCR扩增,然后用毛细管电泳检测PCR产物,分析确定各个样品的矮化基因型。【结果】在24份中国苹果砧木中鉴定出8份携带Dw1矮化基因,5份携带Dw2矮化基因,3个自育杂交品种同时携带Dw1和Dw2矮化基因;新疆野苹果(李2-3)בM9’组合的147个杂种实生苗中有48株携带Dw1矮化基因,14株同时携带Dw1和Dw2基因,山荆子(野1-2)בM9’的345个杂交后代中仅有11个单株携带Dw1基因型,其余单株均不携带任一矮化基因。【结论】试验中检测的八棱海棠(房2-3)、山荆子(野1-2)和平邑甜茶(野2-22)等中国常用实生砧木均不携带Dw1或Dw2基因,仅新疆野苹果(李2-3)中含有Dw2矮化基因;中国自育的杂交砧木品种中,以‘M9’等矮化品种为亲本的后代大多携带Dw1或Dw2;双亲都含有矮化基因的杂交组合后代能获得更多的携带矮化基因的单株。 | 张恒涛 BUS Vincent G.M. 张亚茹 王欢 王美丽 BOWATTE Deepa GARDINER Susan E. CHAGNE David KIRK Chris KUMAR Satish 王大江 张瑞萍 周喆 YAO Jia-Long 阎振立 | 2020 | 果树学报2020，37，12： | 2 |
| 8 | Genetic and environmental control of fruit maturation,dry matter and firmness in apple(Malus×domestica Borkh.)显示文摘For any given genotype,the environment in which an apple is grown can influence the properties of the fruit considerably.While there has been extensive research on the mechanism of the genetic control of fruit quality traits,less effort has been made to investigate the way that these genetic mechanisms interact with the environment.To address this issue,we employed a large‘Royal Gala’בBraeburn’population of 572 seedlings replicated over sites in three climatically diverse apple-growing regions in New Zealand.Phenotyping for traits including fruit maturation timing,firmness and dry matter content was performed at each of these three sites for a single growing season(2011),and at two sites(Motueka and Hawke’s Bay)for two seasons(2009 and 2010).The phenotype data collected over 2 years at two sites enabled the detection of 190 quantitative trait loci(QTL)that controlled these traits regardless of year or growing location,as well as some chromosomal loci that influenced the traits in a single given environment or year.For those loci that were environmentally stable over three sites,there was an interdependency of fruit maturation date,dry matter content and storage potential within this population,with two regions on Linkage Groups(LGs)10 and 16 strongly contributing.If these loci were used in a marker-assisted selection programme to select for progeny bearing firmer fruit,this would have the unintentional consequence of selecting,high dry matter content,later maturing apples.In addition,a further 113 new QTLs with a smaller effect were identified,some of which were exhibited only in a single growing environment,demonstrating the underlying complexity of control of traits determining fruit quality,in addition to the need for being aware of environmental effects when developing new apple varieties. | David Chagne Daya Dayatilake Robert Diack Murray Oliver Hilary Ireland Amy Watson Susan E Gardiner Jason W Johnston Robert J Schaffer Stuart Tustin | 2014 | Horticulture Research2014，1，1： | 2 |
| 9 | Development of a set of SNP markers present in expressed genes of the apple显示文摘 | David Chagné Ksenija Gasic Ross N. Crowhurst Yuepeng Han Heather C. Bassett Deepa R. Bowatte Timothy J. Lawrence Erik H.A. Rikkerink Susan E. Gardiner Schuyler S. Korban | 2008 | Genomics2008，，5： | 1 |
| 10 | Genome mapping of an apple scab, a powdery mildew and a woolly apple aphid resistance gene from open-pollinated Mildew Immune Selection显示文摘 | Vincent G. M. Bus Heather C. M. Bassett Deepa Bowatte David Chagné Chandra A. Ranatunga Dulantha Ulluwishewa Claudia Wiedow Susan E. Gardiner | 2010 | Tree Genetics & Genomes2010，，3： | 1 |
| 11 | Genome mapping of postzygotic hybrid necrosis in an interspecific pear population显示文摘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 lethality.Identification 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 purposes.Development 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 genes.Although hybrid necrosis has been reported in several plant taxa,including Rosaceae species,this phenomenon has not been described previously in pear.In the interspecific pear population resulting from a cross between PEAR3(Pyrus bretschneideri×Pyrus communis)and‘Moonglow’(P.communis),we observed two types of hybrid necrosis,expressed at different stages of plant development.Using 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 independent.One 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’. | 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 | 2016 | Horticulture Research2016，3，1： | 1 |
| 12 | Automated SNP Detection in Expressed Sequence Tags: Statistical Considerations and Application to Maritime Pine Sequences显示文摘 | Lo?ck Le Dantec David Chagné David Pot Olivier Cantin Pauline Garnier-Géré Frank Bedon Jean-Marc Frigerio Philippe Chaumeil Patrick Léger Virginie Garcia Frédéric Laigret Antoine de Daruvar Christophe Plomion | 2004 | Plant Molecular Biology2004，，3： | 1 |
| 13 | Automated SNP detection in expressed sequence tags: Statistical considerations and application to maritime pine sequences显示文摘 | Loick Le Dantec David Chagne David Pot | 2004 | Plant Molecular Biology2004，54，： | 1 |
| 14 | Genome mapping of an apple scab, a powdery mildew and a woolly apple aphid resistance gene from open-pollinated Mildew Immune Selection显示文摘 | Vincent G. M. Bus Heather C. M. Bassett Deepa Bowatte David Chagné Chandra A. Ranatunga Dulantha Ulluwishewa Claudia Wiedow Susan E. Gardiner | 2010 | Tree Genetics & Genomes2010，，3： | 1 |
| 15 | QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit ( Prunus avium L.)显示文摘 | Suneth S. Sooriyapathirana Amjad Khan Audrey M. Sebolt Dechun Wang Jill M. Bushakra Kui Lin-Wang Andrew C. Allan Susan E. Gardiner David Chagné Amy F. Iezzoni | 2010 | Tree Genetics & Genomes2010，，6： | 1 |
| 16 | Multiple quantitative trait loci contribute to resistance to bacterial canker incited by Pseudomonas syringae pv.actinidiae in kiwifruit(Actinidia chinensis)显示文摘Pseudomonas syringae pv.actinidiae(Psa)biovar 3,a virulent,canker-inducing pathogen is an economic threat to the kiwifruit(Actinidia spp.)industry worldwide.The commercially grown diploid(2×)A.chinensis var.chinensis is more susceptible to Psa than tetraploid and hexaploid kiwifruit.However information on the genetic loci modulating Psa resistance in kiwifruit is not available.Here we report mapping of quantitative trait loci(QTLs)regulating resistance to Psa in a diploid kiwifruit population,derived from a cross between an elite Psa-susceptible‘Hort16A’and a resistant male breeding parent P1.Using high-density genetic maps and intensive phenotyping,we identified a single QTL for Psa resistance on Linkage Group(LG)27 of‘Hort16A’revealing 16–19%phenotypic variance and candidate alleles for susceptibility and resistance at this loci.In addition,six minor QTLs were identified in P1 on distinct LGs,exerting 4–9%variance.Resistance in the F1 population is improved by additive effects from‘Hort16A’and P1 QTLs providing evidence that divergent genetic pathways interact to combat the virulent Psa strain.Two different bioassays further identified new QTLs for tissue-specific responses to Psa.The genetic marker at LG27 QTL was further verified for association with Psa resistance in diploid Actinidia chinensis populations.Transcriptome analysis of Psa-resistant and susceptible genotypes in field revealed hallmarks of basal defense and provided candidate RNA-biomarkers for screening for Psa resistance in greenhouse conditions. | Jibran Tahir Stephen Hoyte Heather Bassett Cyril Brendolise Abhishek Chatterjee Kerry Templeton Cecilia Deng Ross Crowhurst Mirco Montefiori Ed Morgan Andrew Wotton Keith Funnell Claudia Wiedow Mareike Knaebel Duncan Hedderley Joel Vanneste John McCallum Kirsten Hoeata Amardeep Nath David Chagné Luis Gea Susan E.Gardiner | 2019 | Horticulture Research2019，6，1： | 0 |
| 17 | Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts显示文摘Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed worldwide.The industry continues to face a wide variety of production challenges(e.g.disease pressures),as well as a demand for higher-yielding cultivars with improved fruit quality characteristics.Unfortunately,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops.Here,we describe the construction and analysis of the first pangenome for both blueberry and cranberry.Our analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in cranberry.Auxiliary genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality traits.The discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding efforts.The pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database.Lastly,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family. | Alan E.Yocca Adrian Platts Elizabeth Alger Scott Teresi Molla F.Mengist Juliana Benevenuto Luis Felipe V.Ferrão MacKenzie Jacobs Michal Babinski Maria Magallanes-Lundback Philipp Bayer Agnieszka Golicz Jodi L.Humann Dorrie Main Richard V.Espley David Chagné Nick W.Albert Sara Montanari Nicholi Vorsa James Polashock Luis Díaz-Garcia Juan Zalapa Nahla V.Bassil Patricio R.Munoz Massimo Iorizzo Patrick P.Edger | 2023 | Horticulture Research2023，10，11： | 0 |
| 18 | Molecular characterization of intergeneric hybrids between Malus and Pyrus显示文摘Apple(Malus)and pear(Pyrus)are economically important fruit crops well known for their unique textures,f lavours,and nutritional qualities.Both genera are characterised by a distinct pattern of secondary metabolites,which directly affect not only resistance to certain diseases,but also have significant impacts on the f lavour and nutritional value of the fruit.The identical chromosome numbers,similar genome size,and their recent divergence date,together with DNA markers have shown that apple and pear genomes are highly co-linear.This study utilized comparative genomic approaches,including simple sequence repeats,high resolution single nucleotide polymorphism melting analysis,and single nucleotide polymorphism chip analysis to identify genetic differences among hybrids of Malus and Pyrus,and F2 offspring.This research has demonstrated and validated that these three marker types,along with metabolomics analysis are very powerful tools to detect and confirm hybridity of progeny derived from crosses between apple and pear in both cross directions.Furthermore,this work analysed the genus-specific metabolite patterns and the resistance to fire blight(Erwinia amylovora)in progeny.The findings of this work will enhance and accelerate the breeding of novel tree fruit crops that benefit producers and consumers,by enabling marker assisted selection of desired traits introgressed between pear and apple. | Giulia Pasqualetto Luisa Palmieri Stefan Martens Vincent G.M.Bus David Chagné Claudia Wiedow Mickael A.Malnoy Susan E.Gardiner | 2023 | Horticulture Research2023，10，1： | 0 |
| 19 | The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae显示文摘The Rosaceae family has striking phenotypic diversity and high syntenic conservation.Gillenia trifoliata is sister species to the Maleae tribe of apple and~1000 other species.Gillenia has many putative ancestral features,such as herb/sub-shrub habit,dry fruit-bearing and nine base chromosomes.This coalescence of ancestral characters in a phylogenetically important species,positions Gillenia as a‘rosetta stone'for translational science within Rosaceae.We present genomic and phenological resources to facilitate the use of Gillenia for this purpose.The Gillenia genome is the fi rst fully annotated chromosome-level assembly with an ancestral genome complement(x=9),and with it we developed an improved model of the Rosaceae ancestral genome.MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fl eshy fruit development in Rosaceae. | Hilary S.Ireland Chen Wu Cecilia H.Deng Elena Hilario Ali Saei Sylvia Erasmuson Ross N.Crowhurst Karine M.David Robert J.Schaffer David Chagn | 2021 | Horticulture Research2021，8，1： | 0 |
| 20 | A high-throughput S-RNase genotyping method for apple显示文摘Knowledge of the genotypes for the self-incompatibility locus(S-locus)in apple varieties and in genotypes being used as parents is critical for breeding and commercial production.We present a high-throughput set of molecular markers for the identification of 13 common S-RNase alleles(S_(1),S_(2),S_(3),S_(5),S_(7),S_(8),S_(9),S_(10),S_(20),S_(2)3,S_(24),S_(25)and S_(28).This set is composed of seven allele-specific quantitative PCR-based High-Resolution Melting assays and four multi-allelic SSR markers.Validation of these markers was performed using 86 apple accessions,including cultivars with known S-genotypes and recent commercial varieties arising from the Plant&Food Research(PFR)cultivar breeding programme.We also characterized the S-genotypes of 183 genotypes representing some of the most valuable parents within PFR’s cultivar breeding programme.The results of this work demonstrate the practical usefulness of this marker set to provide accurate cross-compatibility information to optimise choice of pollenisers in commercial apple orchard design,and to identify compatible parents and guide parental selection when executing apple breeding programmes,to optimise fruit crop yield and quality. | Elena López-Girona Deepa R.Bowatte Maia EMSmart Sydel Alvares Thyana Lays Brancher David Chagné Richard K.Volz | 2021 | Fruit Research2021，1，1： | 0 |
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