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Molecular characterization of intergeneric hybrids between Malus and Pyrus

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Horticulture Research 2023年第1期10卷 172-182页

作者： Giulia Pasqualetto Luisa Palmieri Stefan Martens Vincent G.M.Bus david chagné Claudia Wiedow Mickael A.Malnoy Susan E.Gardiner Research and Innovation Centre Edmund Mach FoundationSan Michele all’AdigeTN 38010Italy Department of Agricultural FoodEnvironmental and Animal SciencesUniversity of UdineUD 33100Italy The New Zealand Institute for Plant and Food Research Ltd(PFR) Hawke’s Bay Research CentreHavelock North 4442New Zealand PFR Fitzherbert Science CentrePalmerston NorthNew Zealand

Apple(Malus)and pear(Pyrus)are economically important fruit crops well known for their unique textures,f lavours,and nutritional *** 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 *** identical chromosome numbers,similar genome size,and their recent divergence date,together with DNA markers have shown that apple and pear genomes are highly *** 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 *** 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 ***,this work analysed the genus-specific metabolite patterns and the resistance to fire blight(Erwinia amylovora)in *** 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.

关键词： crops utilized breeding

The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae

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Horticulture Research 2021年第1期8卷 3144-3157页

作者： 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 The New Zealand Institute for Plant and Food Research Ltd Private Bag 92196Auckland Mail CentreAuckland 1142New Zealand School of Biological Sciences The University of AucklandPrivate Bag 92019Auckland Mail CentreAuckland 1142New Zealand Genomics Aotearoa %Department of BiochemistryUniversity of OtagoPO Box 56Dunedin 9054New Zealand The New Zealand Institute for Plant and Food Research Ltd Private Bag 11600Palmerston North 4442New Zealand The New Zealand Institute for Plant and Food Research Ltd Private Bag 4704Christchurch Mail CentreChristchurch 8140New Zealand The New Zealand Institute for Plant and Food Research Ltd 55 Old Mill RoadRD 3Motueka 7198New Zealand

The Rosaceae family has striking phenotypic diversity and high syntenic *** trifoliata is sister species to the Maleae tribe of apple and~1000 other *** has many putative ancestral features,such as herb/sub-shrub habit,dry fruit-bearing and nine base *** coalescence of ancestral characters in a phylogenetically important species,positions Gillenia as a‘rosetta stone'for translational science within *** present genomic and phenological resources to facilitate the use of Gillenia for this *** 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 *** 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.

关键词： Rosaceae dynamics striking

Validation of SNP markers for fruit quality and disease resistance loci in apple (Malus × domestica Borkh.) using the OpenArray® platform

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Horticulture Research 2019年第1期6卷 1348-1363页

作者： david chagné Stijn Vanderzande Chris Kirk Natalie Profitt Rosemary Weskett Susan E.Gardiner Cameron P.Peace Richard K.Volz Nahla V.Bassil The New Zealand Institute for Plant&Food Research Ltd(Plant&Food Research) Palmerston North Research CentrePalmerston NorthNew Zealand Department of Horticulture Washington State UniversityPullmanWAUSA Plant&Food Research Hawke’s Bay Research CentreHavelock NorthNew Zealand USDA-ARS National Clonal Germplasm RepositoryCorvallisORUSA

Genome mapping has promised much to tree fruit breeding during the last 10 ***,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 *** 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 *** Thermo Fisher Scientific OpenArray®technology enables multiplexed screening of SNP markers using a real-time PCR instrument with fluorescent probe-based Taqman®*** validated the apple IRSCOA v1.0 multitrait assay by screening 240 phenotyped individuals from the Plant&Food Research apple cultivar breeding *** set of individuals comprised commercial and heritage cultivars,elite selections,and families segregating for traits of importance to *** 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 *** 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.

关键词： Open resistance breeding

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

A high-throughput S-RNase genotyping method for apple

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Fruit Research 2021年第1期1卷 87-95页

作者： Elena López-Girona Deepa R.Bowatte Maia EMSmart Sydel Alvares Thyana Lays Brancher david chagné Richard K.Volz The New Zealand Institute for Plant and Food Research Limited(Plant&Food Research) Private Bag 11600Palmerston North 4442New Zealand Hawke’s Bay Research Centre Private Bag 1401Havelock North 4157New Zealand

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 *** 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 *** 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 *** also characterized the S-genotypes of 183 genotypes representing some of the most valuable parents within PFR’s cultivar breeding *** 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.

关键词： breeding cultivar apple

Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

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Horticulture Research 2018年第1期5卷 868-878页

作者： 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 The New Zealand Institute for Plant&Food Research Limited Private Bag 11600Palmerston North4474New Zealand USDA-ARS National Clonal Germplasm Repository 33447 Peoria RoadCorvallisOR97333USA Department of Horticulture Michigan State UniversityEast LansingMI48824-2604USA Phase Genomics SeattleWA98195USA USDA-ARS Horticultural Crops Research Unit CorvallisOR97330USA B.C.Blueberry Council(in Partnership with Agriculture and Agri-Food Canada)Agassiz Food Research Centre AgassizBCV0M 1A0Canada The Donald Danforth Plant Science Center St.LouisMO63132USA Department of Genome Sciences University of Washington School of MedicineSeattleWA98195USA

Black raspberry(Rubus occidentalis L.)is a niche fruit crop valued for its flavor and potential health *** improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference *** recently released draft genome for black raspberry(ORUS 4115-3)lacks assembly of scaffolds to chromosome *** 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 *** 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 *** 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 *** 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 *** conclude that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.

关键词： breeding black interaction

Multiple quantitative trait loci contribute to resistance to bacterial canker incited by Pseudomonas syringae *** in kiwifruit(Actinidia chinensis)

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Horticulture Research 2019年第1期6卷 471-488页

作者： 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 The New Zealand Institute for Plant and Food Research Limited Private Bag 11030Manawatu Mail CentrePalmerston North 4442New Zealand The New Zealand Institute for Plant Food Research Limited HamiltonNew Zealand The New Zealand Institute for Plant and Food Research Limited Private Bag 92–169Auckland 1025New Zealand New Plant via Malpighi 5Forlì47122Italy The New Zealand Institute for Plant and Food Research Limited LincolnNew Zealand The New Zealand Institute for Plant and Food Research Limited 412 No 1 RoadRD2Te Puke 3182New Zealand

Pseudomonas syringae ***(Psa)biovar 3,a virulent,canker-inducing pathogen is an economic threat to the kiwifruit(Actinidia spp.)industry *** commercially grown diploid(2×)*** *** is more susceptible to Psa than tetraploid and hexaploid *** information on the genetic loci modulating Psa resistance in kiwifruit is not *** 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 *** 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 *** addition,six minor QTLs were identified in P1 on distinct LGs,exerting 4–9%*** 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 *** different bioassays further identified new QTLs for tissue-specific responses to *** genetic marker at LG27 QTL was further verified for association with Psa resistance in diploid Actinidia chinensis *** 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.

关键词： breeding trait

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

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

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Horticulture Research 2023年第11期10卷 96-105页

作者： 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 Department of Horticulture Michigan State UniversityEast LansingMI48824United States Department of Plant Biology Michigan State UniversityEast LansingMI48824United States Genetics and Genome Sciences Michigan State UniversityEast LansingMI48824United States Plants for Human Health Institute North Carolina State UniversityKannapolisNC United States Horticultural Sciences Department University of FloridaGainesvilleFL 32611United States Department of Biochemistry and Molecular Biology Michigan State UniversityEast LansingMI48824United States University of Western Australia Perth 6009 Australia Justus Liebig University Giessen35390 Germany Department of Horticulture Washington State UniversityPullmanWA99163United States The New Zealand Institute for Plant and Food Research Limited(PFR) AucklandNew Zealand The New Zealand Institute for Plant and Food Research Limited(PFR) PalmerstonNew Zealand The New Zealand Institute for Plant and Food Research Limited(PFR) MotuekaNew Zealand SEBS Plant BiologyRutgers UniversityNew Brunswick NJ 01019 United States Department of Viticulture and Enology University of CaliforniaDavisDavisCA 95616United States National Clonal Germplasm Repository USDA-ARSCorvallisOR 97333United States Department of Horticulture North Carolina State UniversityKannapolisNC United States MSU AgBioResearch Michigan State UniversityEast LansingMI48824United States

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 *** industry continues to face a wide variety of production challenges(*** pressures),as well as a demand for higher-yielding cultivars with improved fruit quality ***,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value ***,we describe the construction and analysis of the first pangenome for both blueberry and *** 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 *** 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 *** 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 *** 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 ***,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.

关键词： breeding cultivar crops