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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

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prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNp array

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Horticulture Research 2019年第1期6卷 1623-1637页

作者： Craig M.Hardner Ben J.Hayes Satish Kumar Stijn Vanderzande Lichun Cai Julia piaskowski JoséQuero-Garcia JoséAntonio Campoy Teresa Barreneche Daniela Giovannini Alessandro Liverani Gérard Charlot Miguel Villamil-Castro Nnadozie Oraguzie cameron p.peace University of Queensland Queensland Alliance for Agriculture and Food InnovationBrisbaneQLD 4072Australia The New Zealand Institute for plant and Food Research Limited Hawke’s Bay Research CentreHastings 4130New Zealand Department of Horticulture Washington State UniversityPullmanWA 99164USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA UMR 1332 BFp INRAUniversity of Bordeaux33140 Nouvelle-AquitaineFrance Council for Agricultural Research and Economics(CREA) Fruit Unit of ForlìVia la Canapona1 bis47121 Emilia-RomagnaItaly Centre Technique Interprofessionnel des Fruits et Légumes(CTIFL) 751 Chemin de Balandran30127 BellegardeFrance Department of Horticulture Washington State UniversityIrrigated Agriculture Research and Extension Center24106N Bunn RoadProsserWA 99350USA

The timing of fruit maturity is an important trait in sweet cherry production and *** variation for phenology of fruit maturity in sweet cherry appears to be under strong genetic control,but that control might be complicated by phenotypic instability across *** such genotype-by-environment interaction(G×E)is a common phenomenon in crop plants,knowledge about it is lacking for fruit maturity timing and other sweet cherry *** this study,1673 genome-wide SNp markers were used to estimate genomic relationships among 597 weakly pedigree-connected individuals evaluated over two seasons at three locations in Europe and one location in the USA,thus sampling eight‘environments’.The combined dataset enabled a single meta-analysis to investigate the environmental stability of genomic *** disequilibrium among marker loci declined rapidly with physical distance,and ordination of the relationship matrix suggested no strong structure among *** most parsimonious G×E model allowed heterogeneous genetic variance and pairwise covariances among ***-sense genomic heritability was very high(0.60–0.83),as was accuracy of predicted breeding values(>0.62).Average correlation of additive effects among environments was high(0.96)and breeding values were highly correlated across *** indicated that genomic models can be used in cherry to accurately predict date of fruit maturity for untested individuals in new *** G×E for this trait indicated that phenotypes of individuals will be stable across similar *** analyses for other sweet cherry traits,for which multiple years of data are commonly available among breeders and cultivar testers,would be informative for predicting performance of elite selections and cultivars in new environments.

关键词： maturity environments breeding

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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

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GLOBAL GENOMIC pREDICTION IN HORTICULTURAL CROpS:pROMISES,pROGRESS,CHALLENGES AND OUTLOOK

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Frontiers of Agricultural Science and Engineering 2021年第2期8卷 353-355页

作者： Craig HARDNER Satish KUMAR Dorrie MAIN cameron peace Queensland Alliance for Agriculture and Food Innovation University of Queensland St Lucia QLD4072Australia New Zealand Institute plant&Food Res Ltd Hawkes Bay Research CentreHavelock North4130New Zealand Department of Horticulture Washington State UniversityPullmanWA 99164USA.

Only when all contribute their firewood can they build up a big fire(众人拾柴火焰高).Horticultural crops are a major source of high value nutritious food,and new improved cultivars developed through breeding are required for sustainable production in the face of abiotic and biotic stresses,and to deliver novel,premium products to ***,grower confidence in the performance of new germplasm,particularly across environmental variability,is important for commercial adoption and germplasm-environ-ment matching to optimize production.

关键词： pROGRESS crops breeding

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DNA-informed breeding of rosaceous crops: promises, progress and prospects

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Horticulture Research 2017年第1期4卷 335-347页

作者： cameron p.peace Department of Horticulture Washington State UniversityPO Box 646414Pullman99164-6414WAUSA

Crops of the Rosaceae family provide valuable contributions to rural economies and human health and *** solutions to production challenges and market demands can be met with genetically improved new *** rosaceous crop breeding is expensive and time-consuming and would benefit from improvements in efficiency and *** of DNA information is becoming conventional in rosaceous crop breeding,contributing to many decisions and operations,but only after past decades of solved challenges and generation of sufficient *** in deployment of DNA-based knowledge and tools have arisen when the‘chasm’between genomics discoveries and practical application is bridged *** steps are establishing breeder desire for use of DNA information,adapting tools to local breeding utility,identifying efficient application schemes,accessing effective services in DNA-based diagnostics and gaining experience in integrating DNA information into breeding operations and ***-informed germplasm characterization for revealing identity and relatedness has benefitted many programs and provides a compelling entry point to reaping benefits of genomics ***-informed germplasm evaluation for predicting trait performance has enabled effective reallocation of breeding resources when applied in pioneering ***-based diagnostics is now expanding from specific loci to genome-wide *** the full potential of this expansion will require improved accuracy of predictions,multi-trait DNA profiling capabilities,streamlined breeding information management systems,strategies that overcome plant-based features that limit breeding progress and widespread training of current and future breeding personnel and allied scientists.

关键词： breeding crops operations

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Fruit cracking and firmness DNA test development and evaluation in sweet cherry

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Fruit Research 2022年第1期2卷 129-139页

作者： W.Wesley Crump cameron peace Zhiwu Zhang per McCord Department of Horticulture Washington State UniversityProsserWA 99350United States Department of Horticulture Washington State UniversityPullmanWA 99164United States Department of Crop and Soil Sciences Washington State UniversityPullmanWA 99164United States

One application of DNA-informed breeding,which has potential to increase the effectiveness of traditional breeding methods,is the use of DNAbased diagnostic tests to estimate genetic potential of breeding *** sweet cherry(prunus avium L.),cracked or soft fruit are major industry *** research detected two quantitative trait loci(QTLs)for fruit cracking and firmness differing in trait levels associated with QTL haplotypic ***,a DNA test for cracking(pav-G5Crack-SSR),using two simple sequence repeat(SSR)markers,was previously developed but not yet validated on breeding *** addition to SSR markers,single nucleotide polymorphism(SNp)markers can be used for developing locus-specific DNA tests and run as simple assays such as high-resolution melting(HRM).The objective of this research was to develop and evaluate the predictiveness of DNA tests for fruit cracking and firmness in sweet *** seedlings from pedigreeconnected families were screened with the pav-G5Crack-SSR DNA *** tests were also created from four SNp markers with HRM assays,using two years of cracking and firmness data for ***-G5Crack-SSR explained 12–15%of the cracking phenotypic variance,while pav-G1Crack-SNp and pav-G5Crack-SNp(which targeted the same QTL as pav-G5Crack-SSR)together explained 16%–30%of the cracking phenotypic ***-G1Firm-SNp and pav-G3Firm-SNp together explained 22%–28%of the firmness phenotypic *** three DNA tests can be implemented in breeding programs to enhance effectiveness in breeding for decreased cracking incidence and increased fruit firmness in sweet cherry.

关键词： fir breeding cracking

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Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

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Horticulture Research 2016年第1期3卷 257-266页

作者： Sushan Ru Craig Hardner patrick A Carter Kate Evans Dorrie Main cameron peace Department of Horticulture Washington State UniversityPO Box 646414Pullman99164-6414WAUSA Queensland Alliance for Agriculture and Food Innovation University of QueenslandSt Lucia4072BrisbaneAustralia School of Biological Sciences Washington State UniversityPullman99164-4236WAUSA Department of Horticulture Washington State University Tree Fruit Research and Extension CenterWenatchee98801WAUSA

Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of ***,genetic potential is determined by phenotypic *** the availability of DNA tests for some agronomically important traits,breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection.A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative *** models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops,as clonal propagation captures all genetic effects,not just *** study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation,based on a generalized seedling selection scheme of clonally propagated *** trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation *** derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense *** from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available.

关键词： seedling crops cultivar

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Elucidation of the ‘Honeycrisp’ pedigree through haplotype analysis with a multi-family integrated SNp linkage map and a large apple (Malus×domestica) pedigree-connected SNp data set

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Horticulture Research 2017年第1期4卷 358-364页

作者： Nicholas p Howard Eric van de Weg David S Bedford cameron p.peace Stijn Vanderzande Matthew D Clark Soon Li Teh Lichun Cai James J Luby Department of Horticultural Science University of MinnesotaSt Paul55104MNUSA Department of plant Breeding Wageningen University and ResearchWageningen6700AJThe Netherlands Department of Horticulture and Landscape Architecture Washington State UniversityPullman99164WAUSA Department of Horticulture Michigan State UniversityEast Lansing48824MIUSA

The apple(Malus×domestica)cultivar Honeycrisp has become important economically and as a breeding *** earlier study with SSR markers indicated the original recorded pedigree of‘Honeycrisp’was incorrect and‘Keepsake’was identified as one putative parent,the other being *** objective of this study was to verify‘Keepsake’as a parent and identify and genetically describe the unknown parent and its grandparents.A multi-family based dense and high-quality integrated SNp map was created using the apple 8 K Illumina Infinium SNp *** map was used alongside a large pedigree-connected data set from the RosBREED project to build extended SNp haplotypes and to identify pedigree relationships.‘Keepsake’was verified as one parent of‘Honeycrisp’and‘Duchess of Oldenburg’and‘Golden Delicious’were identified as grandparents through the unknown *** this finding,siblings of‘Honeycrisp’were identified using the SNp *** records from several of these siblings suggested that the previously unreported parent is a University of Minnesota selection,*** selection is no longer available,but now is genetically described through imputed SNp *** also present the mosaic grandparental composition of‘Honeycrisp’for each of its 17 chromosome *** new pedigree and genetic information will be useful in future pedigree-based genetic studies to connect‘Honeycrisp’with other cultivars used widely in apple breeding *** created SNp linkage map will benefit future research using the data from the Illumina apple 8 and 20 K and Affymetrix 480 K SNp arrays.

关键词： Golden linkage connected

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Fire blight QTL analysis in a multi-family apple population identifies a reduced-susceptibility allele in ‘Honeycrisp’

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Horticulture Research 2021年第1期8卷 355-367页

作者： Sarah A.Kostick Soon Li Teh John L.Norelli Stijn Vanderzande cameron peace Kate M.Evans Tree Fruit Research and Extension Center Department of HorticultureWashington State UniversityWenatcheeWA 98801USA United States Department of Agriculture Agricultural Research ServiceAppalachian Fruit Research LaboratoryKearneysvilleWV 25430USA Department of Horticulture Washington State UniversityPullmanWA 99164USA

Breeding apple cultivars with resistance offers a potential solution to fire blight,a damaging bacterial disease caused by Erwinia *** resistance alleles at quantitative trait loci(QTLs)were previously characterized in diverse Malus germplasm with poor fruit quality,which reduces breeding *** study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to *** breeding ***-seven important breeding parents(IBps)were represented by 314 offspring from 32 full-sib families,with‘Honeycrisp’being the most highly represented *** resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data,QTLs were consistently mapped on chromosomes(Chrs.)6,7,and *** QTLs together explained~28% of phenotypic *** Chr.6 and Chr.15 QTLs colocalized with previously reported QTLs,while the Chr.7 QTL is possibly novel.‘Honeycrisp’inherited a rare reduced-susceptibility allele at the Chr.6 QTL from its grandparent‘Frostbite’.The highly resistant IBp‘Enterprise’had at least one putative reduced-susceptibility allele at all three *** general,lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across *** study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding *** gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.

关键词： blight breeding cultivar

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The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

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Horticulture Research 2021年第1期8卷 2785-2797页

作者： Nicholas p.Howard cameron peace Kevin A.T.Silverstein Ana poets James J.Luby Stijn Vanderzande Charles-Eric Durel Helene Muranty Caroline Denance Eric van de Weg Institut fur Biologie und Umweltwissenschaften Carl von Ossietzky UniversityOldenburgGermany Department of Horticultural Science University of MinnesotaSt.PaulMNUSA Department of Horticulture and Landscape Architecture Washington State UniversityPullmanWashingtonWAUSA Minnesota Supercomputing Institute University of MinnesotaMinneapolisMNUSA Universited’Angers Institut AgroINRAEIRHSSFR 4207 QuaSaVBeaucouzeFrance plant Breeding Wageningen University and ResearchWageningenThe Netherlands

pedigree information is of fundamental importance in breeding programs and related genetics ***,many individuals have unknown *** methods to identify and confirm direct parent–offspring relationships are routine,those for other types of close relationships have yet to be effectively and widely implemented with plants,due to complications such as asexual propagation and extensive *** objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes(referred to in this study as“summed potential lengths of shared haplotypes”,SpLoSH).A custom python script,HapShared,was developed to generate SpLoSH data in apple and sweet *** was used to establish empirical distributions of SpLoSH data for known relationships in these *** distributions were then used to estimate previously unknown *** studies in each crop demonstrated various pedigree reconstruction scenarios using SpLoSH *** cherry,a full-sib relationship was deduced for‘Emperor Francis,and‘Schmidt’,a half-sib relationship for‘Van’and‘Windsor’,and the paternal grandparents of‘Stella’were *** apple,29 cultivars were found to share an unknown parent,the pedigree of the unknown parent of‘Cox’s pomona’was reconstructed,and‘Fameuse’was deduced to be a likely grandparent of‘McIntosh’.Key genetic resources that enabled this empirical study were large genome-wide SNp array datasets,integrated genetic maps,and previously identified pedigree *** with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

关键词： python breeding crops

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