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| 1 | DNA-informed breeding of rosaceous crops: promises, progress and prospects显示文摘Crops of the Rosaceae family provide valuable contributions to rural economies and human health and enjoyment.Sustained solutions to production challenges and market demands can be met with genetically improved new cultivars.Traditional rosaceous crop breeding is expensive and time-consuming and would benefit from improvements in efficiency and accuracy.Use 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 resources.Successes in deployment of DNA-based knowledge and tools have arisen when the‘chasm’between genomics discoveries and practical application is bridged systematically.Key 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 decisions.DNA-informed germplasm characterization for revealing identity and relatedness has benefitted many programs and provides a compelling entry point to reaping benefits of genomics research.DNA-informed germplasm evaluation for predicting trait performance has enabled effective reallocation of breeding resources when applied in pioneering programs.DNA-based diagnostics is now expanding from specific loci to genome-wide considerations.Realizing 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. | Cameron P Peace | 2017 | Horticulture Research2017，4，1： | 11 |
| 2 | 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显示文摘The apple(Malus×domestica)cultivar Honeycrisp has become important economically and as a breeding parent.An 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 unknown.The 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 array.This 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 parent.Following this finding,siblings of‘Honeycrisp’were identified using the SNP data.Breeding records from several of these siblings suggested that the previously unreported parent is a University of Minnesota selection,MN1627.This selection is no longer available,but now is genetically described through imputed SNP haplotypes.We also present the mosaic grandparental composition of‘Honeycrisp’for each of its 17 chromosome pairs.This 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 programs.The 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. | 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 | 2017 | Horticulture Research2017，4，1： | 9 |
| 3 | Prunus genetics and applications after de novo genome sequencing:achievements and prospects显示文摘Prior to the availability of whole-genome sequences,our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources.With public release of the peach genome and others that followed,significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued.In this review,we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences.Within the structural and evolutionary contexts,we summarize:(1)the current status of Prunus whole-genome sequences;(2)preliminary and ongoing work on the sequence structure and diversity of the genomes;(3)the analyses of Prunus genome evolution driven by natural and man-made selection;and(4)provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide.Functionally,we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits.These include phenology,fruit quality,allergens,disease resistance,tree architecture,and self-incompatibility.Translationally,we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement.Finally,we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae(GDR)and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry. | Maria JoséAranzana Véronique Decroocq Elisabeth Dirlewanger Iban Eduardo Zhong Shan Gao Ksenija Gasic Amy Iezzoni Sook Jung Cameron Peace Humberto Prieto Ryutaro Tao Ignazio Verde Albert G.Abbott Pere Arús | 2019 | Horticulture Research2019，6，1： | 8 |
| 4 | RosBREED:bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops显示文摘The Rosaceae crop family(including almond,apple,apricot,blackberry,peach,pear,plum,raspberry,rose,strawberry,sweet cherry,and sour cherry)provides vital contributions to human well-being and is economically significant across the U.S.In 2003,industry stakeholder initiatives prioritized the utilization of genomics,genetics,and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality.However,rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding—a“chasm”existed between existing genomics and genetic information and the application of this knowledge in breeding.The RosBREED project(“Ros”signifying a Rosaceae genomics,genetics,and breeding community initiative,and“BREED”,indicating the core focus on breeding programs),addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative.RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S.rosaceous crop breeding programs,thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality.This review presents a synopsis of the approach,deliverables,and impacts of RosBREED,highlighting synergistic global collaborations and future needs.Enabling technologies and tools developed are described,including genome-wide scanning platforms and DNA diagnostic tests.Examples of DNA-informed breeding use by project participants are presented for all breeding stages,including pre-breeding for disease resistance,parental and seedling selection,and elite selection advancement.The chasm is now bridged,accelerating rosaceous crop genetic improvement. | Amy F.Iezzoni Jim McFerson James Luby Ksenija Gasic Vance Whitaker Nahla Bassil Chengyan Yue Karina Gallardo Vicki McCracken Michael Coe Craig Hardner Jason D.Zurn Stan Hokanson Eric van de Weg Sook Jung Dorrie Main Cassia da Silva Linge Stijn Vanderzande Thomas M.Davis Lise L.Mahoney Chad Finn Cameron Peace | 2020 | Horticulture Research2020，7，1： | 2 |
| 5 | Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops显示文摘Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest.Traditionally,genetic potential is determined by phenotypic evaluation.With 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 strategies.Existing 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 additive.This 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 crops.Various 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 patterns.Both 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 heritability.Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. | Sushan Ru Craig Hardner Patrick A Carter Kate Evans Dorrie Main Cameron Peace | 2016 | Horticulture Research2016，3，1： | 1 |
| 6 | Fire blight QTL analysis in a multi-family apple population identifies a reduced-susceptibility allele in ‘Honeycrisp’显示文摘Breeding apple cultivars with resistance offers a potential solution to fire blight,a damaging bacterial disease caused by Erwinia amylovora.Most resistance alleles at quantitative trait loci(QTLs)were previously characterized in diverse Malus germplasm with poor fruit quality,which reduces breeding utility.This 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 U.S.apple breeding programs.Twenty-seven important breeding parents(IBPs)were represented by 314 offspring from 32 full-sib families,with‘Honeycrisp’being the most highly represented IBP.Analyzing 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 15.These QTLs together explained~28% of phenotypic variation.The 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 QTLs.In general,lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs.This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm.Knowledge 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. | Sarah A.Kostick Soon Li Teh John L.Norelli Stijn Vanderzande Cameron Peace Kate M.Evans | 2021 | Horticulture Research2021，8，1： | 1 |
| 7 | Fruit cracking and firmness DNA test development and evaluation in sweet cherry显示文摘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 individuals.In sweet cherry(Prunus avium L.),cracked or soft fruit are major industry challenges.Recent research detected two quantitative trait loci(QTLs)for fruit cracking and firmness differing in trait levels associated with QTL haplotypic variation.Also,a DNA test for cracking(Pav-G5Crack-SSR),using two simple sequence repeat(SSR)markers,was previously developed but not yet validated on breeding germplasm.In 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 cherry.Unselected seedlings from pedigreeconnected families were screened with the Pav-G5Crack-SSR DNA test.DNA tests were also created from four SNP markers with HRM assays,using two years of cracking and firmness data for evaluation.Pav-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 variance.Pav-G1Firm-SNP and Pav-G3Firm-SNP together explained 22%–28%of the firmness phenotypic variance.All 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. | W.Wesley Crump Cameron Peace Zhiwu Zhang Per McCord | 2022 | Fruit Research2022，2，1： | 0 |
| 8 | GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS:PROMISES,PROGRESS,CHALLENGES AND OUTLOOK显示文摘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 consumers.However,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. | Craig HARDNER Satish KUMAR Dorrie MAIN Cameron PEACE | 2021 | Frontiers of Agricultural Science and Engineering2021，8，2： | 0 |
| 9 | The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry显示文摘Pedigree information is of fundamental importance in breeding programs and related genetics efforts.However,many individuals have unknown pedigrees.While 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 inbreeding.The 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 cherry.HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops.These distributions were then used to estimate previously unknown relationships.Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data.For 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 confirmed.For 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 relationships.Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction. | 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 | 2021 | Horticulture Research2021，8，1： | 0 |
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