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| 1 | 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 |
| 2 | 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 |
| 3 | 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 |
| 4 | 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 |
| 5 | Cost and accuracy of advanced breeding trial designs in apple显示文摘Trialing advanced candidates in tree fruit crops is expensive due to the long-term nature of the planting and labor-intensive evaluations required to make selection decisions.How closely the trait evaluations approximate the true trait value needs balancing with the cost of the program.Designs of field trials of advanced apple candidates in which reduced number of locations,the number of years and the number of harvests per year were modeled to investigate the effect on the cost and accuracy in an operational breeding program.The aim was to find designs that would allow evaluation of the most additional candidates while sacrificing the least accuracy.Critical percentage difference,response to selection,and correlated response were used to examine changes in accuracy of trait evaluations.For the quality traits evaluated,accuracy and response to selection were not substantially reduced for most trial designs.Risk management influences the decision to change trial design,and some designs had greater risk associated with them.Balancing cost and accuracy with risk yields valuable insight into advanced breeding trial design.The methods outlined in this analysis would be well suited to other horticultural crop breeding programs. | Julia M Harshman Kate M Evans Craig M Hardner | 2016 | Horticulture Research2016，3，1： | 0 |
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