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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 | Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends显示文摘 | James E. Frelichowski Michael B. Palmer Dorrie Main Jeffrey P. Tomkins Roy G. Cantrell David M. Stelly John Yu Russell J. Kohel Mauricio Ulloa | 2006 | Molecular Genetics and Genomics2006，，5： | 1 |
| 4 | 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 |
| 5 | A roadmap for research in octoploid strawberry显示文摘The cultivated strawberry(Fragaria×ananassa)is an allo-octoploid species,originating nearly 300 years ago from wild progenitors from the Americas.Since that time the strawberry has become the most widely cultivated fruit crop in the world,universally appealing due to its sensory qualities and health benefits.The recent publication of the first highquality chromosome-scale octoploid strawberry genome(cv.Camarosa)is enabling rapid advances in genetics,stimulating scientific debate and provoking new research questions.In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture.Among these are the origins of the genome,characterization of genetic variants,and big data approaches to breeding.Key areas of research in molecular biology will include the control of flowering,fruit development,fruit quality,and plant–pathogen interactions.In order to realize this potential as a global community,investments in genome resources must be continually augmented. | Vance M.Whitaker Steven J.Knapp Michael A.Hardigan Patrick P.Edger Janet P.Slovin Nahla V.Bassil Timo Hytönen Kathryn K.Mackenzie Seonghee Lee Sook Jung Dorrie Main Christopher R.Barbey Sujeet Verma | 2020 | Horticulture Research2020，7，1： | 1 |
| 6 | Functional genomics of cell elongation in developing cotton fibers显示文摘 | A. Arpat Mark Waugh John P. Sullivan Michael Gonzales David Frisch Dorrie Main Todd Wood Anna Leslie Rod Wing Thea Wilkins | 2004 | Plant Molecular Biology2004，，6： | 1 |
| 7 | Functional genomics of cell elongation in developing cotton fibers显示文摘 | A. Arpat Mark Waugh John P. Sullivan Michael Gonzales David Frisch Dorrie Main Todd Wood Anna Leslie Rod Wing Thea Wilkins | 2004 | Plant Molecular Biology2004，，6： | 1 |
| 8 | 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 |
| 9 | Defining the‘HoneySweet’insertion event utilizing NextGen sequencing and a de novo genome assembly of plum(Prunus domestica)显示文摘HoneySweet’plum(Prunus domestica)is resistant to Plum pox potyvirus,through an RNAi-triggered mechanism.Determining the precise nature of the transgene insertion event has been complicated due to the hexaploid genome of plum.DNA blots previously indicated an unintended hairpin arrangement of the Plum pox potyvirus coat protein gene as well as a multicopy insertion event.To confirm the transgene arrangement of the insertion event,‘HoneySweet’DNA was subjected to whole genome sequencing using Illumina short-read technology.Results indicated two different insertion events,one containing seven partial copies flanked by putative plum DNA sequence and a second with the predicted inverted repeat of the coat protein gene driven by a double 35S promoter on each side,flanked by plum DNA.To determine the locations of the two transgene insertions,a phased plum genome assembly was developed from the commercial plum‘Improved French’.A subset of the scaffolds(2447)that were>10 kb in length and representing,>95%of the genome were annotated and used for alignment against the‘HoneySweet’transgene reads.Four of eight matching scaffolds spanned both insertion sites ranging from 157,704 to 654,883 bp apart,however we were unable to identify which scaffold(s)represented the actual location of the insertion sites due to potential sequence differences between the two plum cultivars.Regardless,there was no evidence of any gene(s)being interrupted as a result of the insertions.Furthermore,RNA-seq data verified that the insertions created no new transcriptional units and no dramatic expression changes of neighboring genes. | Ann M.Callahan Tetyana N.Zhebentyayeva Jodi L.Humann Christopher A.Saski Kelsey D.Galimba Laura L.Georgi Ralph Scorza Dorrie Main Christopher D.Dardick | 2021 | Horticulture Research2021，8，1： | 0 |
| 10 | 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 |
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