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| 1 | 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 |
| 2 | Genetic and phenological variation of tocochromanol(vitamin E)content in wild(Daucus carota L.var.carota)and domesticated carrot(D.carota L.var.sativa)显示文摘Carrot roots(Daucus carota L.var.sativa)produce tocochromanol compounds,collectively known as vitamin E.However,little is known about their types and amounts.Here we determined the range and variation in types and amounts of tocochromanols in a variety of cultivated carrot accessions throughout carrot postharvest storage and reproductive stages and in wild-type roots(Daucus carota L.var.carota).Of eight possible tocochromanol compounds,we detected and quantified α-,and the combined peak for β-and γ-forms of tocopherols and tocotrienols.Significant variation in amounts of tocochromanol compounds was observed across accessions and over time.Large increases in a-tocopherol were noted during both reproductive growth and the postharvest stages.The variation of tocochromanols in carrot root tissue provides useful information for future research seeking to understand the role of these compounds in carrot root tissue or to breed varieties with increased levels of these compounds. | Claire H Luby Hiroshi A Maeda Irwin L Goldman | 2014 | Horticulture Research2014，1，1： | 6 |
| 3 | A next-generation marker genotyping platform(AmpSeq)in heterozygous crops:a case study for marker-assisted selection in grapevine显示文摘Marker-assisted selection(MAS)is often employed in crop breeding programs to accelerate and enhance cultivar development,via selection during the juvenile phase and parental selection prior to crossing.Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery.To bridge the gap between marker development and MAS implementation,this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery,low-cost genotyping through amplicon sequencing(AmpSeq)and decision making.The results document the development of a MAS package derived from genotyping-by-sequencing using three traits(flower sex,disease resistance and acylated anthocyanins)in grapevine breeding.The vast majority of sequence reads(⩾99%)were from the targeted regions.Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data,most amplicons(83 to 87%)had<10%missing data,and read depth had a median of 220–244×.Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy,flexibility,speed,high-throughput,low-cost and easily automated analysis. | Shanshan Yang Jonathan Fresnedo-Ramíre Minghui Wang Linda Cote Peter Schweitzer Paola Barba Elizabeth M Takacs Matthew Clark James Luby David C Manns Gavin Sacks Anna Katharine Mansfield Jason Londo Anne Fennell David Gadoury Bruce Reisch Lance Cadle-Davidson Qi Sun | 2016 | Horticulture Research2016，3，1： | 2 |
| 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 | Functional magnetic resonance imaging in a visual oddball task显示文摘 | McCarthy G Luby M Gore JC | 1996 | Neuroimage1996，3，： | 2 |
| 6 | How to Construct Pseudo-Random Permutations from Pseudo-Random Functions显示文摘 | Luby M Rackoff C | 1988 | SIAM Journal on Computing1988，17，2： | 1 |
| 7 | Nitrogen and solution pH effects on root anatomy of cranberry显示文摘 | FINN C E ROSEN C J LUBY J J | 1990 | HortScience1990，25，： | 1 |
| 8 | Genotypic and environmental variation in antioxidant activity, total phenolic content, and anthocyanin content among blueberry cultivars显示文摘 | CONNOR A M LUBY J J TONG C B S | 2002 | Journal of American Society for Horticultural Science2002，127，1： | 1 |
| 9 | Distal hyperintense vessels on FLAIR:an MRI marker for collateral circulation in acute stroke显示文摘 | Lee KY Latour LL Luby M | | 0，，： | 1 |
| 10 | Effect of handwashing on child health: a randomised controlled trial显示文摘 | Luby SP Agboatwalla M Feikin DR | 2005 | Lancet2005，366，9481： | 1 |
| 11 | Efficient Erasure Correcting codes 显示文摘 | Luby M Mitzenmacher M Shokrollahi A | 2001 | IEEE Transactions on Information Theory2001，47，2： | 1 |
| 12 | Child and adolescent bipolar disorder:a review of the past 10 years显示文摘 | Geller B Luby J | 1997 | J Am Acad Child Adolesc Psychiatry1997，36，9： | 1 |
| 13 | Improved Low-Density Parity-Check Codes Using Irregular Graphs显示文摘 | Luby M G Mitzenmacher M Shokrollahi M A | 2001 | IEEE Transactions on Information Theory2001，47，2： | 1 |
| 14 | Efficient erasure correcting codes 显示文摘 | Luby M G Mitzenmacher M Shokrollahi M A | 2001 | IEEE Trans Info Theo2001，47，2： | 1 |
| 15 | Hemodynamic physiology and thermoregulation in liposuction显示文摘 | Kenkel JM Lipschitz AH Luby M | 2004 | Plast Reconstr Surg2004，114，2： | 1 |
| 16 | Distal hyperintense vessels on FLAIR:an MRI marker for collateral circulation in acute stroke显示文摘 | Lee KY Latour LL Luby M | | 0，，13： | 1 |
| 17 | Intermixing inimmiscible molybdenum/coppermultilayered metallization under excimer laser irradiation显示文摘 | S Luby E Majkova M Jergerl | 1996 | Applied SurfaceScience1996，106，： | 1 |
| 18 | Physicochemical and functional properties of fermented starch from four cassava varieties 显示文摘 | Julianti E Lubis Z Ridwansyah Yusraini E | 2011 | Asian journal of agricultural research2011，5，6： | 1 |
| 19 | A dig- ital fountain approach to asynchronous reliable mul- ticast显示文摘 | Byers J W Luby M Mitzenmacher M | 2002 | IEEE Journal on Selected Areas in Com-munications2002，20，8： | 1 |
| 20 | Plant breeders' perspectives on improving yield and quality traits in horticultural food crops显示文摘 | Luby J Shaw D | 2009 | Hort Science2009，44，1： | 1 |
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