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Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria×ananassa) breeding populations using pedigree-based QTL analysis

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Horticulture Research 2017年第1期4卷 85-93页

作者： Sujeet Verma Jason D Zurn Natalia Salinas Megan M Mathey Beatrice Denoyes James F Hancock chad E finn Nahla V Bassil Vance M Whitaker IFAS/Department of Horticulture University of FloridaGulf Coast Research and Education Center14625 CR 672Wimauma33598FLUSA USDA-ARS National Clonal Germplasm Repository 33447 Peoria RoadCorvallis97333ORUSA Department of Horticulture Oregon State University4017 Agriculture and Life Sciences BuildingCorvallis97331ORUSA Department of Horticulture UMR 1332 Biologie du Fruit et PathologieINRAUniv.BordeauxVillenave d’OrnonF-33140France Michigan State University East Lansing48824MIUSA USDA-ARS HCRU3420 NW Orchard AvenueCorvallis97330ORUSA

The cultivated strawberry(Fragaria×ananassa)is consumed worldwide for its flavor and nutritional *** analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this *** several quantitative trait loci(QTL)have been previously detected for fruit quality and flowering traits using low-density genetic maps,clarity on the sub-genomic locations of these QTLs was *** discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism(SNP)array,enabling high-density genetic maps and finer resolution QTL *** this study,breeder-specified traits were evaluated in the Eastern(Michigan)and Western(Oregon)United States for a common set of breeding populations during 2 *** QTLs were validated for soluble solids content(SSC),fruit weight(FWT),pH and titratable acidity(TA)using a pedigree-based QTL analysis *** fruit quality,a QTL for SSC on linkage group(LG)6A,a QTL for FWT on LG 2BII,a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were *** addition,a large-effect QTL for flowering was detected at the distal end of LG 4A,coinciding with the FaPFRU *** haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal *** probes in the FaPFRU region may help facilitate marker-assisted selection for this trait.

关键词： breeding straw Fragaria

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Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

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Horticulture Research 2018年第1期5卷 868-878页

作者： Rubina Jibran Helge Dzierzon Nahla Bassil Jill M.Bushakra Patrick P.Edger Shawn Sullivan chad E.finn Michael Dossett Kelly J.Vining Robert VanBuren Todd C.Mockler Ivan Liachko Kevin M.Davies Toshi M.Foster David Chagné The New Zealand Institute for Plant&Food Research Limited Private Bag 11600Palmerston North4474New Zealand USDA-ARS National Clonal Germplasm Repository 33447 Peoria RoadCorvallisOR97333USA Department of Horticulture Michigan State UniversityEast LansingMI48824-2604USA Phase Genomics SeattleWA98195USA USDA-ARS Horticultural Crops Research Unit CorvallisOR97330USA B.C.Blueberry Council(in Partnership with Agriculture and Agri-Food Canada)Agassiz Food Research Centre AgassizBCV0M 1A0Canada The Donald Danforth Plant Science Center St.LouisMO63132USA Department of Genome Sciences University of Washington School of MedicineSeattleWA98195USA

Black raspberry(Rubus occidentalis L.)is a niche fruit crop valued for its flavor and potential health *** improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference *** recently released draft genome for black raspberry(ORUS 4115-3)lacks assembly of scaffolds to chromosome *** used high-throughput chromatin conformation capture(Hi-C)and Proximity-Guided Assembly(PGA)to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven *** seven pseudo-chromosomes cover~97.2%of the total contig length(~223.8 Mb).Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic *** regions were inferred from recombination frequencies of genetic markers,alignment of 303 bp centromeric sequence with the PGA,and heat map showing the physical contact matrix over the entire *** demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry(Fragaria vesca L.)assembled using only PacBio long-read *** conclude that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.

关键词： breeding black interaction

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RosBREED:bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

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Horticulture Research 2020年第1期7卷 527-549页

作者： 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 Michigan State University East LansingMI 48824USA Washington State University WenatcheeWA 98801USA University of Minnesota St.PaulMN 55108USA Clemson University ClemsonSC 29634USA University of Florida WimaumaFL 33598USA USDA-ARS CorvallisOR 97333USA Washington State University PuyallupWA 98371USA Washington State University PullmanWA 99164USA Cedar Lake Research Group PortlandOR 97215USA University Queensland BrisbaneQLDAustralia Wageningen University and Research 6700 AA WageningenThe Netherlands University of New Hampshire DurhamNH 03824USA

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 *** 2003,industry stakeholder initiatives prioritized the utilization of genomics,genetics,and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural ***,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 *** 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 *** was designed to enable the routine application of modern genomics and genetics technologies in *** crop breeding programs,thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural *** review presents a synopsis of the approach,deliverables,and impacts of RosBREED,highlighting synergistic global collaborations and future *** technologies and tools developed are described,including genome-wide scanning platforms and DNA diagnostic *** 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 *** chasm is now bridged,accelerating rosaceous crop genetic improvement.

关键词： breeding cultivar crops

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