title: Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa.
abstract: BACKGROUND
  A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array.
  
  
  RESULTS
  About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing "haploSNPs" (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative "codon-based" SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix's "SNPolisher" R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family 'Holiday' × 'Korona' with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM.
  
  
  CONCLUSIONS
  The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array's high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.
authors.affiliation: USDA-ARS, NCGR, Corvallis, OR, USA. nahla.bassil@ars.usda.gov.
authors.forename: Nahla V
authors.initials: NV
authors.lastname: Bassil
authors.affiliation: University of New Hampshire, Durham, NH, USA. tom.davis@unh.edu.
authors.forename: Thomas M
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authors.affiliation: University of New Hampshire, Durham, NH, USA. Hailong.Zhang@unh.edu.
authors.forename: Hailong
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authors.affiliation: Washington State University, Pullman, WA, USA. spficklin@gmail.com.
authors.forename: Stephen
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authors.lastname: Ficklin
authors.affiliation: Affymetrix, Santa Clara, CA, USA. Mike_Mittmann@affymetrix.com.
authors.forename: Mike
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authors.lastname: Mittmann
authors.affiliation: Affymetrix, Santa Clara, CA, USA. Teresa_Webster@affymetrix.com.
authors.forename: Teresa
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authors.affiliation: University of New Hampshire, Durham, NH, USA. Lise.Mahoney@unh.edu.
authors.forename: Lise
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authors.affiliation: University of New Hampshire, Durham, NH, USA. dge9@wildcats.unh.edu.
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authors.affiliation: USDA-ARS, NCGR, Corvallis, OR, USA. liz.alperin@ars.usda.gov.
authors.forename: Elisabeth S
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authors.affiliation: Michigan State University, East Lansing, MI, USA. rosyara@wisc.edu.
authors.forename: Umesh R
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authors.affiliation: Wageningen-UR Plant Breeding, Wageningen, The Netherlands. herma.koehorst@wur.nl.
authors.forename: Herma
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authors.lastname: Koehorst-Vanc Putten
authors.affiliation: IRTA-Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain. amparo.monfort@irta.cat.
authors.forename: Amparo
authors.initials: A
authors.lastname: Monfort
authors.affiliation: Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, 38010, TN, Italy. dan.sargent@fmach.it.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Sargent
authors.affiliation: IFAPA-Centro de Churriana, Málaga, Spain. iraida.amaya@juntadeandalucia.es.
authors.forename: Iraida
authors.initials: I
authors.lastname: Amaya
authors.affiliation: INRA, UMR BFP, Bordeaux, France. denoyes@bordeaux.inra.fr.
authors.forename: Beatrice
authors.initials: B
authors.lastname: Denoyes
authors.affiliation: Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, 38010, TN, Italy. luca.bianco@fmach.it.
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authors.affiliation: Wageningen-UR Plant Breeding, Wageningen, The Netherlands. thijs.vandijk@wur.nl.
authors.forename: Thijs
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authors.lastname: van Dijk
authors.affiliation: Affymetrix, Santa Clara, CA, USA. Ali_Pirani@affymetrix.com.
authors.forename: Ali
authors.initials: A
authors.lastname: Pirani
authors.affiliation: Michigan State University, East Lansing, MI, USA. iezzoni@msu.edu.
authors.forename: Amy
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authors.lastname: Iezzoni
authors.affiliation: Washington State University, Pullman, WA, USA. dorrie@wsu.edu.
authors.forename: Dorrie
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authors.lastname: Main
authors.affiliation: Washington State University, Pullman, WA, USA. cpeace@wsu.edu.
authors.forename: Cameron
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authors.lastname: Peace
authors.affiliation: University of New Hampshire, Durham, NH, USA. ytj2@wildcats.unh.edu.
authors.forename: Yilong
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authors.affiliation: University of Florida, GCREC, Wimauma, FL, USA. vwhitaker@ufl.edu.
authors.forename: Vance
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authors.lastname: Whitaker
authors.affiliation: University of Florida, GCREC, Wimauma, FL, USA. sujeet.verma@ufl.edu.
authors.forename: Sujeet
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authors.lastname: Verma
authors.affiliation: Affymetrix UK Ltd, Wooburn Green, High Wycombe, UK. Laurent_Bellon@affymetrix.com.
authors.forename: Laurent
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authors.lastname: Bellon
authors.affiliation: Affymetrix UK Ltd, Wooburn Green, High Wycombe, UK. Fiona_Brew@affymetrix.com.
authors.forename: Fiona
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authors.lastname: Brew
authors.affiliation: Instituto Ciencias Biologicas, Universidad de Talca, Talca, Chile. raherre@utalca.cl.
authors.forename: Raul
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authors.affiliation: Wageningen-UR Plant Breeding, Wageningen, The Netherlands. eric.vandeweg@wur.nl.
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mesh_terms: D002874:Chromosome Mapping; D031985:Fragaria / Q000235:genetics*; D060005:Genotyping Techniques / Q000379:methods*; D006824:Hybridization, Genetic; D054643:INDEL Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D017422:Sequence Analysis, DNA