5f13c2300b94b1cf342059dbeeb74349 Development_and_preliminary_evaluation_of_a.pdf 14468f5ebc4a315847674a369f7ea3ac35116992 Development_and_preliminary_evaluation_of_a.pdf 9365df40fe9cf837cc2a0ac746715f9968618bb9370de111a2bf49988165043f Development_and_preliminary_evaluation_of_a.pdf Title: Development and preliminary evaluation of a 90ŁK AxiomŁ SNP array for the allo-octoploid cultivated strawberry Fragaria Ł ananassa Subject: 2015, :. doi:10.1186/s12864-015-1310-1 Keywords: Fragaria; Genotyping array; Plant breeding; Polyploidy; Strawberry; Single nucleotide polymorphism; Reduced ploidy Author: Nahla V Bassil Creator: Arbortext Advanced Print Publisher 9.1.440/W Unicode Producer: Acrobat Distiller 10.1.5 (Windows); modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (AGPL-version) CreationDate: Wed Mar 25 19:56:05 2015 ModDate: Wed Mar 25 21:19:34 2015 Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 30 Encrypted: no Page size: 595.276 x 793.701 pts Page rot: 0 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FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Abstract Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1488968a Children: Item: Title: Background Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1353488e Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@40c06c8b Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@19163ae3 Item: Title: Background Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@27419f3 Children: Item: Title: Polyploidy is challenging for SNP discovery and genotyping Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1453a1c7 Item: Title: Polyploidy in the cultivated strawberry Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7ea21a3d Item: Title: SNP detection in strawberry Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4468dbbe Item: Title: Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4032ba08 Children: Item: Title: Sequence resources Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@42538425 Item: Title: Validation set Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7908bb27 Item: Title: Library preparation and sequencing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@2c373b85 Item: Title: Sequence alignment Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5e24af70 Item: Title: Variant discovery and filtration panels Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3a7a1259 Item: Title: Variant filtering in octoploids Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@244aaf0d Item: Title: HaploSNP strategies and filters Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@232a9118 Item: Title: Variant discovery in diploid F. iinumae Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3f9bd0b1 Item: Title: Non-discovery-based approach Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ea23517 Item: Title: Affymetrix filtering and axiom array design and construction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3b4b8082 Item: Title: Genotyping in octoploid strawberry Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@59e1f537 Item: Title: Cluster plot characterization Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1aa1bfb Item: Title: Genotyping in diploid strawberry Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4712fc97 Item: Title: Inheritance-based SNP validation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@2f8541f5 Item: Title: Linkage mapping of PHR, NMH and OTV SNPs in the ‘Holiday’⁜琀휠᠀䬀漀爀漀渀愠ᤀ 瀀漀瀀甀氀愀琀椀漀温⽄敳琨sectionSec20 Item: Title: Inheritance-based SNP validation in the F. iinumae F2D population Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@55ad5432 Item: Title: Sequence-based SNP validation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6672ca8f Item: Title: Analyses of SNP data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a50a6d4 Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@44f8e708 Children: Item: Title: SNP discovery Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3107e198 Item: Title: Di-allelic SNP pipeline (Additional file 3) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7c6bdb4d Item: Title: Multi-allelic SNP pipeline (Additional file 4) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@d0adc0c Item: Title: Di-allelic indel pipeline (Additional file 5) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@43f49e84 Item: Title: HaploSNP pipelines (Additional files 6, 7 and 8) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@70d30ef6 Item: Title: Diploid (F. iinumae F1D) SNP discovery (Additional file 9) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@307b7258 Item: Title: Codon-based SNPs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@78900845 Item: Title: SNP genotyping in octoploid strawberry Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@380f27d9 Children: Item: Title: Step 1 Only co-cluster F. ×ananassa accessions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6b01344f Item: Title: Step 2 Execute axiom best practices genotyping workflow Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1c11656b Item: Title: Step 3. Increase the stringency of sample calling Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3a196232 Item: Title: Genotyping success Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@587dde6a Item: Title: Cluster characteristics Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@2f952e89 Item: Title: Inheritance-based SNP validation: Parent–child concordance Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6b223cc6 Item: Title: Inheritance-based SNP validation: performance in mapping Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@14c4221d Item: Title: Validation of F1D SNPs by mapping in F. iinumae Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@589ba891 Item: Title: Sequence-based validation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5357f509 Item: Title: Codon-based approach Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@33984c9e Item: Title: SNP polymorphism in the cultivated strawberry Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@53ce3388 Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@69950b4 Children: Item: Title: Performance of the array in linkage mapping Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3b815cce Item: Title: Success rate & number of informative and high quality SNPs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@29f3f6e7 Item: Title: Synteny and divergence among subgenomes Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4fd6cd35 Item: Title: Biological ploidy reduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1f3a7b86 Item: Title: Approaches for technical ploidy reduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3883aa6e Item: Title: Transferability to diploid F. iinumae Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4c2a38be Item: Title: The codon-based strategy Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@67f36902 Item: Title: Array design in allo-octoploids Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1d73379f Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7748b6d3 Item: Title: Additional files Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46db13d3 Item: Title: Abbreviations Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@58f2a5fc Item: Title: Competing interests Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@226f7103 Item: Title: Authors’ contributions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@42648d9e Item: Title: Authors’ information Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@578da21f Item: Title: Acknowledgements Destination: 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Fragaria Genotyping array Plant breeding Polyploidy Strawberry Single nucleotide polymorphism Reduced ploidy Development and preliminary evaluation of a 90ŁK AxiomŁ SNP array for the allo-octoploid cultivated strawberry Fragaria Ł ananassa Nahla V Bassil True Fragaria; Genotyping array; Plant breeding; Polyploidy; Strawberry; Single nucleotide polymorphism; Reduced ploidy Acrobat Distiller 10.1.5 (Windows); modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (AGPL-version) uuid:a8771e89-5cf8-4a69-b103-d0ee3a8d0544 uuid:d2223363-5cb5-434b-b5ed-ca21d2efb605 default 1 converted uuid:a8771e89-5cf8-4a69-b103-d0ee3a8d0544 converted to PDF/A-1b pdfToolbox 2015-03-25T22:00:51+08:00 1 B http://ns.adobe.com/pdf/1.3/ pdf Adobe PDF Schema internal A name object indicating whether the document has been modified to include trapping information Trapped Text http://ns.adobe.com/xap/1.0/mm/ xmpMM XMP Media Management Schema internal UUID based identifier for specific incarnation of a document InstanceID URI internal The common identifier for all versions and renditions of a document. 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