Delivery – Plant Science PBMASS (Pedigree Based Marker Assisted Selection System) David Rodgers

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Text of Delivery – Plant Science PBMASS (Pedigree Based Marker Assisted Selection System) David Rodgers

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Delivery Plant Science PBMASS (Pedigree Based Marker Assisted Selection System) David Rodgers Slide 2 Delivery Plant Science Change database Or File->Open New blank database Or File->New Create a new blank database called PBMASSDemo.mdb Slide 3 Delivery Plant Science Change Background image: Tools->Options->Theme->Select Background Image Slide 4 Delivery Plant Science Tools->Options->Prompt Update Existing Germplasm Tools->Options->Prompt Update Preferred Name Slide 5 Delivery Plant Science Import->Pedigrees->From File Female Parent, Male Parent Format (Me, My Mum, My Dad) Column headings: Genotype, Aliases, Female Parent, Male Parent, Selection History, Comment Slide 6 Delivery Plant Science Import->Pedigrees->From File Purdy Format Column Headings: Genotype, Aliases, Parentage, Selection History, Comment Slide 7 Delivery Plant Science Slide 8 Tools->List Manager->Import Slide 9 Delivery Plant Science List Manager->Import Select WorkshopDemo\Lists\ParentalLines.xls Select Save Import WorkshopDemo\Lists\SwornXSoberPopulationList.xls Save Close and reopen List Manager To combine two lists: Select Source List : SwornxSober Parental Lines Select >> button to add to destination list Select Source List : SwornxSober Population Select >> button to add to destination list Enter a name and comment for the destination list Save Close List Manager Slide 10 Delivery Plant Science Display Pedigree Results->Descentogram Select List: SwornXSober Population Select Genotype: SwornXSober-10 Set Generations to 6 click Genotype text box + Enter Right-click Confraadential Copy Genotype Right-click Genotype text box and paste Enter to display pedigree of Confraadential Check Exclude Backcrosses Click in Genotype text box + Enter Click D to show descendents Increase Generations to 2 Click Genotype text box + Enter Slide 11 Delivery Plant Science Display Pedigree Results->Descentogram Click F to display Family Click Aphrodisiac*3/Classifieds to expand Click again to contract Click P to return to Ancestor mode Display pedigree of SwornXSober-10 Mouse over SwornXSober-10 to display pedigree in task bar Increase Purdy Levels to 2 to expand male parent Increase Purdy Levels to 3 to expand both sides Right-click Sober and select Aliases Right-click Court Courting (NZ) and select Comment Right-click Court Courting (NZ) and select Descendents Save the resulting file Slide 12 Delivery Plant Science Display Pedigree Results->Descentogram Slide 13 Delivery Plant Science Display Pedigree Results->Descentogram Open a new Word document Right-click SwornXSober-10 select Copy Pedigree String Paste in the Word document Right-click SwornXSober-10 select Copy Pedigree Tree Paste in the Word document Slide 14 Delivery Plant Science Export Pedigrees Export->Pedigree List Export ancestors to 4 generations in founder order Slide 15 Delivery Plant Science Slide 16 Add Pedigrees to Fieldbook Tools->Add Pedigrees To Fieldbook Select Files to add pedigrees to Select WorshopDemo\Pedigree\AddPedigrees.xls Slide 17 Delivery Plant Science Add Pedigrees to Fieldbook Tools->Add Pedigrees To Fieldbook Click Update Slide 18 Delivery Plant Science Update Genotype Names Tools->Update Genotype Names Select Files to update preferred names in Select WorshopDemo\Pedigree\UpdateGenoNames.xls Slide 19 Delivery Plant Science Update Genotype Names Tools->Update Genotype Names Slide 20 Delivery Plant Science Finding Genotypes Wildcard searches Results->Descentogram Type corridor[*] in the genotype text box Enter The drop down list box will be populated with all genotypes starting with corridor including as an alias Repeat with Sworn[*] Slide 21 Delivery Plant Science Checking Marker Names Create a new blank database called PBMASSMarkers.mdb File->New Import WorkshopDemo\Marker\MarkerNamesImport.xls Import->Pedigrees->From File We can now use Update Genotype Names to check marker names Tools->Update Genotype Names Open WorkshopDemo\Marker\UpdateMarkerNames.xls TX 3612 is not found Results->Descentogram Type [*]3612 in the Genotype text box and press Enter Change database back to WorkshopDemo\PBMASSDemoDB.mdb Slide 22 Delivery Plant Science Marker Data Importing marker data State matrix State sequential Dart Maps Graphical Genotypes Slide 23 Delivery Plant Science Import State (matrix format) Import->Marker->State (matrix) Open Data File Select WorkshopDemo\Marker\SwornXSoberStateMatrix.xls 426 markers x 160 genotypes -> 68,000 data points Slide 24 Delivery Plant Science Import State (matrix format) Import->Marker->State (matrix) Click Import Data Slide 25 Delivery Plant Science Import State (sequential format) Import->Marker->State (Sequential) Open Data File Select WorkshopDemo\Marker\SwornXSoberParentalLinesStateSequential.xls Slide 26 Delivery Plant Science Import State (sequential format) Import->Marker->State (sequential) Click Import Data Slide 27 Delivery Plant Science Import Dart data Import->Marker->Dart Open Data File Select WorkshopDemo\Marker\DART\SWORNXSOBERParentalLinesDartMatrix.xls Repeat for WorkshopDemo\Marker\DART\SWORNXSOBERDartMatrix.xls Slide 28 Delivery Plant Science Import Maps Import->Marker->Distance Data Population map Open Data File : WorkshopDemo\Marker\SWORNXSOBER-map_columns.xls Import Data Slide 29 Delivery Plant Science Import Maps Import->Marker->Distance Data Concensus map Open data file: WorkshopDemo\Marker\SWORNXSOBER-Consensus-map.xls Import Data Slide 30 Delivery Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Tools->Options->IBD Slide 31 Delivery Plant Science Graphical Genotypes Set Genotype Colours Slide 32 Delivery Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Select Population and Map Slide 33 Delivery Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Select Genotype: SWORNXSOBER-10 Select Linkage Group: G Slide 34 Delivery Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Select Region Slide 35 Delivery Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Set options IBS, no inference Slide 36 Delivery Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Set options IBS + Pedigree inference Slide 37 Delivery Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Set options IBD, no inference Slide 38 Delivery Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Set options IBD + Pedigree inference + Flanking Marker inference Slide 39 Delivery Plant Science IBS, no inferenceIBS, Pedigree Inference IBD, no inferenceIBD + Pedigree and Flanking Marker inference Slide 40 Delivery Plant Science Export Dart Data Import List: WorkshopDemo\Lists\ExportDartList.xls Slide 41 Delivery Plant Science Export Dart Data Right-click De-Select All Select some rows Right-click Select Selected Rows Slide 42 Delivery Plant Science Slide 43 Phenotypic Data Import->Phenotype->Phenotypic Data Open Spreadsheet: WorkshopDemo\Phenotype\PhenotypicData.xls Import Data Slide 44 Delivery Plant Science Phenotypic Data Results->Phenotype Slide 45 Delivery Plant Science Phenotypic Data