delivery – plant science pbmass (pedigree based marker assisted selection system) david rodgers
TRANSCRIPT
Delivery – Plant Science
PBMASS(Pedigree Based Marker Assisted Selection System)
David Rodgers
Delivery – Plant Science
Change databaseOr File->Open New blank database
Or File->New
Create a new blank database called PBMASSDemo.mdb
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Change Background image:Tools->Options->Theme->Select Background Image
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Tools->Options->Prompt Update Existing GermplasmTools->Options->Prompt Update Preferred Name
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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
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Import->Pedigrees->From File
Purdy FormatColumn Headings:
Genotype, Aliases, Parentage, Selection History, Comment
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Tools->List Manager->Import
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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”
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Display PedigreeResults->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
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Display PedigreeResults->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
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Display PedigreeResults->Descentogram
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Display PedigreeResults->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
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Export PedigreesExport->Pedigree List
• Export ancestors to 4 generations in founder order
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Add Pedigrees to FieldbookTools->Add Pedigrees To Fieldbook
• “Select Files to add pedigrees to”• Select WorshopDemo\Pedigree\AddPedigrees.xls
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Add Pedigrees to FieldbookTools->Add Pedigrees To Fieldbook
• Click “Update”
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Update Genotype NamesTools->Update Genotype Names
• “Select Files to update preferred names in”• Select WorshopDemo\Pedigree\UpdateGenoNames.xls
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Update Genotype NamesTools->Update Genotype Names
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Finding GenotypesWildcard 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[*]
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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
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Marker Data
• Importing marker data– State matrix– State sequential– Dart– Maps
• Graphical Genotypes
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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
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Import State (matrix format)Import->Marker->State (matrix)
• Click “Import Data”
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Import State (sequential format)Import->Marker->State (Sequential)
•Open Data File•Select WorkshopDemo\Marker\SwornXSoberParentalLinesStateSequential.xls
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Import State (sequential format)Import->Marker->State (sequential)
• Click “Import Data”
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Import Dart dataImport->Marker->Dart
•Open Data File•Select WorkshopDemo\Marker\DART\SWORNXSOBERParentalLinesDartMatrix.xls•Repeat for WorkshopDemo\Marker\DART\SWORNXSOBERDartMatrix.xls
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Import MapsImport->Marker->Distance Data
• Population map– “Open Data File” : WorkshopDemo\Marker\SWORNXSOBER-map_columns.xls
– Import Data
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Import MapsImport->Marker->Distance Data
• Concensus map– Open data file: WorkshopDemo\Marker\SWORNXSOBER-Consensus-map.xls
– Import Data
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Graphical GenotypesResults->Genotype->Graphical Genotype
• Tools->Options->IBD
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Graphical Genotypes
• Set Genotype Colours
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Graphical GenotypesResults->Genotype->Graphical Genotype
• Select Population and Map
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Graphical GenotypesResults->Genotype->Graphical Genotype
• Select Genotype: SWORNXSOBER-10• Select Linkage Group: G
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Graphical GenotypesResults->Genotype->Graphical Genotype
• Select Region
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Graphical GenotypesResults->Genotype->Graphical Genotype
• Set options – IBS, no inference
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Graphical GenotypesResults->Genotype->Graphical Genotype
• Set options – IBS + Pedigree inference
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Graphical GenotypesResults->Genotype->Graphical Genotype
• Set options – IBD, no inference
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Graphical GenotypesResults->Genotype->Graphical Genotype
• Set options – IBD + Pedigree inference + Flanking Marker inference
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IBS, no inference IBS, Pedigree Inference IBD, no inference IBD + Pedigree and Flanking Marker inference
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Export Dart Data
• Import List: WorkshopDemo\Lists\ExportDartList.xls
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Export Dart Data
• Right-click• De-Select All• Select some rows• Right-click• Select Selected Rows
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Phenotypic Data
• Import->Phenotype->Phenotypic Data• Open Spreadsheet: WorkshopDemo\Phenotype\PhenotypicData.xls• Import Data
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Phenotypic Data
• Results->Phenotype
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Phenotypic Data