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

Delivery – Plant Science

PBMASS(Pedigree Based Marker Assisted Selection System)

David Rodgers

Change databaseOr File->Open New blank database

Or File->New

Create a new blank database called PBMASSDemo.mdb

Change Background image:Tools->Options->Theme->Select Background Image

Tools->Options->Prompt Update Existing GermplasmTools->Options->Prompt Update Preferred Name

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

Import->Pedigrees->From File

Purdy FormatColumn Headings:

Genotype, Aliases, Parentage, Selection History, Comment

Tools->List Manager->Import

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”

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

• 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

• 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

Export PedigreesExport->Pedigree List

• Export ancestors to 4 generations in founder order

Add Pedigrees to FieldbookTools->Add Pedigrees To Fieldbook

• “Select Files to add pedigrees to”• Select WorshopDemo\Pedigree\AddPedigrees.xls

Add Pedigrees to FieldbookTools->Add Pedigrees To Fieldbook

• Click “Update”

Update Genotype NamesTools->Update Genotype Names

• “Select Files to update preferred names in”• Select WorshopDemo\Pedigree\UpdateGenoNames.xls

Update Genotype NamesTools->Update Genotype Names

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[*]

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

Marker Data

• Importing marker data– State matrix– State sequential– Dart– Maps

• Graphical Genotypes

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

Import State (matrix format)Import->Marker->State (matrix)

• Click “Import Data”

Import State (sequential format)Import->Marker->State (Sequential)

•Open Data File•Select WorkshopDemo\Marker\SwornXSoberParentalLinesStateSequential.xls

Import State (sequential format)Import->Marker->State (sequential)

• Click “Import Data”

Import Dart dataImport->Marker->Dart

•Open Data File•Select WorkshopDemo\Marker\DART\SWORNXSOBERParentalLinesDartMatrix.xls•Repeat for WorkshopDemo\Marker\DART\SWORNXSOBERDartMatrix.xls

Import MapsImport->Marker->Distance Data

• Population map– “Open Data File” : WorkshopDemo\Marker\SWORNXSOBER-map_columns.xls

– Import Data

Import MapsImport->Marker->Distance Data

• Concensus map– Open data file: WorkshopDemo\Marker\SWORNXSOBER-Consensus-map.xls

– Import Data

Graphical GenotypesResults->Genotype->Graphical Genotype

• Tools->Options->IBD

Graphical Genotypes

• Set Genotype Colours

• Select Population and Map

• Select Genotype: SWORNXSOBER-10• Select Linkage Group: G

• Select Region

• Set options – IBS, no inference

• Set options – IBS + Pedigree inference

• Set options – IBD, no inference

• Set options – IBD + Pedigree inference + Flanking Marker inference

IBS, no inference IBS, Pedigree Inference IBD, no inference IBD + Pedigree and Flanking Marker inference

Export Dart Data

• Import List: WorkshopDemo\Lists\ExportDartList.xls

Export Dart Data

• Right-click• De-Select All• Select some rows• Right-click• Select Selected Rows

Phenotypic Data

• Import->Phenotype->Phenotypic Data• Open Spreadsheet: WorkshopDemo\Phenotype\PhenotypicData.xls• Import Data

Phenotypic Data

• Results->Phenotype

Phenotypic Data

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

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