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

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Presentation on theme: "Delivery – Plant Science PBMASS (Pedigree Based Marker Assisted Selection System) David Rodgers."— Presentation transcript:

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

2 Delivery – Plant Science Change database Or File->Open New blank database Or File->New Create a new blank database called PBMASSDemo.mdb

3 Delivery – Plant Science Change Background image: Tools->Options->Theme->Select Background Image

4 Delivery – Plant Science Tools->Options->Prompt Update Existing Germplasm Tools->Options->Prompt Update Preferred Name

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

6 Delivery – Plant Science Import->Pedigrees->From File Purdy Format Column Headings: Genotype, Aliases, Parentage, Selection History, Comment

7 Delivery – Plant Science

8 Tools->List Manager->Import

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”

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

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

12 Delivery – Plant Science Display Pedigree Results->Descentogram

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

14 Delivery – Plant Science Export Pedigrees Export->Pedigree List Export ancestors to 4 generations in founder order

15 Delivery – Plant Science

16 Add Pedigrees to Fieldbook Tools->Add Pedigrees To Fieldbook “Select Files to add pedigrees to” Select WorshopDemo\Pedigree\AddPedigrees.xls

17 Delivery – Plant Science Add Pedigrees to Fieldbook Tools->Add Pedigrees To Fieldbook Click “Update”

18 Delivery – Plant Science Update Genotype Names Tools->Update Genotype Names “Select Files to update preferred names in” Select WorshopDemo\Pedigree\UpdateGenoNames.xls

19 Delivery – Plant Science Update Genotype Names Tools->Update Genotype Names

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[*]

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

22 Delivery – Plant Science Marker Data Importing marker data –State matrix –State sequential –Dart –Maps Graphical Genotypes

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

24 Delivery – Plant Science Import State (matrix format) Import->Marker->State (matrix) Click “Import Data”

25 Delivery – Plant Science Import State (sequential format) Import->Marker->State (Sequential) Open Data File Select WorkshopDemo\Marker\SwornXSoberParentalLinesStateSequential.xls

26 Delivery – Plant Science Import State (sequential format) Import->Marker->State (sequential) Click “Import Data”

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

28 Delivery – Plant Science Import Maps Import->Marker->Distance Data Population map –“Open Data File” : WorkshopDemo\Marker\SWORNXSOBER-map_columns.xls –Import Data

29 Delivery – Plant Science Import Maps Import->Marker->Distance Data Concensus map –Open data file: WorkshopDemo\Marker\SWORNXSOBER-Consensus-map.xls –Import Data

30 Delivery – Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Tools->Options->IBD

31 Delivery – Plant Science Graphical Genotypes Set Genotype Colours

32 Delivery – Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Select Population and Map

33 Delivery – Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Select Genotype: SWORNXSOBER-10 Select Linkage Group: G

34 Delivery – Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Select Region

35 Delivery – Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Set options – IBS, no inference

36 Delivery – Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Set options – IBS + Pedigree inference

37 Delivery – Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Set options – IBD, no inference

38 Delivery – Plant Science Graphical Genotypes Results->Genotype->Graphical Genotype Set options – IBD + Pedigree inference + Flanking Marker inference

39 Delivery – Plant Science IBS, no inferenceIBS, Pedigree Inference IBD, no inferenceIBD + Pedigree and Flanking Marker inference

40 Delivery – Plant Science Export Dart Data Import List: WorkshopDemo\Lists\ExportDartList.xls

41 Delivery – Plant Science Export Dart Data Right-click De-Select All Select some rows Right-click Select Selected Rows

42 Delivery – Plant Science

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

44 Delivery – Plant Science Phenotypic Data Results->Phenotype

45 Delivery – Plant Science Phenotypic Data


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