Phenom Networks

1. Phenom Networks • An integrated system for breeding management and complex phenotype analysis This demo shows some of the breeding management capabilities of Phenom-Networks

2. Content • Basic view • Germplasm sets • Studies • Selections • Extract lines based on their phenotypic value • Create new study in the system based on the selected lines • Output study reports for doing selections • Define selections and enter their measurements • Crosses • Plan crossing scheme • Extract crosses • Manage crosses

3. Browse->germplasm->Sets • This page shows lists of germplasms that exist in the system. These lists are organized in folders (left side), and can be fetched to view their content (right side). These are the columns of the list: • designation – pedigree name of the germplasm • entry code – typically name of the seed’s envelop • source – typically source of origin where this line came from • Group – the last cross (if any) in the pedigree used to derive this germplasm.if no cross, then the ancestor line is used. • GID – system’s ID of the germplasm.

4. Browse->Study This page shows studies (experiments) that exist in the system. These studies are organized in folders (left side), and can be fetched to view traits measured in them (right side). Going to other tab will provide more information about the study (see separate demo for a detailed description)

5. Selections • Extract lines based on their phenotypic value • Create new study in the system based on selected lines and traits • Output study reports for colllecting data in the field/nursery • Define selections and enter their measurements

6. Breeding->selection tool (parents) This page is used to select lines based on their phenotypic values.

7. Breeding->selection tool (Germplasm list) Selected germplasm can be saved in a new list (germplasm set).

8. Browse->Germplasm->Sets Selected list saved as a set named “NS-2011”. This set is displayed here.

9. Breeding->new study (germplasms) The new study page provides a wizard that goes through several steps to define new study in the system. The first step is to define the germplasms to be planted in this study. Here I select the new list that I just created before (NS-2011).

10. Breeding->new study (traits) Here I select traits to be measured in this study (listed here as T1, T2 …), and put them (drag & drop) in the variates lists (bottom right).

11. Breeding->new study (traits) Here I select the factor “Plot nane” and put it (drag & drop) under the factors lists (top right).

12. Breeding->new study (description) Here I give the study a name, and can review the list of factors and variates that I selected previously.

13. Breeding->new study (observation) Here I can review previously available data of the selected germplasm (if any).

14. Breeding->new study (observation) Here I can give new plot names for the study by automatic sequence (prefix, running index and suffix).

15. Breeding->new study (observation) Under the plot column (on the left), there is the new assigned plot names.

16. Breeding->study Finally, after we complete the new study, it can be viewed in the study list.

17. Breeding->study (selections) This is the sowing list of the newly created study

18. Breeding->study (reports) Under the reports tab you can define reports to be printed for data collection. This is an example of such a report, where the first row shows inforamtion about the paretnal line (seed envelop), and below there are 4 empty rows saved for selections, to be filled in the nursery. This report can be downloaded as Excel or PDF (right top icons).

19. Example of a PDF format of the previous report

20. Breeding->study (selections) The selection tab is used to define selections. For example, in the first row here, the user defined a breeding method: “selection”, and a number of 3 (means 3 selections). Then he click on “Generate” button (top toolbar on the right).

21. Breeding->study (selections) After clicking on “generate”, 3 lines appear below the germplasm’s row, that represent its selections. Their plot name and designation (which is the germplasm’s preferred name) are like their parent’s, with an extension (-1, -2, -3). The generation is advance (F11->F12). By default, their phenotypic data is the same as their parent. This can be change manually y the user.

22. Breeding->study (selections) Here I want to define selection based on different breeding method: Bulk. For this I select Bulk from the methods list, and repeat the same steps as before.

23. Breeding->study (selections) And now another selection (bulk) appears in the sub table (number 4), with a ‘B’ extension to the plot and designation.

24. Breeding->study (observations) The observation tab contains only the selections. Here it shows the 4 selection that currently exists. You can edit measurement data and enter new values instead of the parent’s values.

25. Breeding->study (selections) The “selection status” column shows the number of selections for each row. 0 selections are colored red, and more than zero is green.

26. Breeding->study (observations) Here is the observation table with all selections so far. The user can enter manually new values, while the system performs automatic checks to keep database integrity.

27. Browse>germplasm sets Finally, once I finished all selections in the study, they are automatically moved to the relevant list (NS-2011), such that I can view the germplasm preferred name (under designation column), entry code (this is the plot from the study), source (source of the original parent) and group (last cross in the pedigree used to derive this germplasm). As shown in the separate interface Demo, each such line can be clicked, to view all its data and info.

28. Crosses • Plan crossing scheme • Extract crosses • Manage crosses

29. Breeding->crossing tool This page is used to plan crossing scheme. You can view germplasm’s data of the first study (left panel), and a second study (right panel). Then you can select rows in both tables to cross among the corresponding germplasms.

30. Breeding->crossing tool Double click on the first column of each table will show a pop up window with all measurements of that row as a list.

31. Breeding->crossing tool Another display possibility where two table represented as horizontal rows.

32. Breeding->crossing tool (germplasm list) Once you defined all crosses, you can save these in a new set.

33. Browse->germplasm->sets This is the list of the newly created crosses. You can see their (automatic) name under designation. Source display plot names of both female and male parents (separated by a “/”), and Group displays preferred names of female and male (separated by a “/”).

34. Breeding->Study (selections) This study is used for hybrid extraction. It is ordered as male parent, and then all females that are supposed to crossed with (see under the column CROSS ROLE).

35. Breeding->Study (selections) Same as for the selections, you can define a “cross” breeding method for each female parent.

36. Breeding->Study (observation) Newly extracted crossed are listed separately under in the observation table.

37. Breeding->manage crosses The “Manage crosses” page shows a list of all crosses, and highlight those that were already extracted (so that you have seeds for them). Next step is to select the extracted crosses and define a new study to measure phenotypes on them.