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Molecular Marker Evaluation Data

Molecular Marker Evaluation Data. Laura Fredrick Marek. ISU/NCRPIS, Ames, IA. supporting presentations by:. Chuck Simon. Clare Coyne. PGRU, Geneva, NY. WRPIS, Pullman, WA. grape SSR information. pea SNP information. Molecular Session.

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Molecular Marker Evaluation Data

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  1. Molecular Marker Evaluation Data Laura Fredrick Marek ISU/NCRPIS, Ames, IA supporting presentations by: Chuck Simon Clare Coyne PGRU, Geneva, NY WRPIS, Pullman, WA grape SSR information pea SNP information

  2. Molecular Session Provide an overview of current organization of molecular descriptors/information in GRIN. Present and solicit suggestions about what information should be included in GRIN. What do users want to see? Present and solicit suggestions about how the data should be organized and presented in GRIN. Does standardization of presentation format make searching GRIN easier and assist database connectivity?

  3. Crops with defined molecular descriptors clover sorghum cucumis sugar beet grape sunflower hazelnut vaccinium maize woody-landscape Not many crops; good time to evaluate/modify data organization and content. Molecular category can be strictly defined.

  4. A sampling of molecular descriptors GRIN link name Currently every molecular descriptor is unique; DQ name and definition. There is significant variation in definition field content.

  5. Molecular Descriptors Molecular category can be strictly defined; descriptors involve specific DNA marker information. indirect detection (gene products): isozymes, allozymes* direct detection (DNA sequence): RFLPs RAPDs* AFLPs SSRs* STRs SNPs others *marker types with data in GRIN

  6. Example of molecular GRIN data: isozymes data from multiple crops data for the same enzyme from multiple crops

  7. Isozyme Raw Data PI 599761 PI 599761 PI 599761 A PI 240660 C allelle 1 D B E invariant mito. band allelle 2 l-102 B-4 MDH gel by M. Brothers Malate Dehydrogenase (MDH1) sunflower gel

  8. Isozyme data set in GRIN MDH1 in study SUNFLOWER.SUN.ISOZYME.CORE.03 Sample size is critical information to include. One way to get data in an excel file is to search by descriptor in Oracle forms database (curators’ GRIN).

  9. Isozyme descriptors in GRIN

  10. Field size limitation: link names for different descriptors appear identical. Cucumis molecular descriptors in GRIN

  11. Isozyme descriptors in GRIN * Summary statistics listed by accession. Should a naming convention be used across crops for molecular descriptors? In general, this is done with morphological descriptors.

  12. A sampling of molecular descriptors GRIN link name Vaccinium DQ name derived from EST source name. Currently every molecular descriptor is unique; DQ name and definition. There is significant variation in definition field content.

  13. MWM MWM Yonca Aragon Hunter River Ted Kisha, W6, SSR gel image and information. SSR gel (Licor) of individuals from three alfalfa cultivars.

  14. SSR and other PCR-based descriptors in GRIN Blueberry descriptor definition field includes more information than any other crop.

  15. Blueberry SSR data model A tour through public GRIN… or, what the information looks like to our users…. Nahla Bassil, Corvallis

  16. Select “Research Crops and Descriptor/Evaluation Data Queries”.

  17. Select “VACCINIUM”

  18. Select “List of Descriptors”

  19. Abbreviated SSR definition on this page. Combined GRIN/information based choice? Select “SSR-CA112F” CA stands for “cold acclimated”. (Only defined in embedded excel worksheet.) Actual descriptor name does not include SSR- (affects ability to search in oracle forms database version).

  20. Actual descriptor name does not include SSR- (affects ability to search in oracle forms database version). Full descriptor definition on this page. Contains descriptor specific information for this evaluation. More detail than any other descriptor. Select “Observed values” In sunflower, the equivalent field is named “code values”.

  21. Definition indicated allele range of 142-184 bp. Go back to the full descriptor definition page.

  22. Actual descriptor name does not include SSR- (affects ability to search in oracle forms database version). (Called study or environment on this page.) Select “CULTIVATED BLUEBERRY.SSR.2005”

  23. (Called evaluation on this page.) Actual descriptor name does not include VACCINIUM (affects ability to search in oracle forms database version). If select “VACCINIUM CA112F”, will go back to full definition page. If select “54 Accessions …

  24. Blueberry accessions are clonal. In an out crossing seed crop, data in this category could look like….

  25. Population sample size critical information to include. Back to the evaluation page…

  26. Select “an Excel Spreadsheet”.

  27. Partial listing of CA-type Vaccinium SSRs (descriptors) and observation values. Other SSR types (NA, VCC) listed on separate worksheets in the file.

  28. Is useful information missing from the blueberry model? Publication reference BLAST date, search algorithm and database(s) searched Population size or sampling information Summary statistics (in publication?) Information Organization Put all common descriptor data in evaluation page description.

  29. Grape SSR data presented by Chuck

  30. What information should be included? Experimental details, raw data: Information to allow use of markers by other labs. Summary statistics: Information to assess accession diversity. How to name descriptors? Currently each molecular descriptor is unique. Most will be. Should descriptors follow a naming convention across crops? Introduce a new field containing molecular marker type (SSR, SNP etc) to facilitate cross-genera searching. Descriptor definitions should contain descriptor unique information. How to define evaluation (environment)? Significant variation in content in definition and evaluation fields. Should definitions contain similar information across data types and crops? Evaluation/environment definitions should contain information in common to all descriptors in that evaluation.

  31. Structure of molecular data in GRIN Three models are currently in use. B is most common. A B C CROP CROP CROP molecular molecular CROP-isozyme isozyme#1 isozyme CROP-SSR enzyme locus SSR#1 SSR CROP-SNP SSR#2 DQ name etc. SSR#3 DQ name SNP#1 SNP SNP#2 DQ name etc. DQ name etc. Consider how data organization affects searching ability in GRIN curators database version (oracle forms). Which format best handles multiple accessions with multiple descriptors within multiple data types (blueberry model of 54/28 is a conservative amount of data)?

  32. Re-categorize some molecular descriptors other chromosome related information presented in the category “cytologic” other cytoplasmic male sterility data presented in the category “cytoplasm type”

  33. Summary: Molecular Session What information should be included in GRIN? What do users want to see? Information to include in descriptor definition (as per SSR data model). Experimental details unique to individual descriptor such as: Primer sequences Population sampling size GenBank reference Publication reference or information source. For BLAST search results, include search algorithm, date of search and database(s) searched. Information to include in evalutation/environment definition. Experimental details in common to all descriptors in environment. Sample gel image(s) with standards (molecular weight and standard accession). Include allele sizes and frequency data in GRIN.

  34. Summary: Molecular Session How should the data be organized and presented in GRIN? Would standardization of presentation format make searching GRIN easier and assist database connectivity? Select descriptor name to allow cross crop searching. Introduce a new field containing molecular marker type (SSR, SNP etc) to facilitate cross crop searches. Embed information links in GRIN not on local WEB pages. Consider re-categorization of descriptors to streamline searching.

  35. Helianthus niveus ssp. niveus endemic to Baja California, only Heilanthus taxa not represented in NPGS on the Pacific coast sand dunes west of Vincente Guerrero, BC, Mex

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