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

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. 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? What do users want to see?

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

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

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

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

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

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

Isozyme descriptors in GRIN

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

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.

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

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

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

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

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

Select “VACCINIUM”

Select “List of Descriptors”

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). Select “SSR-CA112F” Abbreviated SSR definition on this page. Combined GRIN/information based choice?

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

Definition indicated allele range of bp. Go back to the full descriptor definition page.

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

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

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

Select “an Excel Spreadsheet”.

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

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

Grape SSR data presented by Chuck

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

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

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”

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

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.

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