SGN Map Data Submission Guidelines

1. A mapping file which contains the information about the markers positions each linkage group.
2. One or more marker data files describing the markers used. The file format describing each type of marker is different, so that for one map, many marker description files may be required.
3. Marker polymorphism survey data can also be submitted, even if the markers are not mapped.
4. Accession information is needed for accessions that are not already in the SGN database.

These files should be tab-delimited text files (In Excel, choose type "Text (tab delimited)" in the Save As dialog). To submit the files send them as email attachments to sgn-feedback@sgn.cornell.edu. Please make sure to include the column headings.

The mapping file

This file gives the location of the markers on the map. When submitting a map, be sure to also provide a marker data file and accession information. These are the columns defined for the mapping file:

• marker name: Should be identical to the SGN marker name if already available on SGN.
• marker id: (optional) If the marker is already in SGN, providing its marker id (SGN-M number) will allow us to process your map more quickly.
• linkage group: The name or number of the chromosome or linkage group.
• position: The position in cM on the linkage group.
• confidence: Mapmaker's confidence for this marker - one of I, I(LOD2), F(LOD3), CF(LOD3). If your mapping software doesn't calculate a confidence, just omit this column.
• protocol: The type of experiment used to map the marker. Currently we support CAPS, SSR, RFLP, SNP, and AFLP. We can accept most PCR-based markers; contact SGN if you would like to submit marker types that are not listed here.

The marker data file

This file has a different format for each marker type. Please provide these columns:

CAPS markers:

  marker_name. The marker name.
  fwd primer. The sequence of the forward primer.
  rev primer. The sequence of the reverse primer.
  temperature. The annealing temperature used in the PCR.
  Mg concentration. The Mg++ concentration used in the PCR.
  bands for parent 1. The band sizes for parent1 (see examples below).
  bands for parent 2. The band sizes for parent2 (see examples below).
  enzyme. The enzyme used for the digestion.
  size. The band size before digestion.

SSR markers:

  marker_name. The marker name.
  fwd primer. The sequence of the forward primer.
  rev primer. The sequence of the reverse primer.
  temperature. The annealing temperature used in the PCR.
  Mg concentration. The Mg++ concentration used in the PCR.
  bands for parent 1. The band sizes for parent1 (see examples below).
  bands for parent 2. The band sizes for parent2 (see examples below).
  repeat motif. The repeat motif (for example AAT).

RFLP markers:

  marker_name. The marker name.
  clone name. The clone used as a probe.
  fwd sequence read name. The forward sequence read name. 
  rev sequence read name. The reverse sequence read name.
  bands for parent 1. The band sizes for parent1.
  bands for parent 2. The band sizes for parent2.

For other types of markers, contact SGN.

Polymorphism data

The polymorphism data file should have the following columns:

  marker name.
  band sizes accession 1. (see example below).
  band sizes accession 2.
  band sizes accession 3.
  band sizes accession 4.
  ...
  band sizes accession n.

Accession information

We need the following information for each accession used in the mapping or polymorphism data files. (Some accessions are already in our database; Contact us if you're not sure). This information can be sent in an email or text file.

• The accession's identifier, for example "TA210"
• The accession's name (optional), for example "Sunpear"
• The accession's species and (optional) common name

If you have identified the accessions in the files as "parent 1", "parent 2", etc, remember to state which accession is which.

Notes and examples

1. Marker names should either correspond to SGN marker names, if the markers are identical, or have a new name that is not yet in the SGN database, as the marker correspondences will be established on a name matching basis.
2. The band sizes should be given separated by + symbols, if more than one band is detected, such as: 420+230. The original band size, prior to digestion, can be given in a separate column.
3. For RFLP markers, if possible, provide sequence data for the clone, as chromatogram files (.ab1 or .scf). Usually, a forward and reverse read is taken. The file names can be indicated in the RFLP marker file.