Polymorphism Between Two Accessions (Step One)

From this search utility you can choose a pair of maize or teosinte germplasm accessions and then retrieve the genotypes of the set of Panzea SNP or SSR markers that have been assayed on both accessions. All assayed markers can be shown, or markers can be limited to those that are polymorphic between the two accessions, monomorphic between the two, or not available because of missing data. The position of each marker on the IBM2 neighbors genetic map is provided, and it is also possible to limit the search to markers that map to a particular chromosome or chromosomal region.

To obtain this information, use the interactive search form at the right. The search is a two step process. In Step One you must first choose a marker type (SNP or SSR) and then perform a search to find the first accession of interest. To obtain a complete list of the available accessions with data from the chosen marker type, leave the remaining search parameters in their default state, and click Submit. Otherwise, modify the search criteria appropriately to limit the results. Provided that you kept the output format as 'HTML', after clicking Submit, the list of accessions matching your search criteria will then be displayed in a table below the search form. To complete Step One of the search, find the first accession of interest in this table and then click on its name in the Accession1 column.

Step Two of the search involves choosing the second accession of interest, and then the genotypic comparison type and chromosomal region of interest. The drop down box in the Accession 2 field provides a list of all accessions with markers in common with Accession 1, with the total number of corresponding SNPs or SSRs displayed in parentheses. To complete Step Two of the search, choose the second accession from this drop down list, and then choose the desired Comparison type, chromosomal region and output format. The default comparison type is 'ALL', but you can modify this to show only the markers polymorphic between the two accessions ('Polymorphic'), those with matching genotypes ('Match'), or those for which the comparison is invalid because of missing data in one or both of the accessions ('Not Available'). By default, all markers are shown regardless of their map position, but you can limit the results to the IBM2 Chromosome and even the chromosomal region of interest (the latter by typing values in the Position (from cM) and Position (to cM) boxes). The default output format is HTML, but you can change this to Excel format or fixed-width, comma-separated or tab-delimited text. Also, you can modify the sorting order of the output via the Sort by parameters. Columns on which the resulting table can be resorted are indicated by a circled 'S' in a small yellow square in the column heading of the HTML table.

Download a Polymorphism Search tutorial