GMT Tutorial Exercise 19

Select an "Automated Designer" to automate your work with MRT^TM markers

• The "Automated Designer" Excel macros streamline high throughput work with MRT^TM markers. They support marker selection, PCR set-up, and sample and marker tracking during capillary analysis on the ABI3730 and the subsequent GeneMapper^® analysis.
• All the "Automated Designer" macros on these pages can be downloaded from GENica Marker Tools FILES»LIST. See the following GMT Tutorial Exercises for full details.
• The Automated Designer macros support three broad aspects of designing and carrying out a genetic analysis (see below):
  • Marker Selection
  • Marker Screening
  • Genetic Analysis
• The different types of macros can be used in combination or independently of each other, e.g. the Genetic Analysis macro can be used either on its own, using default marker data, or with custom marker information generated by one of the Marker Screening macros.
• Click on the name of an Automated Designer macro for step-by-step use instructions.

Marker Selection:

• For both barley and wheat, "polymorphism viewer" macros identify the locations of MRT^TM markers on several published maps.
  • Barley_Polymorphism_Viewer_vX.X.xls
  • Wheat_Polymorphism_Viewer_vX.X.xls
• Markers that tend to be highly polymorphic have been pre-selected to form "whole genome scan" kits for wheat and barley¹. The names and map locations of these markers can be highlighted in these macros. Alternatively, a user-defined list of MRT^TM markers can be entered to highlight their map positions.
• If markers have been pre-screened (see step 2), the polymorphism viewers can display which of the pre-screened markers were found to be polymorphic, e.g. to identify areas with poor marker coverage.

Marker Screening:

• Marker screening macros are designed to analyse a small number of DNA samples (e.g. the parental lines of a mapping population or complex cross, or the DNA pools for bulk segregant analysis) with a high number of markers to select informative markers for the subsequent genetic analysis e.g. of a segregating population (step 3 below).
• Use this table to choose a "marker screening" macro for your work:

Genetic Analysis:

• The "genetic analysis" macros are used to analyse an unlimited number of DNA samples (e.g. representing a segregating population, or from a set of germplasm to be analysed for genetic diversity) with up to four marker panels, each composed of up to six MRT^TM markers.
• If markers have been pre-screened with a "marker screening" macro (step 2 above), output files from that macro can be used directly as input for the "genetic analysis" macros. Using this custom data helps reduce the number of capillaries needed to analyse samples, and to ignore non-informative "peaks" during scoring.
• If markers have not been pre-screened, the "genetic screening" macros use default values.
• Two different "genetic screening" macros exist, a "Standard" version and a "University of Adelaide Special" version. The latter was customised to suit local user preferences. General users should choose the "Standard Edition".
  • Automated_Designer_for_Genetic_Analysis_v5.0_-_Standard_Edition.xls
  • Automated_Designer_for_Genetic_Analysis_v5.0_-_Uni_of_Adel_Special_Edition.xls. (Please contact Julia Brueggemann if you are interested in this version. It is not distributed through the GENica Marker Tools website. Jbrueggemann 07:44, 16 September 2009 (UTC))

¹Please contact Matt Hayden for further information and for access to the "Whole Genome Scan Kits". Note that markers in the wheat whole genome scan kits "build 1 improved" and "build 3" (the currently - June 2009 - recommended versions) are non-redundant. Combining the two kits therefore corresponds to screening a total of 907 wheat MRT^TM markers.