GMT Tutorial Exercise 21
The Automated Designers - How to perform marker screening using the "Whole Genome Scan" marker kits
- This macro is designed to analyse up to eight DNA samples (e.g. the parental lines of a mapping population or complex cross, or the DNA pools for bulk segregant analysis) with pre-selected markers from one of the Whole Genome Scan kits to select informative markers for the subsequent genetic analysis, e.g. of a segregating population.
Please note:
The information regarding the number of markers available in the different "Whole Genome Scan" kits (see brown box below) needs to be updated.
Please refer to the information on this page instead: GMT_Tutorial_Exercise_19#Marker_Screening:
Jbrueggemann 00:49, 2 June 2009 (UTC)
The Whole Genome Scan Kits:
- The Whole Genome Scan kits are pre-selected sets of markers that tend to be highly polymorphic and provide good whole genome coverage.
- Ready-to-use primer aliquots for the markers forming a Whole Genome Scan kit are provided in a 96-well format.
- For wheat, two Whole Genome Scan kits are available; "Build#1" has 462, "Build#2" has 387 markers.
The markers in the two kits are non-redundant, so by using the two kits together, 849 different markers can be screened, offering increasingly dense genome coverage.
- For barley, currently only the Whole Genome Scan kit "Build#1" with two marker sets, each containing ca. 192 markers, is available.
- Click here to find out how the names and map locations of markers in a "Whole Genome Scan" kit can be displayed with the "Polymorphism Viewer" macros ("workflow 2").
- Please contact Matt Hayden for further information and access to the kits.
|
- Below is a workflow showing how the "Automated Designer for Whole Genome Scan" and "GeneMapper" can be used in combination to pre-screen the MRTTM markers in a given "Whole Genome Scan" kit.
- Click on a step for details. Move between the steps forming a workflow with the [previous step] and [next step] links in the top right-hand corner of each step-wise instruction.
Design the experiment
- Download the Automated Designer for Whole Genome Scan macro for wheat or barley (as applicable) from GMT.
- Open the macro and enable the macro functions.
- Check the macro's version number.
- Using the macro - the Data Entry worksheet.
- Using the macro - the Primer Dilution Plate Layout worksheet.
- Using the macro - the PCR setup worksheet.
- Using the macro - the PCR Master Mixes worksheet.
Carry out marker assays
- Prepare PCR products.
- Using the macro - the SAMPLE File Writer worksheet.
- Separate PCR products on the ABI3730.
Score marker data
- Using the macro - the PANEL File worksheet.
- Using the macro - the Primer Screening Assistant worksheet.
- Import panel information into GeneMapper.
- Import sample electrotraces into GeneMapper and determine peak sizes.
- Pre-score marker data in GeneMapper.
- Export the GeneMapper marker data table.
Identify polymorphic markers and their allele size ranges
- Using the macro - the Primer Screening Analyser worksheet.
- Using the macro - the Polymorphism Summary worksheet.
|
