PBG/MCB 620 DNA Fingerprinting - Barley World

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1 Οκτ 2013 (πριν από 3 χρόνια και 11 μήνες)

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PBG/MCB 620 DNA Fingerprinting


Exercise 10/08/2012.


A collection of oat varieties from different European countries has been genotyped with 8 SSR
markers. The dataset with the genotypes is called
OATs.txt
. Download the file from:

http://barleyworld.org/molecular
-
breeding

to your desktop.


We will analyze the marker data using PowerMarker


1.


Creating a project


1.1

Launch the PowerMarker application by double
-
clicking its icon on St
art
-
>
All programs
-
>

Bioinformatics
-
>

Powermarker.

1.2

Choose
File
-
>

Close All Projects
to close all default projects

1.3

Choose File
-
>

Add New Project

to open the file dialog to save the new project.

1.4

Accept the default directory name, and type
PBG620

in the file

name field.


2.

Importing a dataset


2.1

Choose File
-
>

Import
-
>

Dataset

2.2

Click Browse button to open the file dialog. Choose the file
OATs
.txt from the Desktop

2.3

Select the first two columns
Name

and
Country
, and click the link Categorical

to change
these two col
umns to categorical types. All the other columns are

accepted as marker

types.



Select
Name

from the drop down list of Level
-
1 Column combobox.



Select
Country

from the drop down list of Level
-
2 Column combobox.

2.4

Click Next
-
>
Next
-
>
Finish


3.

Producing a table
of summary statistics


3.1

Choose Analysis
-
>

Summary
-
>

Summary Statistics to open the analysis dialog

3.2

Select
OATs

in the Data ListBox.

3.3

Click Submit


4.

Phylogenetic analysis


4.1

Click
Analysis
-
>
Phylogeny
-
>
Compute Frequencies
. Select dataset OATs and compute
freque
ncies at level 1

4.2

Click Analysis
-
>
Phylogeny
-
>

Frequency
-
based distance

and use the index of Nei 1973.
Select the dataset Oats.frequency created in 4.1

4.3

Click Analysis
-
>
Phylogeny
-
>

UPGMA/NJ tree. Use the distance matrix created in 4.2

4.4

Click Analysis
-
>
Phylogeny
-
>

Bootstrap
. Select the dataset Oats.frequency created in 4.1.
Distance Method= Nei 1973; Tree method=UPGMA; Bootstrap number=100