Sections:

Marker-assisted Breeding

Selection of Markers

Genetic Diversity

Genetic diversity

Importance of diversity in plant breeding

Importance of diversity for molecular marker work

Definition: polymorphism

Crop Domestication: From plants in the wild to our kitchen

Crop Domestication

Traits selected for by humans

Consequences of loss of genetic diversity:

Germplasm banks

Wild relatives are also a good source of diversity

Phenotype does not equal genotype

Selecting the germplasm to use

Criteria for selecting germplasm

Genetic Diversity Assessment

Methods of genetic diversity assessment

Measures of genetic diversity

Using markers to assess diversity

Results of diversity analyses

Selecting parents

Software resources for genetic diversity assessment

Tips for Phenotyping

Genetic Linkage Mapping

Quantitative Trait Analysis

Applications & Future Directions

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Software resources for genetic diversity assessment

Here are just a few of the free software programs available (see de Vicente, Lopez, and Fulton 2004 for a more exhaustive list). Note: you should always get statistical assistance when analyzing your data!

Arlequin http://lgb.unige.ch/arlequin/

PowerMarker http://statgen.ncsu.edu/powermarker/

PHYLIP http://evolution.genetics.washington.edu/phylip.html

DnaSP http://www.ub.edu/dnasp/

MEGA http://www.megasoftware.net/

Structure http://pritch.bsd.uchicago.edu/structure.html