Measuring Genetic Diversity

Before selecting the parents you wish to use for your MAB work, you may need to assess the genetic diversity that is available in your germplasm set (or that which you have acquired from genebanks or other sources), unless this work has been done previously. The goal is to select parents that are genetically diverse enough that you can identify differences – polymorphisms – in the progeny.   This may include the need for a particular trait that appears in an accession, or just a general need for more diversity.  There is no set level of genetic diversity required, and each crop is different.

There are many methods of measuring genetic diversity in potential parents. We will not go over the various methods of genetic diversity assessment here, but we refer you to the resources at the end of this section. In general the methods can include in-depth calculations of allele frequencies, genetic distance calculations, etc. or can be just a simple measure of what percentage of molecular markers assessed show polymorphism between two parents. This could give you enough information to be able to select parents for a new breeding population. 

In brief, here are just a few of the measures of genetic diversity:

• Based on the number of variants among the alleles
• Polymorphism or rate of polymorphism (Pj)
• Proportion of polymorphic loci
• Number of alleles (A) and allelic richness (As)
• Average number of alleles per locus
• Based on the frequency of variant alleles
• Average expected heterozygosity           (He; Nei’s genetic diversity

The genetic distance between two samples is described as the proportion of genetic elements (alleles, genes, gametes, genotypes) that the two samples do not share. See de Vicente, Lopez and Fulton 2004 for more details, in particular Chapter 3.

Clearly the use of markers is needed for these measures of genetic diversity. Many different types of markers can be used. The Resources at the end of this module include examples and comparisons, as well as software programs available for the calculations. As with most statistics in MAB, there are no specific cut-offs for what levels of diversity are “good” – this is something you must decide, with your goals and germplasm specifics in mind. The results of genetic diversity analyses can be a simple measure of genetic distance, or the commonly seen phenograms/dendrograms (“trees”) or cluster diagrams (Figure 12). 

In general, one crossing parent in a MAB project is a cultivated variety that needs improvement in one or more traits, and the other parent is selected either because it exhibits some particular desired trait or is only distantly related to the first parent (and therefore has the potential to have new alleles for a number of traits).

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!

GenAlEx: http://biology-assets.anu.edu.au/GenAlEx/Welcome.html

Arlequin:  http://cmpg.unibe.ch/software/arlequin35/

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: https://web.stanford.edu/group/pritchardlab/structure.html