Penetrance

 

Definition: Penetrance is the proportion of genotypes that show expected phenotypes.

The penetrance values for any genotype can only be assigned by observation and breeding analyses.  Penetrance values not a property of the gene. The values may change in different genetic backgrounds or strains.
 

Example:  Lobe eye is a dominant trait.  Flies from a pure-breeding population of Drosophila with the Lobe gene are scored for their phenotypes.  Only 90% of the flies from this colony have the Lobe phenotype; 10% of the flies look wild-type.

Observation shows that the proportion of flies with the homozygous genotype (LL) that show the expected Lobe phenotype is 90%.  Thus, the penetrance is 90% in this strain of Lobe homozygous flies.

Next, flies with a known heterozygous genotype Ll are scored for their phenotypes.  These flies are obtained by crossing homozygous Lobe females to homozygous wildtype (non-Lobe males).  The F1 progeny are scored for eye shape.  70% were observed to be Lobe and 30% were observed to be wildtype. The proportion of heterozygous genotypes (Ll) that show the expected phenotypes is 70%.  Thus, the penetrance of Lobe is 70% in heterozygous Lobe flies.

 Pure breeding wildtype flies (ll) never show the Lobe phenotype. Thus, the penetrance of Lobe is 0% in homozygous wildtype flies.

With this information, it is possible to predict the distribution in other generations.

Problem: What would be the expected phenotypic frequencies in the F2 generation for the Lobe flies described above?

This problem is best solved systematically.  You know that the cross producing the F2 generation is Ll x Ll.

 The corresponding genotypic array is: 

1/4 LL + 1/2 Ll + 1/4 ll

The Expected Ratio based on penetrance less than 100% is given in the table below:

  Phenotypes
Genotype Freq. Penetrance
  L     l		 Lobe Wildtype
LL 1/4 9/10 : 1/10 9/40 1/40
Ll 1/2 = 2/4 7/10 : 3/10 14/40 6/40
ll 1/4 0 : 1 0 10/40
  Total 23/40 17/40

If  you are given a single fly from the F2 generation with a wildtype phenotype it might have the genotype of LL, Ll or ll.

Using conditional probability,  the probabilities that an F2 fly that looks wildtype has the genotypes LL, Ll or ll would be 1/17; 6/17 and 10/17, respectively.

Confused by Conditional Probabilities? Click here
 

New use for a test cross:  You have a organism with a unknown recessive phenotype but unknown genotype because of penetrance.   To determine its genotype, cross that organism to a totally recessive individual from a pure-breeding strain and observe the progeny ratios.

Example of the new use of a TEST Cross

Test Cross with Lobe

Using the experimentally determined penetrance values for the homozygote and heterozygote (given above) the cross is: 

Unknown Wildtype x ll

Possibility 1: The unknown fly has genotype LL but the Lobe phenotype did not penetrate for this individual fly.  All of the progeny would  have the same genotype (Ll).   With penetrance you expect a phenotypic ratio of 70% Lobe and 30% wildtype (see table below.

LL x ll = 100% Ll

Phenotypes
Genotype Freq. Penetrance Lobe Wildtype
Ll 1.0 7/10 : 3/10 7/10 3/10
Total 7/10 3/10

 

Possibility 2: The unknown fly has genotype Ll but the Lobe phenotype did not penetrate for this individual fly.  Half of the progeny would  have the genotype Ll and half of the progeny would  have the genotype ll .  With penetrance you expect a phenotypic ratio of 35% Lobe and 65% wildtype (see table below).
 

Ll x ll = 50% Ll: 50% ll
 

Phenotypes
Genotype Freq. Penetrance Lobe Wildtype
Ll 1/2 7/10 : 3/10 7/20 3/20
ll 1/2 0/1 0 10/20
Total 7/20 13/20

 
Possibility 3: The Unknown fly has genotype ll.  All of the progeny would have the ll genotype.  All of them should have the wildtype phenotype.

ll x ll = 100% ll

You may wish to test your knowledge of penetrance and conditional probability. Click number 2 below

Penetrance and Conditional Probability
1 Penetrance
2 Test Your Understanding of Conditional Probability and Penetrance
3 Answers to "Test Your Understanding ..."
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