Genotyping Example, Step 5 - Interpreting The Results

Once again, we are ready for the final step, interpreting the results of our chi-square calculation. This allows us to determine if our CosOH57 marker is segregating (or inherited) in the ratios we expect.  If it is not, it could be the marker is linked to our disease resistance gene, Rx-4, or some other genetic forces are at play with regard to the marker's inheritance in our particular plant population. We will consult a Chi-Square Distribution Table, using degrees of freedom. In this case the degrees of freedom = 2 because we have 3 genotypic classes: banding pattern A (OH88119), banding pattern B (6.8068) and banding pattern H (heterozygous, a combination of our two parents).

In our genotyping example, the X2 value of 36.8884 and degrees of freedom of 2 are associated with a P value of far less than 0.01 (Table 8). Therefore in our tomato breeding example, we reject our hypothesis that the CosOH57 DNA marker is inherited in a normal Mendelian pattern.  We can assume that the deviations we saw between what we expected and actually observed in terms of the number of plants found in each banding pattern could not be due to mere chance. Therefore, we must revise our current hypothesis. The deviation could occur because our marker, CosOH57 is linked with bacterial spot resistance. One way to evaluate this hypothesis is to perform single marker trait analysis. You can learn more about single marker trait analysis in the e-extension page Introduction to Single Marker Analysis (SMA). However, the deviation from the expected results could also be due to other genetic and evolutionary factors including selection which have led to a higher frequency of one banding pattern in the tomato population. The analyses to evaluate these alternative hypotheses are beyond the scope of this lesson.

Table 8:  Chi-square probability distribution and the result of the genotypic data analysis.

Click below to watch a video tutorial further explaining how to calculate the  X2 value and read the probability distribution chart.