Genotyping Example, Step 2 - Measuring The Observations

The second step is where the researchers do the lab procedures for visualizing DNA marker patterns in their testing population to compile their "observed data".

Fig. 7 Sample gel photo of CAPS marker CosOH57, genotyped in an Fpopulation. Photo credit: Matthew Robbins, The Ohio State University

The gel photo to the right (Fig. 7) shows the results of screening F2 individuals from our same OH88119 x 6.8068 cross with the CosOH57 DNA marker. Lane 1 is the ladder, lanes 2 and 3 are DNA patterns from the parents and lanes 4 - 33 are DNA samples from the F2 individuals. Notice the 3 different patterns seen in the F2s with: 1) a pattern like parent OH88119, 2) parent 6.6068 or 3) a heterozygous pattern which combines both parental patterns (same as seen in the F1s).

Each F2 individual plant is then scored with an A, B, or H code, as outlined in Table 4 below. For more information or practice on scoring a gel, you can go to the eXtension lesson, Genotyping With Molecular Markers: Scoring a Molecular Marker on an Agarose Gel or to an interctive animation in the Plant and Soil Sciences eLibrary where you can practice scoring a gel and coding it (Gel Scoring).

Table 4: Codes used when scoring a genotyping gel.
Code Genotype
A homozygous for parent 1 allele (OH88119 in this case)
B homozygous for parent 2 allele (6.8068 in this case)
H heterozygous, containing one allele from each parent

We then total up our scoring data and enter it into a chi-square table, much like we did in the phenotyping example.The observed column is the data collected from the gel (Table 5).

Table 5: Plugging observed genotypic data summaries into a chi-square calculation table.
Class Observed (O) Expected Frequency Expected (E)
A (OH88119) 85 0.25 49.25
B (6.8068) 46 0.25 49.25
H (heterozygous) 66 0.50 98.50
TOTAL 197 1 197