Genetics
The controlled matting of organisms allowed for the basic patterns of inheritance to be deduced. Understanding patterns of inheritance was instrumental in developing the study of genetics and has grown from typing of physical traits (Phenotyping) to very complex molecular analysis of DNA.
Controlled matting experiments are highly dependent on the organism being studied. A simple cross using the nematode C. elegans can be performed in less than a week, while fruit files need months and corn requires 6-9 months!
Based on Mendel’s laws of inheritance, fairly complex genetic problem can be investigated with computer simulation to allow genetic experiments to be performed during a normal class period rather than months.
In this exercise you will use StarGenetics to simulate mating experiments with pea plants. The purpose is to analyze the nature and mode of the inheritance of specific genetic traits. Additionally, inferring genotypes from phenotypes will be investigated.
The genetics simulator we will use is found at https://star-genetics.surge.sh/ and should work in both Firefox and chrome
Watch the video on how to work with the simulator before doing the following.
Mendel’s Peas Exercise 1 Part 1
Start simulation
Navigate to https://star-genetics.surge.sh/
From the pulldown menu select “Mendel’s Peas Exercise 1 Part 1”
Which stock plants are pure breeding?
Identify which stock strains are pure breeding by performing a self-cross with each plant.
Pure breeding strains are ones that when self-crossed will produce the same phenotype in the next generation and only that phenotype.
You can self-cross each plant by selecting the plant twice to the matting site
Generate at least 80 progeny.
Record your observation and if it is pure breeding.
Strain Stock
Observed phenotype(s) and percentages
Is it pure breeding?
White parent
100%
Phenotypes: Unisex, it’s tall and white, pod color is green, pod shape inflated, and pea color is smooth and green.
Yes, it has the same phenotypes as it’s parents.
Purple Parent 1
100%
Phenotypes: Unisex, it’s tall and purple, green pod color, inflated pod shape, green pea color and smooth.
Yes it has the same phenotype as it’s parents.
Purple Parent 2
It is 24% the white plant and 76% the of the purple parent 2. At total of 19 white peas, and 61 purple parent 2 peas.
Phenotypes: there is a mix
White plant:
Unisex, it’s tall and white, pod color is green, pod shape inflated, and pea color is smooth and green.
Purple plant 2:
Unisex, it’s tall and purple, green pod color, inflated pod shape, green pea color and smooth.
No, it has a mixed gene or Aelle from the white plant, and the purple plant 2.
Which phenotype is dominate?
Determine the dominate phenotype by crossing White Parent with Purple Parent 1 and report the phenotype(s) of the F1
Observed Phenotype(s)
Number of individuals
What is the dominate phenotype?
unisex, tall, purple, axial pod position. inflated pod shape and inflated, green pea color, and smooth.
2 parent indiviauls.
And 1 indivual made from the two.
The purple parent 1 has the dominant phenotype.
What are the genotypes?
Based on the results you have collected so far what genotypes would you predict for the listed plants?
Phenotypes
Probable Genotypes
White Parent
Tall, White, recessive, green pea color, and smooth.
pp
Purple Parent 1
Tall, purple, green pea color, and smooth.
PP
F1 progeny
Tall, purple, green pea color, and smooth.
PP
Prediction of F2 Results
Based on the probable genotypes you recorded in the table above, what phenotype ratio would you predict for the F2 generation if you cross two F1 plants?
https://www.omnicalculator.com/health/punnett-square is a useful online Punnett square app.
Predicted phenotype ratio of the F2 if two F1s are crossed
3:1 ratio.
What are the F2 phenotypes?
Cross two F1 plants and report the phenotypes, number of plants and phenotype ratio
Observed Phenotype(s)
Number of individuals
Observed %
PP and PP
The gene of the plant is
1 classes: total is 80
PP Dominant, so the plant will be purple, and like its parent gene.
Observed F2 ratio (dominate : recessive)
Did you observe the ratio you predicted?
100% it is (dominate: dominate)
Yes, but the ratio is a lot further than the what was shown above.
If you did not observe the ratio you predicted, use the +more Progeny button to increase the sample size. Or if you are curious about changing the sample size, add more plants to the cross.
Record your updated information.
Observed Phenotype(s)
Number of individuals
Observed %
Dominaint
1 class : 160 total
Updated F2 ratio (dominate : recessive)
Did you observe the ratio you predicted after adding more plants?
Why might your ratios vary between your initial data and the data from additional mattings vary?
Explanation of sample size issues
Based on the information collected what are the possible Genotypes for the F2 plants?
Phenotypes
Probable Genotypes
Test Cross
Dominate phenotypes can have multiple possible Genotypes. For example, Aa and AA will have the same phenotype as only one dominate allele is needed to express the phenotype.
In contract, a recessive phenotype must be aa!
A method to determine the genotype is to perform a test cross. This is where a plant with a dominate phenotype is crossed with a recessive one.
There are two possible outcomes in such a situation. Fill in the resulting genotypes for each Punnett square
Recessive plant
Recessive plant
Dominate
a
a
Dominate
a
a
A
Aa
Aa
A
Aa
Aa
A
Aa
Aa
a
aa
aa
Possible Genotypes that produce dominate phenotype
Possible phenotype ratio resulting from test cross
AA, Aa
50:50 (1 to 1 ratio)
You will use the process of the test cross to identify the genotype of several dominate pea plants. Use the predictions you made above on who the test cross will work to make a conclusion about the plant’s genotypes.
Mendel’s Peas Exercise 1 – Part 2
From the pull-down menu, change the experiment to “Mendel’s Peas Exercise 1 – Part 2”
There are several plants in the strain stock region. Perform a test cross to determine the genotype of each purple plant.
Plant
Observed phenotype ratio when crossed with White plant
Genotype of Purple plant
Purple F2-A
Class 1 total – white: 35 (44%)
Class 2 total- purple: 45 (56%)
Ratio: 1:3 to 1
Pp
Purple F2-B
Class 1 total – purple:46 (58%)
Class 2 total – white: 34 (43%)
Ratio: 1:1
Pp or pp
Purple F2-C
Class 1 total – purple: 80 (100%)
Ratio: 1:3 ratio
Pp
Purple F2-D
Class 1 total – purple: 29 (36%)
Class 2 total – white: 51 (64%)
Ratio: 1:1
Pp or pp
Purple F2-E
Class 1 total – purple: 80 (100%)
Ratio:
Pp
Purple F2-F
Class 1 total – purple:
Class 2 total – white:
Ratio:
Purple F2-G
Class 1 total – purple:
Class 2 total – white:
Ratio:
Purple F2-H
Class 1 total – purple:
Class 2 total – white:
Ratio:
Purple F2-I
Class 1 total – purple:
Class 2 total – white:
Ratio:
Purple F2-J
Class 1 total – purple:
Class 2 total – white:
Ratio:
Dihybrid Crosses
Mendel proposed the law of independent assortment where different traits do not affect the inheritance of each other. Be aware that examining two traits at once generates a more complex set of phenotype classes due to the possible combinations that can occur.
You will examine two traits, Pea color and Pea shape. The simulator tracks several traits but for this activity you’ll focus on just these two.
Rough Yellow Pea
Rough Yellow Pea
Plant B has rough yellow peas, and you can observe this in the image or by using the “show Phenotypes” button to see a list of the phenotypes. But remember it will also show you phenotypes for other traits that we are not interested in.
NOTE: IGNORE the pod color, pod shape, and flower color.
Parental Cross
From the pull-down menu select “Mendel’s Peas Guided Exercise”
Mate Plant A with Plant B
What observations can you make about the F1 progeny from this cross?
The pea shape of class 1 is inflated and smooth. The pod is green, and the height is tall.
The pease shape of class 2 is inflated and smooth. The pod is yellow, and the height is tall.
What phenotype is dominate for Seed Color and for Seed Shape?
The dominate seed color is green and the seed shape is smooth and inflated.
Based on these results what genotypes would you predict for Plant A and Plant B?
Recall that you need different symbols for the two traits.
Plant
Probable Genotype for Seed Color
Probable Genotype for Seed shape
Plant A
Plant B
Based on your above results and your predictions for the parental Plant A and B, what genotype do you predict for the F1?
Plant
Probable Genotype for Seed Color
Probable Genotype for Seed shape
F1
Cross F1 to Generate F2
What Phenotype ratio would you predict for the F2 based on the F1 Probable Genotypes?
https://www.omnicalculator.com/health/punnett-square
Select an F1 plant and perform a self-cross with at least 200 progeny.
Examine ONLY the pea color and pea shape. And report the results in the table.
NOTE: You may have to use the green arrows to see all the plants.
NOTE: The simulator will have organized results based on ALL of the traits, so you will have to add together classes of phenotypes. See example below.
Phenotype observed for Pea Color and Shape
Number of individuals
Example data collection: Class 2 and Class 3 are both round and yellow seeds, so they are the same phenotype at the traits we are measuring. You would add the number of individuals in each class together (10+21) = 31 have round yellow seeds in this example.
What phenotype ratio did you observe?
Does it agree with your prediction? Why or why not? What might you do if the ratio is “close” to the prediction?
Complete the table below, remember some phenotypes will have multiple genotypes.
Phenotype observed for Seed Color and shape
Possible Genotypes for each phenotype
Explain at least two ways the genotypes predicted for each phenotype can be determined
BONUS Questions:
Bonus Problem
Determine the Genotypes for Plant A and Plant B at the Pod Color and pod shape traits.
Pant
Genotype for Pod Color (Green/Yellow)
Genotype for Pod Shape (Inflated/wrinkled)
Plant A
Plant B
Explain how you determined the genotypes.