The Greenhouse and Gardens at Genome

Experiments in the Greenhouse and Gardens illustrate the Mendelian principles explained in the Abbey slideshow presentations 1-8. You can begin with these slideshows and then proceed to various activities in the Greenhouse and Gardens.  You can also begin directly with the experiments and then use the Abbey slideshows for a review of principles. 

Principles of Inheritance

Additional Activities

Monohybrid Cross (F1, F2, F3): The Greenhouse  Guess the Parents: The Greenhouse The Mating Game: The Greenhouse Intermediate Dominance: The North Garden Monohybrid Test Cross: The North Garden Two Trait (Dihybrid) Cross: The Greenhouse Dihybrid Cross: The South Garden

Dihybrid Test Cross : The North Garden Test Cross with Linkage: The North Garden Kernel Color in Maize: The Corn Patch behind the Greenhouse The Pansy Challenge: Greenhouse Inheritance in Honeybees: The North Garden The Cattery: southwest of The Terrace The Bunny Hutch: lower platform of The Terrace Caminalcules:  east of the Terrace The Mixollama Herd: east of The Terrace The Fly Room: Tower levels 13-15

The Greenhouse

Monohybrid CrosS:

The Monohybrid Cross activity includes two instructional posters, the F1 Hybrid pea and two dishes of peas representing the F2 progeny. One set of F2 progeny appear when the F1 pea is clicked. The other is on the bench and is used for producing the F3.

• Clicking on the posters gives background and instructions for the activity. In addition, an Excel spreadsheet is offered and may be used to record, summarize and analyze your data.
• The poster shown here illustrates the phenotypes of the two parental strains – yellow seeds and green seeds -- crossed to get the hybrid, and that of the F1 hybrid as well.
• The yellow color of the hybrid identifies yellow as the dominant phenotype. Clicking on the F1 pea produces a population of F2 peas in the blue bowl below the poster. You may examine these peas to count the number of yellow and green peas. Note: the “lifetime” of the peas is about a minute. However, another set of peas can be produced by clicking on the F1 pea again at any time.
  
  

Ratio of yellow:green = 3:1

• Clicking on the peas in the F2 bowl produces additional sets of progeny, and also enters the number of green and yellow seeds in each set into the Chat Record. The data from the Chat Record can be copied and pasted into an Excel file or into any word processing document for analysis.
• Clicking on individual peas in the second F2 bowl produces a set of F3 progeny from each pea.  The peas with the recessive trait can only have the green gene and will produce all green progeny.  However, the peas with the dominant trait may have either two yellow genes or one yellow and one green gene, and will produce either all yellow or a mixed yellow and green progeny. 
• On the bench near the F2 dishes is a sheet of data from Mendel's crosses between peas with different seed colors and different seed shape.  There are 10 sets of data from different crosses.  Mendel makes the point that the progeny ratios of an individual population may deviate from the predicted 3:1 ratio.  Students can also compare ratios from individual F2 populations with those of combined populations. 

Seven Traits: 

On the partition between the main greenhouse and the workroom is a poster that illustrates the seven pairs of traits that Mendel worked with.  On the bench in the workroom is a summary of the F2 data from Mendel's crosses with all seven pairs of traits.  Four of the seven traits (seed color, pod color, plant height and flower color) are represented in Second Life activities. 

 

Guess the Parents:

This activity tests the visitor's ability to predict parents from the progeny of a cross.
A usefuly preparatory activity is the Test Cross activity in the garden north of the Abbey.
The Guess the Parents activity includes the instructional poster, the red progeny dish below the poster, a Chi Square table and Chi Square notebook for testing your hypothesis about the parents you propose.

• Clicking on the poster gives a notecard with instructions about how to perform the experiment.
• Clicking on the red dish will produce a set of 24 progeny, and also offers a data notecard for recording your data. Your task is to count the green and yellow peas in the dish, and enter the data in the spaces indicated by the instructions on the notecard. Note that you should REPLACE the # symbol on the notecard with the number of peas you counted in each category.
• Then decide which set of parents could have produced the progeny in the numbers you counted. Aa x Aa parents will produce a different progeny ratio than Aa x aa parents. The default value is Aa x Aa, so if you think your parents were both heterozygotes, leave that in place. If you think your parents were Aa x aa, then replace the “Aa x Aa” with “Aa x aa”.
• Save your edited notecard to your inventory, and then drag it from your inventory to one of the blue Chi Square notebooks.
• Click on the Chi Square table to get information about performing Chi Square analysis. The notecard explains that Chi Square tests how well your data fit the hypothesis you are testing, and also tells you how the Chi Square value is calculated and how to use the Chi Square table.
• When you are ready to do the Chi Square analysis, click on the notebook. Click twice to get a summary of your data and to get the Chi Square value calculated for the parents you suggested.
• Check your Chi Square value against the table to see if you should accept or reject your hypothesis. The “critical value” to which you should compare the Chi Square value calculated by the notebook will be found at the intersect between the number of degrees of freedom in your data set and the p value of 0.05. How many degrees of freedom for a data set with two classes of progeny? If your Chi Square value is lower than the critical value, your hypothesis has been supported. If your Chi Square value is higher than the critical value, you should reject the hypothesis.
• You may repeat this activity to produce additional Data notecards. Once the Chi Square value has been calculated for a given notecard, it will disappear from the notebook. New parents will be assigned at random each time you do the experiment.

The Mating Game:

This activity also tests your understanding of the types of progeny that can be produced by parents with various genotypes. The Mating Game includes the instructional Mating Game sign and six different peas, each of which represents one of six possible crosses involving a single pair of genes: AA x AA, AA x aa, aa x aa, AA x Aa, Aa x aa, and Aa x Aa.

• Clicking on the sign will give the instructions for playing the game, lists the six possible crosses, and asks you to identify the genotype of each of the nine peas involved in the crosses.
• In each group of three peas, the pea at the top of the triangle is mated to one of the two peas below. For example, Yellow A can be mated either to Yellow B or to Yellow C. Clicking on one of the two lower peas produces the progeny of the cross.
• What are the possibilities for the genotype of a yellow pea? Given those possibilities what kind of crosses can occur between two yellow peas?
• Progeny will appear in the dish below each set of three peas. Examine the peas and decide what the possibilities are for the parents that produced those progeny.
• Before you put more peas into the same dish, click on the progeny peas to dismiss them. Stacking progeny sets can lead to misleading data.
• If you simply leave the peas in the dish, they will disappear after about a minute.
• The top pea in each set is the same genotype, so crossing this pea to both of the other two peas can help you infer what this genotype is.
• Five of the genotypes can be determined directly by examination of the progeny. The sixth genotype must be determined by exclusion, that is, whichever of the possible patterns has not yet been assigned to one of the crosses.

Two Trait Cross: Peas and Pods:

This is one of two activities involving the segregation of alleles for two different traits: pea color and pod color. This combination is interesting because the dominance relationships of the two colors are different for peas and pods.

The activity includes the instructional poster, the F1 hybrid pod with peas, and the rezzed dish of F2 peas in their pods. The F2 progeny appear when one of the F1 peas is clicked.

• Clicking on the poster explains the traits, and gives instructions for performing the cross. The poster will also offer a link to a spreadsheet that can be used to record, summarize and analyze your data.
• The following information is NOT included in the instructions for the cross, although it is given in the slideshow of Abbey Presentation #8. Pea color and pod color actually appear in separate generations. Pod color is a parental trait and will express the genotype of the flower that produces the peas. Peas represent the next generation of progeny, so their color represents THEIR genotype, and not their mother's. This means that the traits as they are illustrated here would not actually appear in the same generation. Because of this, the pea color and pod color are listed as separate traits. What you should examine is the combinations of pea and pod color. Do all possible combinations appear?
• The poster give the color of peas and pods in the parents of the cross, and also the pea and pod color of the F1 progeny. According to the traits expressed in the F1, which color is dominant in the peas? Which color is dominant in the pods?
• Clicking on any of the peas in the F1 pod will produce a dish of peas in their pods in the dish below the poster.
• Examine the peas and pods. Do both pea colors appear? Do both pod colors appear? Do both pea colors appear in the pods of both colors?
• Click on the peas in the dish to produce more sets of progeny and to enter progeny data into the Chat Record.
• The spreadsheet provided for the activity will calculate ratios of yellow to green peas and pods if you enter the data into the boxes as indicated by the instructions on the spreadsheet itself.

Inheritance of Kernel Color in Corn:

This activity is about how several alleles can interact in the production of a single trait. The activity includes the instructional sign, and three cobs, with one, two and three pair of alleles segregating respectively.

• Clicking on the sign gives background information about pigment production in the aleurone and endosperm of a maize kernel. In the endosperm, a single pair of alleles regulates the production of yellow pigment. In the overlying aleurone, several pair of alleles determine enzymes in a multi-step pigment pathway that can end in either red or purple pigment in the aleurone. The genes involved in part of the aleurone pigment pathway are:

C--	R--	P--
Precursor =>	colorless product =>	red pigment =>	purple pigment.

Since aleurone pigment can mask endosperm pigment, the visible color of a kernel will depend on which alleles are active in both parts of the kernel.

• The sign also offers a spreadsheet in which the number of kernels of each type can be recorded. The task is to examine the kernel color and predict the genotypes of the parents that produced the population of kernels on the cob.
• Clicking on Cob 1 produces a notecard describing the determination of either purple or yellow color by one pair of alleles. The dominant allele results in purple kernels, while the recessive allele results in yellow kernels. In this cob, all of the kernels have the yellow allele active in the endosperm, but the presence of purple pigment in the aleurone can mask the yellow color. Parental genotype is determined by looking at the ratios of purple and yellow kernels.
• Clicking on Cob 2 produces a notecard explaining the interaction between one pair of alleles in the endosperm and one in the aleurone. If the aleurone is colorless the color of the endosperm, due to the presence or absence of yellow pigment, is visible. In the aleurone of this cob, purple pigment may or may not be produced, due to the activity of a second pair of alleles. Again, the genotype of the parents can be predicted by looking at the ratios of purple, yellow and white kernels.
• Clicking on Cob 3 produces a notecard explaining that three pair of alleles are operating to determine the final color of a kernel. In the endosperm, either yellow or white pigment may be produced. In the aleurone, either purple, red or no pigment may be produced, depending on the activity of the R and Pr alleles.
• Y / y: Y makes the yellow pigment of the endosperm; y does not.
• C / c; Pr / pr: The R allele is active is all of the kernels. If the C allele acts to make the colorless precursor of the red pigment, then the red pigment can be made. If the the C allele is not present (c/c), neither red nor purple pigment can be made. If the C allele is active AND the Pr allele is also present, then the red pigment is produced, converted to the purple pigment, and the kernels are purple. If the Pr allele is not present (pr/pr), then the kernels are red.
• After completing the activity with Cob 3, you can return to Cob 1 and figure out which of the three aleurone alleles was segregating.

The Pansy Challenge:  The Pansy Challenge is an activity suitable for advanced students.  Color in pansies is due to pigments produced by a pathway similar to that found in maize.  The activity includes the informational notecard containing three data sets crosses between pansies of different colors. Students can examine this data and suggest a mechanism for the inheritance of the colors and possible genotypes for the parents. 

The North Garden

Monohybrid Cross with Intermediate Dominance:

The inheritance patterns in this garden should be contrasted with the patterns seen in the greenhouse with the Dish of Peas.
The Intermediate Dominance activity includes two active objects, an informational sign, and the progeny plot.

Clicking on the sign gives background and instructions for the experiment. An Excel spreadsheet, which can be used to record the data and compare it with that seen in the Dish of Peas experiment in the Greenhouse, is also offered.

At the back of the plot, near the Abbey, are the parents for the cross: pure-breeding red and pure-breeding white flowers. In front of the parents are the F1 progeny, which illustrate intermediate dominance in the heterozygote.

• Clicking on any of the F1 progeny produces F2 progeny in the garden plot in front of the F1 flowers. Data from these progeny are entered into the Chat Record.

  Gametes	A	a
  A	AA	Aa
  a	Aa	aa

Ratio of red:pink:white = 1:2:1

• The spreadsheet provided with the activity will calculate the progeny ratios if you enter the data in the locations indicated by the instructions on the spreadsheet.

Monohybrid Test Cross Plot:

The test cross plot produces one of two progeny sets, depending on whether the parent of unknown genotype was homozygous or heterozygous for the dominant Red allele for flower color.
In the test cross experiment, there are two active objects: the instructional sign and the four test cross parents. In the test cross parents, genotype of the parent is reset each time one of the parents is clicked, so any of the “unknown” flowers may be either heterozygous or homozygous.

• Clicking on the instructional sign gives a notecard explaining the principle of the Test Cross. An individual expressing a dominant trait (A_) is crossed to an individual homozygous for the recessive trait (aa). The progeny set may be either totally red, if the unknown parent was homozygous, or partly white if the unknown parent was heterozygous.

Progeny flowers are all red

Progeny flowers are half red, half white

• Clicking on any of the red parent flowers produces a set of progeny. The type of progeny produced are noted in the Chat Record. You are then asked to identify the genotype of the parent.

Dihybrid Test Cross Plot (Independent Assortment):

The dihybrid test cross verifies the principle of Independent Assortment inferred by Mendel from the F2 progeny of hybrids. This principle states that when individuals differ for two pair of alleles, each pair will sort to the gametes independently of the other pair. In AaBb dihybrids, half the gametes will get allele A and half will get allele a. Likewise, half the gametes will get allele B and half will get allele b. The principle of Independent Assortment proposes that the probability of the combination AB = pA x pB. ½ A x ½ B = ¼ AB. The probability of the other three combinations -- Ab, aB and ab -- is the same. In the test cross the gametes from the dihybrid parent will be expressed in the progeny, since the test cross parent contributes only recessive alleles.

Cross: AaBb x aa bb

Gametes	AB	Ab	aB	ab
All ab	AaBb	Aabb	AaBb	aabb
Phenotypes	Red Center	Red Center	Yellow Center	Yellow Center
	Red Petals	Gold Petals	Red Petals	Gold Petals

In the Dihybrid Test Cross activity, there are two active objects: the instructional sign and the progeny plot.

• Clicking on the instructional sign gived a notecard with background information and instructions for the cross. The sign also offers a spreadsheet for recording and analyzing data.
• The alleles segregating in the test cross are center color and petal color. Centers can be either red or yellow; petals can be either red or gold.
• Clicking on the progeny plot generates a set of 36 progeny. When the flowers appear in the test post, the color of the center and petals for each is recorded in the Chat Record.
• Data from the Chat Record can be pasted into a spreadsheet and then sorted for analysis. Instructions for sorting are contained in the spreadsheet itself.
• The fit of the progeny data with the predictions for independent assortment can be tested by Chi Square analysis. The Mendelian Law of Independent Assortment predicts that equal numbers of all four gamete types are produced. The spreadsheets provided with the activity will calculate the Chi Square value after the student has entered predicated and observed progeny numbers, and calculated deviation from the predicted values.
• Chi Square values can be evaluated using the Chi Square table in the Greenhouse.

Dihybrid Test Cross (Linkage):

The dihybrid test cross can also be used to test for linkage – the location of two or more pairs of alleles on the same chromosome. A second dihybrid test cross illustrates the behavior of linked alleles. Two pairs of alleles display independent assortment if they are on different chromosomes or if they are far enough apart on the same chromosome that they are routinely separated by crossing over between homologous chromosomes. However alleles that are close together on the same chromosome may be separated only occasionally by crossing over, so that the original parental association is favored over the recombinants. For example of the two dominant alleles A and B are on one homolog and the recessive alleles a and b are on the other, then more gametes will show the parental combinations AB and ab, than the recombinant combinations Ab and aB.

In the Genetic Linkage activity, there are two active objects: the instructional sign and the progeny plot that contains the offspring of the test cross.

• Clicking on the instructional sign gets background information about linkage and instructions for performing the experiment. The sign also offers a copy of the dihybrid test cross spreadsheet. The data for the linked markers can be collected on the same spreadsheet as the data for independent assignment for comparison of the two data sets.
• Clicking on the progeny plot produces a set of 36 progeny. Four sets of progeny are suggested to produce a large dataset for analysis.
• The traits represented in the progeny are petal color – red or blue -- and petal position – perky or droopy. Progeny data go into the Chat Record, from which they can be copied and pasted into the spreadsheet for sorting, summarizing and analysis.
• The spreadsheet provided will calculate Chi Square values after predicted and observed values are entered and deviations from the predicted values are calculated.
• Chi Square values can be evaluated using the Chi Square table in the Greenhouse. Significant deviation from independent assortment can be taken as evidence for linkage.

Inheritance in Honeybees:  This activity, suitable for advanced students, is found just north of the walkway that runs beside the North Garden.  It includes the book described below, which provides an informational notecard about inheritance in bees, and three hives:  one for wild type bees, one for mutant bees, and one that produces the progeny of a dihybrid cross.  Click on each hive to start and stop the emergence of its bees.  The bees are not identified by sex, and include both males and females.   

Die Bienensucht: In addition to his work on plants, Mendel was also interested in breeding bees. A monograph on bees – Bee Research by von Morlot (1839) is tucked into one of the beehive stands.  Like hawkweed (see the letters from Naegeli in the Abbey), bees proved to be an exception to the rules for inheritance that Mendel had derived from the experiments with peas. This is because male bees have only one parent -- their mother. Male bees have only one set of chromosomes, while females have the usual two, having inherited one set from both their parents. This leads to inheritance patterns that seem not to follow the rules. 

The South Garden:

Dihybrid Flower Garden:

The dihybrid flower garden demonstrates Mendel's Principle of Independent Assortment. The flowers can be red or white, and short or tall. The flower color alleles sort to the gametes independently of those for height. All possible combinations of phenotypes are seen in the progeny.
In the dihybrid garden, there are four active objects: the informational sign, Parental Flowers, F1 Progeny and the F2 progeny plot.

• The informational sign gives the background of the cross, and describes the principle of independent assortment as all possible random combinations of the progeny of two monohybrid crosses. The sign also offers a spreadsheet for recording, summarizing and analyzing the data from the cross.
• The Parental Flowers display and describe the phenotypes of the pure-breeding parents.
• The F1 Progeny display and describe the phenotype of the F1 progeny.
• The F2 Progeny Plot generates a set of 16 F2 progeny according to the probabilities for each phenotype when F1 progeny mate with one another or self-fertilize.

  In the progeny of the Red Tall Hybrid (Rr Tt) plants:
  1/4 of the progeny will be white; 3/4 will be red
  1/4 of the progeny will be short; 3/4 will be tall
  But by the principle of independent assortment,
  1/4 x 1/4 will be BOTH white and short = 1/16
  1/4 x 3/4 willbe BOTH white and tall = 3/16
  1/4 x 3/4 will be BOTH red and short = 3/16
  3/4 x 3/4 will be BOTH red and tall=9/16

• Progeny data will appear in the Chat Record and can be copied and pasted into the spreadsheet provided by the information sign.
• Interestingly, ALL of the progeny of pure-breeding parents, which look different, will be the same. They have a single genotype and all express the same phenotype. But in following generation, in which all of the parents LOOK tall and red, only a little more than half of their progeny will also be tall and red. The rest will express other combinations of traits.
• Although the predicted progeny ratio for the phenotypes in a dihybrid F2 is 9:3:3:1, you will rarely get exactly this ratio in a single small population, but you will see a mix of characters.
• If you collect the data from 5-6 sets of progeny, you will get closer to the 9:3:3:1 ratio. The spreadsheet provided with the activity will calculate the progeny ratios from the summary data.