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8: Gene Mapping

Two- and three-point test crosses, genetic distances, interference, and tetrad analysis.

Ordered Tetrad Analysis: Estimating Centromere Distance

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Ordered Tetrads in Neurospora crassa

Background Information

Neurospora crassa is an organism that has significantly contributed to the understanding of genetics. This fungus exhibits a distinctive genetic feature: the formation of ordered tetrads. These ordered tetrads result from the typical two rounds of meiotic divisions followed by a single round of mitotic division within an ascus, resulting in eight ascospores arranged in a predictable sequence. The position of each ascospore reflects the series of genetic events during cell division, providing a snapshot of the meiotic process.
The analysis of these ordered tetrads in Neurospora crassa allows for the classification of ascospores based on their allele arrangements into different segregation patterns.
The central principle in this analysis is the distinction between first-division and second-division segregation, which is based on the behavior of alleles in the presence or absence of crossover between a gene and its centromere. When alleles separate during the first meiotic division, it indicates first-division segregation. Conversely, if alleles separate during the second division, this suggests that a crossover event has occurred, leading to second-division segregation.
Counting the frequency of second-division segregation events within these ordered tetrads can provide an estimate of the genetic distance between a gene and its centromere. This frequency, reflective of the crossover events during meiosis, is used to calculate the recombination frequency. Such estimates are crucial for constructing genetic maps, which serve as a guide to the genetic landscape of Neurospora crassa, enhancing our understanding of genetic linkage and the location of genes relative to centromeres.

Experimental Data

In the table below, the six different patterns of ordered asci in Neurospora crassa are listed along with the counts found in an experiment.

Octad Asci
Count
+ + + + a a a a
1,830 
+ + a a + + a a
440 
+ + a a a a + +
414 
a a + + + + a a
433 
a a + + a a + +
468 
a a a a + + + +
1,815 
TOTAL 5,400
Distance Formula
distance between a gene
and its centromere		 = ½ × (asci with second-division segregation patterns)
total number of asci
Question

Using the numbers of asci for each pattern shown in the table above, determine the genetic distance between gene A and its centromere.

 

Unordered Tetrad Analysis: Calculating Gene Distance in a Three-Gene Cross

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Unordered Tetrad Three Gene Mapping

In this problem, you will use unordered tetrads to determine the between a single pair of genes and calculate the distances between them. The yeast Saccharomyces cerevisiae is used in this study. A cross has been performed to study the linkage relationships among three genes, and the resulting genotypes are summarized in the table below.

Characteristics of Recessive Phenotypes

  • Gene A is analogous to the 'amber' phenotype. A budding yeast that is homozygous recessive for Gene A cells develop a rich yellow-orange pigmentation, giving the colony a warm, amber hue.
  • Gene K is related to the 'knotted' phenotype. A budding yeast that is homozygous recessive for Gene K cells grow in twisted, coiled shapes, resulting in a knotted or gnarled appearance.
  • Gene W is connected with the 'webbed' phenotype. A budding yeast that is homozygous recessive for Gene W colonies produce delicate, web-like strands that connect neighboring colonies in a cobweb pattern.
Set # Tetrad Genotypes Progeny
Count
1
+ + +
+ + +
a k w
a k w
38
2
+ + +
+ k w
a + +
a k w
1,224
3
+ + w
+ + w
a k +
a k +
59
4
+ + w
+ k w
a + +
a k +
1,494
5
+ k +
+ k +
a + w
a + w
22
6
+ k w
+ k w
a + +
a + +
3,763
TOTAL = 6,600

The resulting phenotypes are summarized in the table above.

Step-by-Step Instructions
  • Step 1: Find the row for the Parental Type for all three genes.
  • Step 2: Looking at only your two genes, assign PD, NPD, TT.
  • Step 3: Determine if the two genes are linked.
    • PD >> NPD → linked; PD ≈ NPD → unlinked
  • Step 4: Determine the map distance between the two genes.
    • D = ½ (TT + 6 NPD) / total = (3 NPD + ½ TT) / total
Determine the distance between the two genes A and W
 

Unordered Tetrad Analysis: Calculating Gene Distance in a Two-Gene Cross

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Unordered Tetrad Two Gene Mapping

In this problem, you will use unordered tetrads to determine the between a single pair of genes and calculate the distances between them. The yeast Saccharomyces cerevisiae is used in this study. A cross has been performed to study the linkage relationships among two genes, and the resulting genotypes are summarized in the table below.

Characteristics of Recessive Phenotypes

  • Gene E is correlated with the 'elephant' phenotype. A budding yeast that is homozygous recessive for Gene E cells absorb excessive amounts of liquid, resulting in giant, swollen cells.
  • Gene Y is associated with the 'yolk' phenotype. A budding yeast that is homozygous recessive for Gene Y cells develop a dense, yellowish core that resembles an egg yolk when viewed under a microscope.
Set # Tetrad Genotypes Progeny
Count
1
+ +
+ +
e y
e y
61
2
+ +
+ y
e +
e y
1,166
3
+ y
+ y
e +
e +
1,173
TOTAL = 2,400

The resulting phenotypes are summarized in the table above.

Step-by-Step Instructions
  • Step 1: Find the row for the Parental Type for all three genes.
  • Step 2: Looking at only your two genes, assign PD, NPD, TT.
  • Step 3: Determine if the two genes are linked.
    • PD >> NPD → linked; PD ≈ NPD → unlinked
  • Step 4: Determine the map distance between the two genes.
    • D = ½ (TT + 6 NPD) / total = (3 NPD + ½ TT) / total
Determine the distance between the two genes E and Y
 

Unordered Tetrad Analysis: Testing for Linkage in a Two-Gene Cross

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Characteristics of Recessive Phenotypes

  • Gene F is correlated with the 'fuzzy' phenotype. A budding yeast that is homozygous recessive for Gene F colonies are covered in soft, fine filaments, giving them a fuzzy, cotton-like texture.
  • Gene N is related to the 'nude' phenotype. A budding yeast that is homozygous recessive for Gene N cells have an unusually smooth surface with no visible external features or textures.
Set # Tetrad Genotypes Progeny
Count
1
+ +
+ +
f n
f n
26
2
+ +
+ n
f +
f n
812
3
+ n
+ n
f +
f +
1,362
TOTAL = 2,200

The resulting phenotypes are summarized in the table above.

Step-by-Step Instructions
  • Step 1: Find the row with the Parental Type for both genes.
  • Step 2: Assign PD, NPD, TT for the other rows
  • Step 3: Determine if the two genes are linked.
    • PD >> NPD → linked; PD ≈ NPD → unlinked
Unordered Tetrad Two Gene Determine Linkage

The yeast Saccharomyces cerevisiae has unordered tetrads. A cross is made to study the linkage relationships among two genes.
Using the table above, determine the linkage between the two genes.

 

Three-Point Test Cross: Calculating Genetic Interference

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Three-Point Test Cross Problem

A test cross is a way to explore the relationship between genes and their respective alleles. It is a useful tool for genetic mapping and deciphering the inheritance of traits. Specifically, a three-point test cross examines three (3) genes at the same time to learn about their assortment in gamete formation.
A standard three-point test cross involves crossing a heterozygous organism for all three genes with an organism that is homozygous recessive for all three genes
For this problem, a test cross using a fruit fly (Drosophila melanogaster) heterozygous for three genes was conducted to understand their genetic interactions.

Characteristics of Recessive Phenotypes

  • Gene B is connected with the 'bumpy' phenotype. A fruit fly that is homozygous recessive for Gene B has a skin texture that is not smooth, but rough with small bumps all over.
  • Gene E is linked with the 'eery' phenotype. A fruit fly that is homozygous recessive for Gene E appears to have something off, crooked limbs and other twisted appendages.
  • Gene P is analogous to the 'prickly' phenotype. A fruit fly that is homozygous recessive for Gene P is covered with sharp bristles, giving it a spiky texture.
Phenotype Genotypes Progeny
Count
 bumpy, eery, prickly b e p 888
 bumpy, eery b e + 517
 bumpy, prickly b + p 115
 bumpy b + + 2,506
 eery, prickly + e p 2,578
 eery + e + 131
 prickly + + p 549
 wildtype + + + 916
TOTAL = 8,200

The resulting phenotypes are summarized in the table above.

  • The distance between genes B and P is 25 cM
  • The distance between genes B and E is 35 cM
  • The distance between genes P and E is 16 cM
  • The correct gene order determined from these distances is BPE
Step-by-Step Instructions for Calculating Interference
  • Step 1: Count the observed number of double crossovers from the data table.
  • Step 2: Calculate the probability of independent crossovers between distant genes.
    • Multiply the two individual crossover probabilities (based on their distance) for both adjacent gene pairs.
  • Step 3: Determine the expected number of double crossovers.
    • Multiply the combined probability (from Step 2) by the total progeny count.
  • Step 4: Calculate the Coefficient of Coincidence (CoC).
    • Divide the observed number of double crossovers (from Step 1) by the expected number (from Step 3).
  • Step 5: Calculate Interference.
    • Interference is given by the formula: Interference = 1 - CoC.

In genetic studies, interference refers to the phenomenon where the occurrence of a crossover in one region of a chromosome reduces the likelihood of another crossover occurring nearby, thereby affecting the expected genetic ratios.

Question

Based on the traits expressed in the offspring, select the correct fraction that represents the interference level between genes B and E.

 

Three-Point Test Cross: Calculating Distance for a Single Gene Pair

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Three-Point Test Cross Problem

A test cross is a way to explore the relationship between genes and their respective alleles. It is a useful tool for genetic mapping and deciphering the inheritance of traits. Specifically, a three-point test cross examines three (3) genes at the same time to learn about their assortment in gamete formation.
A standard three-point test cross involves crossing a heterozygous organism for all three genes with an organism that is homozygous recessive for all three genes
For this problem, a test cross using a fruit fly (Drosophila melanogaster) heterozygous for three genes was conducted to understand their genetic interactions.

Characteristics of Recessive Phenotypes

  • Gene A is connected with the 'artsy' phenotype. A fruit fly that is homozygous recessive for Gene A has wings that are colorful and distinctive patterns.
  • Gene H is linked with the 'horsey' phenotype. A fruit fly that is homozygous recessive for Gene H is quite big and strong-looking, much larger than your typical fruit fly.
  • Gene K is connected with the 'kidney' phenotype. A fruit fly that is homozygous recessive for Gene K has a body shape that is curved, similar to a kidney bean.
Phenotype Genotypes Progeny
Count
 artsy, horsey, kidney a h k 707
 artsy, horsey a h + 2,172
 artsy, kidney a + k 13,592
 artsy a + + 7,206
 horsey, kidney + h k 6,988
 horsey + h + 13,938
 kidney + + k 2,180
 wildtype + + + 717
TOTAL = 47,500

The resulting phenotypes are summarized in the table above.
The resulting phenotypes are summarized in the table above.

Question

With the progeny data from the table, and using only the genotypes that result from crossover events between the two genes A and H during meiosis.
calculate the genetic distance between the two genes A and H, expressing your answer in centimorgans (cM)

 

Three-Point Test Cross: Identifying Double Crossover Genotypes

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Three-Point Test Cross Problem

A test cross is a way to explore the relationship between genes and their respective alleles. It is a useful tool for genetic mapping and deciphering the inheritance of traits. Specifically, a three-point test cross examines three (3) genes at the same time to learn about their assortment in gamete formation.
A standard three-point test cross involves crossing a heterozygous organism for all three genes with an organism that is homozygous recessive for all three genes
For this problem, a test cross using a fruit fly (Drosophila melanogaster) heterozygous for three genes was conducted to understand their genetic interactions.

Characteristics of Recessive Phenotypes

  • Gene C is affiliated with the 'chummy' phenotype. A fruit fly that is homozygous recessive for Gene C shows behavior where it always maintains a close distance to other flies.
  • Gene R is associated with the 'rusty' phenotype. A fruit fly that is homozygous recessive for Gene R has a reddish-brown color, much like rusted iron metal.
  • Gene T is correlated with the 'tipsy' phenotype. A fruit fly that is homozygous recessive for Gene T moves in an erratic path, suggesting a lack of coordination, as if intoxicated.
Phenotype Genotypes Progeny
Count
 chummy, rusty, tipsy c r t 840
 chummy, rusty c r + 1,512
 chummy, tipsy c + t 103
 chummy c + + 41
 rusty, tipsy + r t 34
 rusty + r + 122
 tipsy + + t 1,513
 wildtype + + + 835
TOTAL = 5,000

The resulting phenotypes are summarized in the table above.
The resulting phenotypes are summarized in the table above.

Question

Based on the traits expressed in the offspring, identify the double crossover genotype combinations. These allele combinations are a result of two genetic crossover events.
More than one genotype will be correct. Select all that apply.

 

Three-Point Test Cross: Identifying Recombinant Genotypes

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Three-Point Test Cross Problem

A test cross is a way to explore the relationship between genes and their respective alleles. It is a useful tool for genetic mapping and deciphering the inheritance of traits. Specifically, a three-point test cross examines three (3) genes at the same time to learn about their assortment in gamete formation.
A standard three-point test cross involves crossing a heterozygous organism for all three genes with an organism that is homozygous recessive for all three genes
For this problem, a test cross using a fruit fly (Drosophila melanogaster) heterozygous for three genes was conducted to understand their genetic interactions.

Characteristics of Recessive Phenotypes

  • Gene F is linked with the 'fuzzy' phenotype. A fruit fly that is homozygous recessive for Gene F is covered in a dense layer of hairs, giving it a soft appearance.
  • Gene H is connected with the 'horsey' phenotype. A fruit fly that is homozygous recessive for Gene H is quite big and strong-looking, much larger than your typical fruit fly.
  • Gene R is analogous to the 'rusty' phenotype. A fruit fly that is homozygous recessive for Gene R has a reddish-brown color, much like rusted iron metal.
Phenotype Genotypes Progeny
Count
 fuzzy, horsey, rusty f h r 91
 fuzzy, horsey f h + 1,216
 fuzzy, rusty f + r 219
 fuzzy f + + 599
 horsey, rusty + h r 598
 horsey + h + 222
 rusty + + r 1,157
 wildtype + + + 98
TOTAL = 4,200

The resulting phenotypes are summarized in the table above.
The resulting phenotypes are summarized in the table above.

Question

Based on the traits expressed in the offspring, identify the all recombinant genotypes for genes F and H. These genotypes result from crossover events that occur between the two genes F and H during meiosis.
More than one genotype will be correct. Select all that apply.

 

Three-Point Test Cross: Identifying Parental Genotypes

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Three-Point Test Cross Problem

A test cross is a way to explore the relationship between genes and their respective alleles. It is a useful tool for genetic mapping and deciphering the inheritance of traits. Specifically, a three-point test cross examines three (3) genes at the same time to learn about their assortment in gamete formation.
A standard three-point test cross involves crossing a heterozygous organism for all three genes with an organism that is homozygous recessive for all three genes
For this problem, a test cross using a fruit fly (Drosophila melanogaster) heterozygous for three genes was conducted to understand their genetic interactions.

Characteristics of Recessive Phenotypes

  • Gene A is correlated with the 'artsy' phenotype. A fruit fly that is homozygous recessive for Gene A has wings that are colorful and distinctive patterns.
  • Gene N is connected with the 'nerdy' phenotype. A fruit fly that is homozygous recessive for Gene N has large, prominent eyes that stand out, much like thick-rimmed glasses.
  • Gene P is correlated with the 'prickly' phenotype. A fruit fly that is homozygous recessive for Gene P is covered with sharp bristles, giving it a spiky texture.
Phenotype Genotypes Progeny
Count
 artsy, nerdy, prickly a n p 337
 artsy, nerdy a n + 255
 artsy, prickly a + p 58
 artsy a + + 923
 nerdy, prickly + n p 949
 nerdy + n + 54
 prickly + + p 273
 wildtype + + + 351
TOTAL = 3,200

The resulting phenotypes are summarized in the table above.
The resulting phenotypes are summarized in the table above.

Question

Based on the traits expressed in the offspring, identify the parental genotype combinations. These are the allele combinations that the parent fruit flies originally carried.
More than one genotype will be correct. Select all that apply.

 

Two-Point Test Cross: Determining Gene Configuration (Cis vs. Trans)

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Two-Point Test Cross Problem

A test cross is a way to explore the relationship between genes and their respective alleles. It is a useful tool for genetic mapping and deciphering the inheritance of traits. Specifically, a two-point test cross examines two (2) genes at the same time to learn about their assortment in gamete formation.
A standard two-point test cross involves crossing a heterozygous organism for both genes with an organism that is homozygous recessive for both genes
For this problem, a test cross using a fruit fly (Drosophila melanogaster) heterozygous for two genes was conducted to understand their genetic interactions.

Characteristics of Recessive Phenotypes

  • Gene D is analogous to the 'dewy' phenotype. A fruit fly that is homozygous recessive for Gene D appears moist, with its body covered in tiny droplets of water.
  • Gene H is affiliated with the 'horsey' phenotype. A fruit fly that is homozygous recessive for Gene H is quite big and strong-looking, much larger than your typical fruit fly.
Phenotype Genotypes Progeny
Count
 dewy, horsey d h 860
 dewy d + 543
 horsey + h 549
 wildtype + + 848
TOTAL = 2,800

The resulting phenotypes are summarized in the table above.
The phenotype counts resulting from the cross are summarized in the table above.

Question

Using the data presented in the table to determine the configuration of the alleles on the parental chromosomes. Determine whether the alleles for the two genes are in a cis (on the same chromosome) or trans (on different chromosomes) configuration.

 

Two-Point Test Cross: Calculating Distance Between Genes

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Two-Point Test Cross Problem

A test cross is a way to explore the relationship between genes and their respective alleles. It is a useful tool for genetic mapping and deciphering the inheritance of traits. Specifically, a two-point test cross examines two (2) genes at the same time to learn about their assortment in gamete formation.
A standard two-point test cross involves crossing a heterozygous organism for both genes with an organism that is homozygous recessive for both genes
For this problem, a test cross using a fruit fly (Drosophila melanogaster) heterozygous for two genes was conducted to understand their genetic interactions.

Characteristics of Recessive Phenotypes

  • Gene N is affiliated with the 'nerdy' phenotype. A fruit fly that is homozygous recessive for Gene N has large, prominent eyes that stand out, much like thick-rimmed glasses.
  • Gene W is associated with the 'waxy' phenotype. A fruit fly that is homozygous recessive for Gene W has a thick protective layer that is water resistant and opague.
Phenotype Genotypes Progeny
Count
 nerdy, waxy n w 45,935
 nerdy n + 11,576
 waxy + w 11,585
 wildtype + + 45,904
TOTAL = 115,000

The resulting phenotypes are summarized in the table above.
The resulting phenotypes are summarized in the table above.

Question

With the progeny data from the table, calculate the genetic distance between the two genes, expressing your answer in centimorgans (cM)

 

Two-Point Test Cross: Identifying Parental Genotypes

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Two-Point Test Cross Problem

A test cross is a way to explore the relationship between genes and their respective alleles. It is a useful tool for genetic mapping and deciphering the inheritance of traits. Specifically, a two-point test cross examines two (2) genes at the same time to learn about their assortment in gamete formation.
A standard two-point test cross involves crossing a heterozygous organism for both genes with an organism that is homozygous recessive for both genes
For this problem, a test cross using a fruit fly (Drosophila melanogaster) heterozygous for two genes was conducted to understand their genetic interactions.

Characteristics of Recessive Phenotypes

  • Gene P is related to the 'prickly' phenotype. A fruit fly that is homozygous recessive for Gene P is covered with sharp bristles, giving it a spiky texture.
  • Gene X is linked with the 'xanthic' phenotype. A fruit fly that is homozygous recessive for Gene X has a fluorescent bright yellow coloring.
Phenotype Genotypes Progeny
Count
 prickly, xanthic p x 1,281
 prickly p + 31
 xanthic + x 21
 wildtype + + 1,267
TOTAL = 2,600

The resulting phenotypes are summarized in the table above.
The resulting phenotypes are summarized in the table above.

Question

Review the phenotype counts shown in the table. Based on the traits expressed in the offspring, identify the possible parental genotype combinations. These are the allele combinations that the parent fruit flies originally carried. More than one combination will be correct. Select all that apply.

 

Two-Point Test Cross: Identifying Recombinant Genotypes

Click to show Two-Point Test Cross: Identifying Recombinant Genotypes example problem

Two-Point Test Cross Problem

A test cross is a way to explore the relationship between genes and their respective alleles. It is a useful tool for genetic mapping and deciphering the inheritance of traits. Specifically, a two-point test cross examines two (2) genes at the same time to learn about their assortment in gamete formation.
A standard two-point test cross involves crossing a heterozygous organism for both genes with an organism that is homozygous recessive for both genes
For this problem, a test cross using a fruit fly (Drosophila melanogaster) heterozygous for two genes was conducted to understand their genetic interactions.

Characteristics of Recessive Phenotypes

  • Gene C is linked with the 'chummy' phenotype. A fruit fly that is homozygous recessive for Gene C shows behavior where it always maintains a close distance to other flies.
  • Gene F is analogous to the 'fuzzy' phenotype. A fruit fly that is homozygous recessive for Gene F is covered in a dense layer of hairs, giving it a soft appearance.
Phenotype Genotypes Progeny
Count
 chummy, fuzzy c f 618
 chummy c + 251
 fuzzy + f 253
 wildtype + + 678
TOTAL = 1,800

The resulting phenotypes are summarized in the table above.
The resulting phenotypes are summarized in the table above.

Question

Review the phenotype counts shown in the table. Based on the traits expressed in the offspring, identify the possible recombinant genotype combinations. These allele combinations have occurred due to genetic crossover. More than one combination will be correct. Select all that apply.