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8: Gene Mapping

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

LibreTexts reference: Gene Mapping and Recombination

Centromere Distance from Ordered Tetrad Analysis

Click to show Centromere Distance from Ordered Tetrad Analysis example problem

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
2,652 
+ + a a + + a a
787 
+ + a a a a + +
802 
a a + + + + a a
781 
a a + + a a + +
826 
a a a a + + + +
2,652 
TOTAL 8,500
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.

 

Gene Distance in a Three-Gene Cross from Unordered Tetrad Analysis

Click to show Gene Distance in a Three-Gene Cross from Unordered Tetrad Analysis example problem
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 C is related to the 'clumpy' phenotype. A budding yeast that is homozygous recessive for Gene C grows in dense, irregular clusters, with cells clumping together rather than spreading smoothly.
  • Gene F is analogous to 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.
Set # Tetrad Genotypes Progeny
Count
1
+ + +
+ + +
a c f
a c f
417
2
+ + +
+ + f
a c +
a c f
4,980
3
+ + f
+ + f
a c +
a c +
7,180
4
+ + f
+ c f
a + +
a c +
4,326
5
+ c +
+ c +
a + f
a + f
203
6
+ c f
+ c f
a + +
a + +
294
TOTAL = 17,400

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 A and F
 

Gene Distance in a Two-Gene Cross from Unordered Tetrad Analysis

Click to show Gene Distance in a Two-Gene Cross from Unordered Tetrad Analysis example problem
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 M is affiliated with the 'militant' phenotype. A budding yeast that is homozygous recessive for Gene M colonies are small, dense, and secrete compounds that inhibit the growth of nearby colonies.
  • Gene R is correlated with the 'rusty' phenotype. A budding yeast that is homozygous recessive for Gene R colonies develop a reddish-brown pigmentation, reminiscent of rusted metal.
Set # Tetrad Genotypes Progeny
Count
1
+ +
+ +
m r
m r
182
2
+ +
+ r
m +
m r
3,918
3
+ r
+ r
m +
m +
4,500
TOTAL = 8,600

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 M and R
 

Linkage in a Two-Gene Cross from Unordered Tetrad Analysis

Click to show Linkage in a Two-Gene Cross from Unordered Tetrad Analysis example problem
Characteristics of Recessive Phenotypes

  • Gene P is affiliated with the 'pebble' phenotype. A budding yeast that is homozygous recessive for Gene P produces colonies with a rough, uneven surface that resembles a collection of tiny pebbles.
  • Gene X is linked with the 'xenon' phenotype. A budding yeast that is homozygous recessive for Gene X cells emit a faint glow under UV light, as if they were fluorescent.
Set # Tetrad Genotypes Progeny
Count
1
+ +
+ +
p x
p x
3,333
2
+ +
+ x
p +
p x
2,746
3
+ x
+ x
p +
p +
121
TOTAL = 6,200

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.

 

Genetic Interference from Three-Point Test Crosses

Click to show Genetic Interference from Three-Point Test Crosses example problem

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 T is related to 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.
  • Gene X is connected with the 'xanthic' phenotype. A fruit fly that is homozygous recessive for Gene X has a fluorescent bright yellow coloring.
  • Gene Y is connected with the 'yucky' phenotype. A fruit fly that is homozygous recessive for Gene Y gives off an unpleasant odor and has a generally unappealing look.
Phenotype Genotypes Progeny
Count
 tipsy, xanthic, yucky t x y 1,683
 tipsy, xanthic t x + 5
 tipsy, yucky t + y 117
 tipsy t + + 187
 xanthic, yucky + x y 193
 xanthic + x + 103
 yucky + + y 15
 wildtype + + + 1,697
TOTAL = 4,000

The resulting phenotypes are summarized in the table above.

  • The distance between genes T and Y is 10 cM
  • The distance between genes T and X is 15 cM
  • The distance between genes Y and X is 6 cM
  • The correct gene order determined from these distances is TYX
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 T and X.

 

Single-Gene Pair Distance from a Three-Point Test Cross

Click to show Single-Gene Pair Distance from a Three-Point Test Cross example problem

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 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 P is linked with the 'prickly' phenotype. A fruit fly that is homozygous recessive for Gene P is covered with sharp bristles, giving it a spiky texture.
  • Gene W is related to 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
 horsey, prickly, waxy h p w 2,735
 horsey, prickly h p + 643
 horsey, waxy h + w 3,174
 horsey h + + 3,450
 prickly, waxy + p w 3,434
 prickly + p + 3,126
 waxy + + w 651
 wildtype + + + 2,787
TOTAL = 20,000

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, and using only the genotypes that result from crossover events between the two genes P and W during meiosis.
calculate the genetic distance between the two genes P and W, expressing your answer in centimorgans (cM)

 

Double Crossover Genotypes from Three-Point Test Crosses

Click to show Double Crossover Genotypes from Three-Point Test Crosses example problem

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 associated 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 J is related to the 'jerky' phenotype. A fruit fly that is homozygous recessive for Gene J moves in rapid and sudden movements, displaying an unpredictable flight pattern.
  • Gene M is analogous to the 'mushy' phenotype. A fruit fly that is homozygous recessive for Gene M feels soft to the touch and unusually squishy, unlike the usual firmness.
Phenotype Genotypes Progeny
Count
 bumpy, jerky, mushy b j m 151
 bumpy, jerky b j + 693
 bumpy, mushy b + m 2,451
 bumpy b + + 616
 jerky, mushy + j m 656
 jerky + j + 2,478
 mushy + + m 738
 wildtype + + + 167
TOTAL = 7,950

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.

 

Recombinant Genotypes from Three-Point Test Crosses

Click to show Recombinant Genotypes from Three-Point Test Crosses example problem

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 linked 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 correlated 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 J is analogous to the 'jerky' phenotype. A fruit fly that is homozygous recessive for Gene J moves in rapid and sudden movements, displaying an unpredictable flight pattern.
Phenotype Genotypes Progeny
Count
 artsy, horsey, jerky a h j 73
 artsy, horsey a h + 587
 artsy, jerky a + j 228
 artsy a + + 1,801
 horsey, jerky + h j 1,790
 horsey + h + 231
 jerky + + j 628
 wildtype + + + 62
TOTAL = 5,400

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 A and H. These genotypes result from crossover events that occur between the two genes A and H during meiosis.
More than one genotype will be correct. Select all that apply.

 

Parental Genotypes from Three-Point Test Crosses

Click to show Parental Genotypes from Three-Point Test Crosses example problem

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 D is associated with 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 N is correlated 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 affiliated 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
 dewy, nerdy, prickly d n p 76
 dewy, nerdy d n + 2,971
 dewy, prickly d + p 1,118
 dewy d + + 649
 nerdy, prickly + n p 647
 nerdy + n + 1,042
 prickly + + p 3,029
 wildtype + + + 68
TOTAL = 9,600

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.

 

Gene Configuration (Cis vs. Trans) in Two-Point Test Crosses

Click to show Gene Configuration (Cis vs. Trans) in Two-Point Test Crosses 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 H is correlated 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 W is correlated 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
 horsey, waxy h w 190
 horsey h + 407
 waxy + w 397
 wildtype + + 206
TOTAL = 1,200

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.

 

Gene Distance from Two-Point Test Crosses

Click to show Gene Distance from Two-Point Test Crosses 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 N is analogous to 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 associated 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
 nerdy, prickly n p 8,621
 nerdy n + 25,011
 prickly + p 25,128
 wildtype + + 8,740
TOTAL = 67,500

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, calculate the genetic distance between the two genes, expressing your answer in centimorgans (cM)

 

Parental Genotypes from Two-Point Test Crosses

Click to show Parental Genotypes from Two-Point Test Crosses 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 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.
  • Gene R is affiliated with 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
 kidney, rusty k r 228
 kidney k + 628
 rusty + r 704
 wildtype + + 240
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 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.

 

Recombinant Genotypes from Two-Point Test Crosses

Click to show Recombinant Genotypes from Two-Point Test Crosses 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 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.
  • Gene X is connected with the 'xanthic' phenotype. A fruit fly that is homozygous recessive for Gene X has a fluorescent bright yellow coloring.
Phenotype Genotypes Progeny
Count
 kidney, xanthic k x 1,925
 kidney k + 1,190
 xanthic + x 1,104
 wildtype + + 1,981
TOTAL = 6,200

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.

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