Linkage and Genetic Mapping in Eukaryotes

LINKAGE AND GENETIC MAPPING IN EUKARYOTES

LINKAGE AND CROSSING OVER

• Crossing over can produce recombinant genotypes.
• Bateson and Punnett discovered two traits that did not assort independently.
• Morgan proposed that crossing over between X chromosomes can occur and linked X-linked genes.
• Chi-square analysis distinguishes between linkage and independent assortment.
• Creighton and McClintock showed that crossing over produces new combinations of alleles and exchange segments between homologous chromosomes.
• Crossing over can occur during mitosis.

Chromosomal and Genetic Linkage

• Chromosomes contain many genes (hundreds to thousands).
• Linkage refers to two genes on the same chromosome.
• Genes close together are typically transmitted as a group from parent to offspring.
• Chromosomes are called linkage groups because genes are physically connected.
• Genes far apart on a chromosome may assort independently due to crossing over.
• Humans have 22 autosomal linkage groups, an X linkage group, and a Y linkage group.
• Geneticists use dihybrid (two-factor) and trihybrid (three-factor) crosses to follow traits.
• The outcome of a cross depends on whether genes are linked on the same chromosome.

Crossing Over and Recombinant Phenotypes

• Crossing over can alter gene linkage.
• Bivalent chromosomes have two homologous chromosomes, each with a pair of sister chromatids.
• Genetic recombination via crossing over can create new allele combinations on chromosomes.
• Cells with new allelic combinations are called nonparental or recombinant cells.
• Cells with the original allele combinations are called parental cells.

Bateson and Punnett's Experiment

• Bateson and Punnett (1905) were the first to show that not all traits assort independently.
• In sweet peas, crosses involving flower color and pollen length didn't show the expected 9:3:3:1 phenotypic ratio from a dihybrid cross.
• They suggested the traits were coupled.

Morgan's Experimental Evidence of Linkage

• Thomas Hunt Morgan provided the first direct evidence that different genes are physically located on the same chromosome.
• Morgan studied X-linked inheritance patterns using trihybrid crosses with three traits:
  • Body color (gray y^+ or yellow y)
  • Eye color (red w^+ or white w)
  • Wing shape (long m^+ or miniature m)
• The linkage was evident in the F2 generation rather than an equal proportion of eight possible phenotypic classes.
• Parental combinations were most prevalent in the offspring.
• Morgan suggested that these three traits are on the X chromosome and tend to be inherited together.

Quantitative Analysis of Morgan's Results

• Reorganizing the data by gene pairs reveals quantitative differences:
  • Body color and eye color:
    • Gray body, red eyes: 1,159
    • Yellow body, white eyes: 1,017
    • Gray body, white eyes: 17 (nonparental)
    • Yellow body, red eyes: 12 (nonparental)
    • Total: 2,205
  • Eye color and wing shape:
    • Red eyes, long wings: 770
    • White eyes, miniature wings: 716
    • Red eyes, miniature wings: 401 (nonparental)
    • White eyes, long wings: 318 (nonparental)
    • Total: 2,205

Morgan's Hypotheses

• Morgan proposed three hypotheses to explain his results:
  1. All three genes are located on the same chromosome (the X chromosome).
  2. Crossing over produces new combinations of alleles.
  3. The likelihood of crossing over depends on the distance between the two genes. Genes that are far apart are more likely to cross over than genes that are close together.
• Nonparental offspring resulted from crossing over between homologous X chromosomes.

Chi-Square Tests for Linkage

• Researchers use the chi-square test to determine if two genes are linked or assorting independently.

Steps for Chi-Square Analysis:

1.  **Propose a hypothesis:** The null hypothesis (H_0) is that the traits are assorting independently.
2.  **Calculate expected values:** Determine expected values for each phenotype based on the hypothesis.
3.  **Perform Chi-square analysis:** Use the expected values and observed phenotypic data.
4.  **Interpret the Chi-square result:** Rejecting the null hypothesis indicates linkage.

Creighton and McClintock's Experiment

• Creighton and McClintock provided the first direct evidence that crossing over is associated with genetic recombination.
• They worked with corn, which has 10 different chromosomes per set.
• Some corn strains had an unusual chromosome 9 with a darkly staining knob at one end.
• An abnormal version of chromosome 9 had an extra piece of chromosome 8.

Chromosomal Abnormalities:

• They identified two chromosomal abnormalities to track chromosome movement during meiosis.
• These abnormalities involved unusual staining patterns or translocations.
• They traced the movement of alleles for kernel color and kernel endosperm texture.
• Crossing over resulted in chromosomes with either a knob or a translocation.
  • Gene near the knobbed end of chromosome 9: color to corn kernels
  • Gene near the translocated piece from chromosome 8: texture of the kernel endosperm

Experimental System Significance:

• Their system showed that crossing over generates genetic recombinations and involves a physical exchange of material between homologous chromosomes.

Crossing Over During Mitosis

• Mitosis typically doesn't involve homologous chromosome pairing, so crossing over is rare.
• Crossing over during mitosis (mitotic crossing over) can produce recombinant chromosomes with new allele combinations.
• This process is called mitotic recombination.

Twin Spots

• Curt Stern (1936) studied this in Drosophila, noting that adjacent body areas may express different alleles for bristle length and body color.
• Adjacent areas in the same organism with slightly different phenotypes are called twin spots, resulting from mitotic recombination.

GENETIC MAPPING IN PLANTS AND ANIMALS

Purpose of Genetic Mapping

• Genetic mapping determines the linear order and distance of genes on a chromosome.
• Genes have a specific location on a chromosome, called a locus.
• Genetic maps serve several purposes:
  1. Understanding the complexity and genetic organization of species.
  2. Illustrating the underlying basis for inherited traits.
  3. Enabling molecular cloning and study of genes.
  4. Comparison of genetic maps is used in evolutionary studies.
  5. Identifying disease-causing genes for diagnosis and treatment.
  6. Allowing genetic counselors to predict offspring traits/diseases.
  7. Enhancing selective breeding in agriculture.
• The linear order of genes on the chromosome is called a genetic linkage map.

Recombination Frequency and Map Distance

• Genetic mapping allows determining relative distances between genes.
• The farther apart two genes are on a chromosome, the greater the chance of crossing over between them.
• The percentage of recombinant offspring correlates to the distance between genes.

Offspring Classification

• Crosses distinguish between recombinant and nonrecombinant offspring.
• Recombinant offspring have different allele combinations than parental strains.
• Nonrecombinant offspring have the same allele combinations as parental strains.
• Crossing over during meiosis produces recombinant offspring.
• Recombinant offspring are typically fewer in number than nonrecombinant offspring.

Calculation of Map Distance

• Recombination frequency estimates the physical distance between two genes on the same chromosome.
• Map distance = \frac{{\text{Number of recombinant offspring}}}{{\text{Total number of offspring}}} \times 100
• The total includes both recombinant and nonrecombinant offspring.
• Units for map distance are map units (mu) or centiMorgans (cM).
• 1 map unit equals a 1% recombination frequency.

Sturtevant's Genetic Map

• Alfred Sturtevant constructed the first genetic map in 1911 using Drosophila melanogaster.
• The map consisted of X-linked traits.

Experimental Design

• His system produced flies with recombination of traits on the X chromosome.
• The percentage of recombination indicated the relative gene distance.
• Sturtevant assumed that map distances would be more accurate between closely linked genes.
• At map distances approaching 50.0 (50% recombination), multiple undetected crossover events may influence results.

Trihybrid Crosses and Genetic Mapping

• Trihybrid crosses (three traits) determine the map distance and order of genes on a chromosome.
• Procedure for constructing a trihybrid cross:
  • Cross two true-breeding strains differing in three alleles.
  • Example: bb \ prpr \ vgvg♀ \times b^+b^+ \ pr^+pr^+ \ vg^+vg^+♂