LINKAGE AND CROSSING OVER

Application of Mendel’s Rules assumes:

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1. One allele completely dominates the other

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2. All genes have 2 allelic forms

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3. All traits are monogenic (affected by only one

locus)

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4. All chromosomes occur in homologous pairs

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5. All genes assort independently

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Mendel's Law of Independent Assortment

Allele pairs separate independently during the formation of gametes. This means that traits are transmitted to offspring independently of one another.

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Dihybrid cross - phenotypes

Independent assortment

An Interpretation from the Dihybrid cross

• During gamete formation, segregating pairs of unit factors assort independently.
• In other words, segregation of 2 alleles at one genetic locus has no effect on the segregation of 2 alleles at another locus.
• For example, the assortment of yellow and green alleles has no effect on the assortment of round and wrinkled alleles, and vice versa.

Discovery of Linkage

• William Bateson and R.C. Punnett were working with several traits in sweet peas, notably a gene for purple (P) vs. red (p) flowers, and a gene for long pollen grains (L) vs. round pollen grains (l).

Bateson and Punnett also studied peas:

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Flower Color: P = purple p = red

Pollen seed shape: L = long l = round

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True Breeding lines: PPLL x ppll P

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PpLl F1

Phenotype Number Exp Ratio Exp Number

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Purple long 284 9 215

Purple round 21 3 71

Red long 21 3 71

Red round 55 1 24

What is going on????

Crosses produced a deviation from the predicted

Mendelian independent assortment ratios.

• A test cross is a breeding or a mating between an individual of dominant phenotype, who could be either homozygous dominant (SS) or heterozygous (Ss), with an individual that MUST be homozygous recessive (ss).

Test cross F1 to double recessive:

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Parents PpLl X ppll

Gametes PL pl

Pl

pL

pl

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Expect 1:1:1:1 ratio of phenotypes

Bateson and Punnett observed 7:1:1:7

Some gamete types more common that others…but why???

• Because the parental phenotypes reappeared more frequently than expected, the researchers hypothesized that there was a coupling, or connection, between the parental alleles for flower color and pollen grain shape
• This coupling resulted in the observed deviation from independent assortment.

• But why are certain alleles linked? Bateson and Punnett weren't sure.
• In fact, it was not until the later work of geneticist Thomas Hunt Morgan that this coupling, or linkage, could be fully explained.

MORGAN’S EXPERIMENTS

• In Drosophila, Both the white eye gene (w) and a gene for miniature wings (m) are on the X chromosome.
• Morgan (1911) crossed a female white miniature (w m/w m) with a wild-type male (w+ m+/ Y).
• In the F1, all males were white-eyed with miniature wings (w m/Y), and all females were wild-type for eye color and wing size (w+ m+/w m).

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Morgan’s experimental crosses of white-eye and miniature-wing variants of Drosophila melanogaster

In F2, the most frequent phenotypes for both sexes were the phenotypes of the parents in the original cross (white eyes with miniature wings, and red eyes with normal wings).

Non-parental phenotypes (white eyes with normal wings or red eyes with miniature wings) occurred in about 37% of the F2 flies. Well below the 50% predicted for independent assortment, this indicates that non-parental flies result from recombination of linked genes.

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What is Linkage?

• Linkage is defined genetically as the failure of two genes to assort independently.
• Linkage occurs when two genes are close to each other on the same chromosome.
• Genes far apart on the same chromosome assort independently: they are not linked.
• Linkage is based on the frequency of crossing over between the two genes.
• Crossing over occurs in prophase of meiosis 1, where homologous chromosomes break at identical locations and rejoin with each other.

Morgan and Crossing Over

• Morgan proposed that the chiasmata visible on chromosomes were regions of crossing over.

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• Occurs between non-sister chromatids.

Process of Recombination

• From an evolutionary point of view, the purpose of sex is to re-shuffle the combinations of alleles so the offspring receive a different set of alleles than their parents had.
• Natural selection then causes offspring with good combinations to survive and reproduce, while offspring with bad combinations don’t pass them on.
• Genes are on chromosomes. Meiosis is a mechanism for re-shuffling the chromosomes: each gamete gets a mixture of paternal and maternal chromosomes.
• However, chromosomes are long and contain many genes. To get individual genes re-shuffled, there needs to be a mechanism of recombining genes that are on the same chromosome. This mechanism is called “crossing over.

• Crossing over occurs in prophase of meiosis 1, when the homologous chromosomes “synapse”, which means to pair closely with each other. DNA strands from the two chromosomes are matched with each other.
• During synapsis, an enzyme, “recombinase”, attaches to each chromosome at several randomly chosen points. The recombinase breaks both DNA molecules at the same point, and re-attaches them to opposite partners.
• The result of crossing over can be seen in the microscope as prophase continues, as X-shaped structures linking the homologues.
• The genetic consequence of crossing over is that each chromosome that goes into a gamete is a combination of maternal and paternal chromosomes.

Recombination Process

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.

Mechanism of crossing-over

No Linkage: Independent Assortment

Linkage without Recombination

Linkage with Recombination

Linkage Mapping

• Each gene is found at a fixed position on a particular chromosome. Making a map of their locations allows us to identify and study them better. In modern times, we can use the locations to clone the genes so we can better understand what they do and why they cause genetic diseases when mutated.
• The basis of linkage mapping is that since crossing over occurs at random locations, the closer two genes are to each other, the less likely it is that a crossover will occur between them. Thus, the percentage of gametes that had a crossover between two genes is a measure of how far apart those two genes are.
• As pointed out by T. H. Morgan and Alfred Sturtevant, who produced the first Drosophila gene map in 1913. Morgan was the founder of Drosophila genetics, and in his honor a recombination map unit is called a centiMorgan (cM).
• A map unit, or centiMorgan, is equal to crossing over between 2 genes in 1% of the gametes.

Detecting Linkage through Testcrosses

• Linked genes are used for mapping. They are found by looking for deviation from the frequencies expected from independent assortment.
• A testcross (one parent is homozygous recessive) works well for analyzing linkage
• If the alleles are not linked, and the second parent is heterozygous, all four possible combinations of traits will be present in equal numbers in the progeny.
• A significant deviation in this ratio (more parental and fewer recombinant types) indicates linkage.

Sturtevant and Mapping

• Sturtevant, Morgan’s undergraduate student, discovered frequency of crossing over between each pair of the 3 genes:

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• yellow, white 0.5%
• white, miniature 34.5%
• yellow, miniature 35.4%

Sturtevant’s Interpretation

• Sturtevant reasoned that recombination frequencies were additive, so order of genes on chromosome was yellow-white-miniature.

Single Crossovers: Non-crossover (Parental) and Crossover (Recombinant) Gametes

What is the maximum % recombination?

Map Units

• One map unit (centimorgan, cM) = 1% recombination between two genes
• yellow and white are 0.5 cM apart
• yellow and miniature are 35.4 cM apart
• white and miniature are (35.4-0.5) = 34.9 cM apart

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• In Drosophila, crossing over occurs only in females, never in males.

III. Three-Point Mapping

• You can add % recombination between two genes to find the order of genes pretty well.

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• But the only way to be sure of the order of three genes is by Three-Point Mapping, which considers 3 genes at once.

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• You look for rare double-crossover events, and that is the clue to the gene order.

Genetic Map of Drosophila melanogaster

Interference

• There is a second issue with double crossovers: interference.
• Interference is the inability of 2 crossovers to occur very close to each other. Think of the chromosome as a thick rope: it is impossible to bend it too tightly.
• It is possible to measure the amount of interference, by comparing the actual number of double crossovers to the number that you would expect based on the number of single crossovers that occurred.