Friday 13, Chromosome Inheritance, Linkage and Mapping

Chromosome Inheritance

Chromosomes are the units of transmission in inheritance, not genes.
You inherit half of your chromosomes from each parent.
When genes are on the same chromosome, they are linked and tend to be inherited together.
Independent assortment is important, but inheritance is primarily about which chromosome you get.

Linked Genes

Linked genes are genes located on the same chromosome.
Independent assortment, as defined by Mendel, does not apply to linked genes.
However, linkage is not permanent because chromosomes are dynamic and can undergo crossing over during meiosis.

Crossing Over and Recombination

Crossing over involves the exchange of genetic information between paternal and maternal chromosomes.
Recombination occurs whenever DNA is cut and reattached.
Crossing over is a type of recombination event.
Recombination events can be used to map the location of genes relative to one another on a chromosome.

Chromosomal Mapping

Chromosomal mapping helps identify which chromosomes contain specific genes and their relative distances.
This can be done without sequencing, using inheritance patterns.
Mendel's work was based on genes located on different chromosomes, leading to the concept of independent assortment.
Genes on the same chromosome tend to segregate together, disrupting independent assortment.

Independent Assortment

Independent assortment occurs when genes are on separate chromosomes.
Example: Mendel's pea traits (seed color and shape) were inherited independently.
With independent assortment one would expect four different genetically different gametes produced with equal likelihood. If the traits were yellow versus green and round versus wrinkled, there is a $1/4$ chance of getting yellow and round, $1/4$ chance of yellow and wrinkled, $1/4$ chance of getting green and round, and $1/4$ chance of getting green and wrinkled.

Dihybrid Crosses

Mendel performed dihybrid crosses with true-breeding plants differing in two traits (e.g., seed texture and color).
Example: Smooth seeds (S) are dominant over wrinkled seeds (s), and yellow seeds (Y) are dominant over green seeds (y).
True-breeding plants are homozygous for these traits (SSYY vs. ssyy).
F1 generation is heterozygous for both traits (SsYy) and exhibits dominant phenotypes (smooth and yellow).

Gamete Production

The F1 plant can produce four different gamete combinations: SY, Sy, sY, and sy.
Self-crossing of the F1 generation results in a 4x4 Punnett square with 16 possible combinations.
The F2 generation shows nine genotypes, but only four phenotypes due to dominance.
Phenotypic ratio: 9 smooth and yellow, 3 smooth and green, 3 wrinkled and yellow, 1 wrinkled and green.
This 9:3:3:1 ratio is observed when traits are inherited independently.

Mendel's Second Law

Mendel's principle of independent assortment states that factors (genes) for different traits assort independently.
This is related to meiosis and chromosome behavior during gamete formation.

Meiosis and Inheritance

Fertilization results from the fusion of haploid cells produced by meiosis.
Independent assortment occurs when genes are on separate, unlinked chromosomes.
Linked genes (on the same chromosome) do not assort independently.
Crossing over can unlink genes, leading to independent inheritance some of the time.

Crossover Frequency

Even if genes are linked, there's a chance of a crossover event separating them.
Example: If a crossover event occurs 3 out of 100 times, the genes will appear linked 97 times and unlinked 3 times.
The null hypothesis assumes equal combinations if genes are not linked.
With linkage, the linked version is more frequent, but almost never 100% due to crossing over.

Recombinant Gametes

Linkage with a crossover event generates recombinant gametes.
Closer genes are less likely to have a crossover event between them.
Genes very close to each other may appear completely linked, but a crossover event is still possible.
It is statistically impossible to achieve them being completely at the same location on the chromosome, as at some point there will be a crossover event to seperate them.
Complete linkage (no crossover) results in parental gametes 100% of the time, meaning no recombination event has changed the location.
If the parental chromsome contains round and wrinkled traits and there's a crossover event between them, the recombinant chromosome would contain green and smooth traits.

Visualizing Independent Assortment

Independent assortment occurs when genes are on different chromosome pairs.
Each of the four possible gamete combinations has an equal chance (25%) of occurring.

Genes on the Same Chromosome

When gene A and gene B are on the same chromosome, they are physically linked.
Complete linkage would result in only two combinations: AB and ab (maternal).
Without crossing over, there's a 50/50 chance of inheriting either chromosome.

Crossing Over Between Homologous Chromosomes

Crossing over between non-sister chromatids can exchange genes.
Non-crossover gametes are more common than crossover gametes when genes are linked.
Crossover events may occur outside the genes of interest, maintaining linkage.
If genes are very far apart, they may appear to assort independently, but true independent assortment will never be achieved - there will always be a 25% equalibrium between parental gametes.

Linkage Ratio

Genes close together appear almost completely linked, resulting in high linkage ratios.
A linkage group consists of genes linked to one another on the same chromosome.
Humans have 23 linkage groups, one for each haploid chromosome.

Inheritance Numbers

Example: Tracking thin veins (hv) and brown eyes (bw) genes in Drosophila.
Perform a test cross with homozygous recessive individuals.
If genes are completely linked, only two parental gametes are expected.
If there is a crossover event, new combinations will appear.
Complete unlinked genes follow a mendelian ratio of 9:3:3:1 but you won't get that with this configuration.
Quantify the observed numbers to determine linkage.

Crossover Probability

Statistical probability of a crossover event is proportional to the distance between genes.
More crossover events indicate genes are further apart; fewer events indicate closer proximity.

Chiasmata

Chiasmata are the points where chromosomes wrap around each other during meiosis.
Physically where a crossover event can take place because the chromosomes must physically come into contact with each other.
When chiasmata are observed under a microscope, actual breaking and rejoining can occur at a chiasma, resulting in crossing over.
After crossing over, chromosomes are hybrids of maternal and paternal sequences.
Crossing over occurs between non-sister chromatids.
Can only occur of up to 50% of the chromosomes, those chromosomes being adjacent to each other.

Recombination Percentage

The percentage of offspring resulting from recombination events depends on the distance between genes.
Closer genes have fewer crossover events between them.

Thomas Hunt Morgan

Thomas Hunt Morgan discovered X-linked inheritance and crossing over in Drosophila (1911).
Morgan led a lab with PhD students and postdocs who performed most of the experimental work.

Alfred Sturtevant

Alfred Sturtevant, a student of Morgan, used recombination data to map gene order.
He recognized that recombination frequencies between linked genes are additive.
Quantifying crossover events allows numerical predictions to be made.

Sturtevant's Contribution

In 1913, Sturtevant published data showing recombination events and their frequencies.
He crossed wild-type alleles with mutant alleles in Drosophila.

Recombination Events

Example: Yellow (y) and white (w) genes on the X chromosome in Drosophila.
Tracked recombination events by observing the phenotypes of male offspring.
Linked traits stayed linked about 99.5% of the time, with recombination events occurring about 0.5% of the time.
Another experiment tracked white (w) and miniature (m) genes, with recombination events occurring 34.5% of the time.
This indicated that w and m were further apart than y and w.

Centimorgans

Sturtevant defined 1% recombination frequency as one centimorgan (cM) in honor of Morgan.
W and y are 0.5 cM apart, while w and m are 34.5 cM apart.
These distances are relative, not exact.

Limitations of Single Crossovers

With single crossovers, recombination can occur in 50% of gametes if a crossover happens every time and genes are at opposite poles of the chromosome.
The absolute maximum distance is 50 centimorgans.
Therefore, a statement is false if two genes are said to be 65 centimorgans apart.
Genes that are 50 centimorgans apart would appear to cross over 100% of the time and would appear to be unlinked.
There will be two hybrid chromosomes and two noncrossing chromosomes.

Double Crossover

Single crossovers are used to determine the distance between two linked genes, but do not tell you of their relative locations.
Double crossover events can be missed when only two traits are tracked.
These are like a positive and a negative i.e. the genes end up in the same place.
Double crossover events are used to determine the distance between three linked genes.
The genes must be heterozygous or two alleles to do this.

Three-Point Mapping

With linked heterozygotes (Aa, Bb, Cc) that all lie on the same chromosome, the double crossover can provide the most data about the relationship of these genes.
If the double crossover occurs between genes a and c then genes a and c will not change their position. If you track gene B as the allele that is changing, you'll notice that it had to be a double crossover effect.

Three-Point Mapping Criteria

The heterozygous parent must be heterozygous for all three genes under consideration
The phenotype classes must reflect the genotype of the gametes of the parents
You have to do a robust experiment and a large enough scale to be representative of all offspring. The larger, the better.

Triple Cross Outcomes

The one that is the most common is the non crossover event. It is almost impossible for all three alleles across all three locations to all be assorting independently.
The least common is the double crossover event. The more likely that genes remain as they are, the less likely there will be crossover in both locations for any given gene.
You should always have four outcomes

Double Crossover Event

To identify if there is a double crossover event, observe the phenotype that is least common
Because it is a double crossover event, look to see which allele changes places relative to the other two - that is the middle allele.
Therefore, when conducting triple point mapping, you have to look at how many instances each allele occurs.

Reviewing what was Discussed:

Noncrossover Events occur in the greatest proportion within the alleles
Double crossover event will occur as the smallest proportion
The allele that changed position, in the double crossover event of smallest proportion, is the middle allele.

Restriction Fragment Length Polymorphisms (RFLPs)

Restriction Fragment Length Polymorphisms (RFLPs).
Restriction enzymes cut DNA at specific sequences.
Different individuals may have different restriction sites due to polymorphisms.
After cutting DNA with restriction enzymes, you will separate the DNA by using gel electrophoresis (which separates the DNA by size).
There will be different sized bands for different sequences.
If you have two samples next to each other, they will look different if your ladder containing DNA's are of different sizes, or is missing.

Microsatellites and SNPs

Microsatellites are short, repetitive sequences found throughout the genome of variable lengths.
Single nucleotide polymorphisms (SNPs) are single base pair differences found throughout the genome.
SNPs are used by geneticists to identify and locate related genes, and to screen for diseases (e.g., cystic fibrosis, which is located on chromosome 7).
Cystic Fibrosis is a result of a bad SNP.