Linkage and Recombination

Gene interaction quizzes should be graded and returned this evening.
A quiz is due on Sunday, covering three-point mapping. It is recommended to attempt it after Friday's lecture, especially if you're not comfortable with three-point mapping.
An announcement will be sent out, focusing on differentiating independent assortment, incomplete linkage, and complete linkage, which is a common area of confusion for students. This will take the form of a practice problem with a detailed explanation, posted on Monday.

Linkage: Two or more genes are inherited together because they are located on the same chromosome. This is represented in shorthand notation. For example, a genotype like $AaBb$ doesn't indicate linkage, whereas $A<br /> B / a<br /> b$ (or a similar notation with lines indicating the chromosome) does.

Genes are very close together on the same chromosome, such that they are always inherited together. For instance, if genes $A$ and $B$ are completely linked, inheriting $A$ always means inheriting $B$ .
Example: A cross between two pure-breeding individuals (e.g., $CCSS$ and $ccss$ ) results in an $F_1$ heterozygote ( $CcSs$ ). A test cross (back to a homozygous recessive, $ccss$ ) will only produce offspring with the parental phenotypes due to the complete linkage.
With complete linkage, the offspring will only display the parental phenotypes because the alleles travel together as a single unit.
This can be conceptualized as a simple Mendelian cross ( $Aa <br /> eq aa$ ), since the linked genes behave as a single locus.

Morgan's experiments with fruit flies revealed different types of linkage.
Cross: A wild-type fly ( $b^+bg^+$ ) is crossed with a mutant fly ( $bb$ $bg^+bg^+$ , normal color, vestigial wings). Note that the notation "\plus " indicates wild-type alleles.
Notation: Alleles on the same chromosome are written together (e.g., \plus b \plus bg or $b b$ $bg bg$ ), and are always read vertically, not horizontally.
The $F_1$ generation is heterozygous (\plus b \plus bg / b bg), inheriting a normal allele from one parent and a mutant allele from the other.
Test Cross: The heterozygous $F_1$ is test crossed to visualize linkage.
Independent Assortment: If genes assorted independently, the dihybrid cross (\plus b \plus bg
eq bbgg) would result in a 1:1:1:1 ratio of parental and recombinant phenotypes. Recombinants are offspring that combine traits differently from the parents (e.g., wild-type for one trait and mutant for the other).
Complete Linkage: If the genes are completely linked, the notation indicates they are on the same chromosome (\plus b \plus bg / b bg). In the cis (coupled) configuration (wild-type alleles on the same chromosome), only parental phenotypes are observed. In the trans (repulsion) configuration (a wild-type and a mutant allele on each chromosome), only recombinant phenotypes are observed.

The actual cross yielded both parental and recombinant phenotypes, but not in a 1:1:1:1 ratio. This indicates incomplete linkage.
Incomplete Linkage: All four possible phenotypes are observed, but not in a 1:1:1:1 ratio.
Configuration: The configuration of genes (cis or trans) can be inferred from the offspring. Higher proportion of parentals indicates cis configuration, and higher proportion of recombinants suggests trans configuration.
Recombination Frequency: Calculated as the number of recombinants divided by the total number of progeny. For example, with 900 parental and 200 recombinant offspring, the recombination frequency is $(200 + 200) / (900 + 900 + 200 + 200)$ , which approximates to 17.3%.
This means that in approximately 17.3% of the time, the cross will result in recombinant offspring.
To determine the proportion of each recombinant class, divide the total recombinant percentage by two (since there are two recombinant phenotypes).
The parental percentage is calculated by subtracting the recombinant percentage from 100%.

Recombination is the exchange of genetic information between non-sister chromatids during meiosis.
Crossover between sister chromatids has no effect because they're genetically identical.
During prophase I or prophase II of meiosis, homologous chromosomes line up, and breaks can occur, leading to the exchange of genetic information.
Chiasmata: Physical points of contact between non-sister chromatids where crossing over occurs.
Recombination results from crossing over, generating new combinations of alleles.
Incomplete linkage follows the same principles, beginning with pure-breeding individuals and generating an $F_1$ heterozygote, followed by a test cross. The key difference is that crossover occurs a certain percentage of the time, leading to some recombinant offspring.
Visualizing each kernel of corn as an individual offspring helps understand incomplete linkage on a large scale.
Even with crossover, parental combinations are still possible.
In a cis configuration, after replication and meiosis, two out of the four gametes will be normal, while the other two will account for recombination which explains why the number of recombinants would be lower than the number of parentals.

The distance between genes affects recombination frequency. Closer genes have lower recombination frequencies, while genes farther apart have higher recombination frequencies.
Limited space between closely-linked genes restricts the possibility of breakage or potential recombination.
Alfred Sturtevant, a student of Hunt Morgan, realized that recombination frequencies could be used to map gene distances on chromosomes.
The distance from gene $A$ to $C$ can be determined by adding the distances from $A$ to $B$ and $B$ to $C$ , where B is an intermediate gene.
Recombination frequency is proportional to the distance between genes, enabling the construction of genetic maps.
Sturtevant mapped the fruit fly genome by analyzing recombination frequencies between various genes.

Recombination frequency reflects the distance between genes on a chromosome.
18% recombination = 18 centimorgans.
Centimorgans (cM) are units of genetic distance, named after Hunt Morgan.
Synonymous terms: recombination frequency, centimorgans, and map units all refer to the same concept of genetic distance.
Modern mapping techniques use DNA sequencing and computer analysis for genome mapping, where the location of genes can be directly observed.

Recombination frequency of 17.3% indicates incomplete linkage. However, a 1:1:1:1 ratio of offspring (50% recombinants) indicates independent assortment.
Parental combinations are $AABB$ and $aabb$ , while recombinants are $Aabb and aaBb$ .
Independent assortment has a recombination frequency of 50%.
A recombination frequency of 50% is the cutoff for linkage; it means the genes are either on different chromosomes or far apart on the same chromosome.
A recombination frequency of 49.9% is still considered independent assortment, not incomplete linkage.
Recombination frequencies cannot exceed 50%.