Untitled Notes

Linkage & Gene Mapping

Eukaryotic genomes contain hundreds to thousands of genes.
Most species have at most a few dozen chromosomes.
Each chromosome is likely to carry many hundreds or even thousands of different genes.
This genetic arrangement raises questions about the relationship to Mendel’s law of independent assortment.

Independent assortment: Alleles of two different characters assort into gametes and are inherited independently.
Example:
- Parents: RRYY (round, yellow) and rryy (wrinkled, green) produce gametes RY and ry.
- Offspring from F₁ generation: RrYy will yield haploid gametes, leading to combinations in F₂ generation.
- Gametes: (1/4 RY, 1/4 Ry, 1/4 rY, 1/4 ry).
Linked assortment hypothesis: Alleles of two different characters are inherited together if they are located on the same chromosome.
In this case, the gametes produced will show no recombination, e.g., only RY or ry if genes are linked.

William Bateson and Reginald Punnett studied flower color (purple/red) and pollen shape (long/round).
Expectations of simple Mendelian inheritance resulted in a 9:3:3:1 ratio; their observed results deviated from this expectation, indicating lack of independent assortment.
Observed ratios included:
- Purple flowers, long pollen: 296 (expected 240)
- Purple flowers, round pollen: 19 (expected 80)
- Red flowers, long pollen: 27 (expected 80)
- Red flowers, round pollen: 85 (expected 27)

Mechanism: Crossing over occurs during meiosis and allows independent assortment of linked genes.
Crossing over leads to two gametes resembling the parent's chromosomes, and two with new combinations of alleles (recombinants).
Non-recombinant offspring inherit the same combination of alleles, while recombinant offspring result from crossing over.

Hypothesis of linked assortment implies no recombination, leading to gamete types like PL and pl.
Phenotypes produced will resemble parental traits closely, with no recombinant phenotypes.

Genes closer together on a chromosome are less likely to be separated during crossing over.
Statistical likelihood of crossing over decreases linearly with increasing distance between genes.
- Crossing over events are more probable between genes A and C than between A and B if B is in closer proximity to A.
Linkage groups: chromosomes where genes are physically linked and do not assort independently.
Crossing over can occur in multiple places on homologous chromosomes, leading to complexes of co-inheritance.

Thomas Hunt Morgan's studies on Drosophila (fruit flies) revealed linkage between traits such as body color, eye color, and wing length.
Gene linkage was supported via test crosses that showed a higher frequency of non-recombinant offspring than expected under independent assortment.

The chi-square test can determine if the observed ratio of offspring phenotypes is consistent with linkage.
Null hypothesis: The genes assort independently.
For example, using observed and expected phenotype ratios produces a chi-square value that reflects the correlation.

Recombination frequency indicates the distance between genes and helps in genetic mapping.
Formula for recombination frequency (distance in centiMorgans):
\text{Distance (cM)} = \frac{\text{Number of recombinant F2 offspring}}{\text{Total number of offspring in F2 cross}} \times 100
1% recombination frequency corresponds to 1 cM.

Map distances are additive but can be complicated by double crossovers, especially when calculating the distance among genes.
Genes can behave as unlinked at distances beyond 50 cM due to independent assortment or extreme distances between them.
Trihybrid crosses can further elucidate gene order and distances when analyzing multiple traits—showing intermediate ratios for single and double crossovers.

Parental cross: Use true-breeding strains differing in alleles.
F1 test cross: Cross heterozygotes with homozygous recessive to confirm offspring ratios.
Count phenotypes: Determine number of recombinant vs. non-recombinant offspring.
Calculate distance using recombination frequency: To create a genetic map with distances based on observed offspring.
Understand double crossovers: Account for all crossover events for accurate gene mapping.

Not all distances add up perfectly due to double crossovers, which lead to an underestimation of genetic distance.
Maximum detectable recombinant frequency is 50%, due to restrictions imposed by physical linkage on the same chromosome.
Unlinked genes (independent assortment) exhibit a 1:1:1:1 phenotype ratio in F2 crosses, highlighting practical applications in genetic studies and breeding.