Genetic Linkage and Recombination

• Genes present on the same chromosome tend to be inherited together and are referred to as "linked".
• If two genes are on the same chromosome, they won't sort independently and won't follow Mendelian inheritance.
• In a di-hybrid cross, genes on different chromosomes allow independent assortment with an inheritance pattern of 9:3:3:1.
• Genes very close together on the same chromosome may exhibit complete linkage

Incomplete Linkage

• Genes that are located far apart on the same chromosome typically show incomplete (partial) linkage
• Recombination easily separates these genes.

Genetic Linkage

• The propensity of alleles located near each other on a chromosome is genetic linkage
• Genes with close loci are less likely to be separated onto different chromatids during crossover.

Discovery of Genetic Linkage

• William Bateson and Reginald Punnett studied the movement of alleles on the same chromosome in 1905.
• They followed the inheritance pattern of flower color and pollen shape in sweet peas.

Bateson and Punnett Experiment

• Purple flower color (P) is dominant to red (p); long pollen shape (L) is dominant to round (l).
• Researchers crossed true-breeding purple/long (PPLL) and red/round (ppll) plants.
• The F1 generation was 100% purple/long (PpLl).
• Crossing F1 individuals resulted in an F2 generation with four phenotypes: purple/long, purple/round, red/long, and red/round.
• Alleles did not assort independently, and the 9:3:3:1 pattern was not followed.
• The alleles responsible for these traits were linked.

Why Linkage?

• Linkage is how chromosomes are packaged with genes on them
• Chromosomes (and therefore linkage) allow organizing genes for their safe coordinated transmission from cell to cell (parent to offspring)

Types of Linkage:

• Crossing over type
• Genes involved type
• Chromosomes involved type

Based on Crossing Over

• Linkage can be complete or incomplete depending on whether new combinations or non-parental combinations are present or absent.

Complete Linkage

• Two or more characters are inherited together in two or more generations in parental combinations
• These do not produce non-parental combinations.
• Genes showing complete linkage are closely located in the same chromosome.

Incomplete Linkage

• Genes exhibit this characteristic when they produce some percentage pf non-parental combinations
• These genes are located distantly on the chromosome and happens because of chromosomal segments breaking during crossing over.

Based on Genes

• Linkage is placed into coupling and repulsion phases
• This depends on whether several dominant or some dominant and some recessive alleles are linked together.

Coupling phase

• All dominant alleles are present on the same chromosome.
• All recessive alleles are present on same chromosome.

Repulsion Phase

• Dominant alleles of some genes are linked with recessive alleles of the other genes on the same chromosome

Based on Chromosomes

• Linkage is categorized based on gene location on the chromosomes: autosomal or X-chromosomal.

Autosomal Linkage

• Genes located in autosomes (not sex chromosomes) are linked.

X-chromosomal Linkage

• Genes located in sex chromosomes are linked.

Significance of Linkage

• For breeders it is difficult to combine desired characters in one variety if there is linkage of these traits
• Maintains parental characteristics together by reducing likelihood of recombination of genes

Crossing Over and Inheritance

• Linked genes do not stay linked all the time
• Genetic linkages can be separated by crossing over during prophase I of meiosis.
• Genetic variation results from crossing over in meiosis

Crossing Over

• Genes previously linked become unlinked during crossing over generating four different types of chromosomes, or gametes.
• Unequal quantities occur because crossing over isn't constant during meiosis.
• Crossing over is a random DNA exchange between non-sister chromatids of homologous chromosomes.
• It results in the recombination of the genetic material.

Recombination Prevalence

• The frequency of recombination depends on the distance separating connected genes.

Factors Affecting Crossing Over

• Sex: a reduction of crossing over in male mammals
• Mutation: Mutation reduces crossing over
• Temperature: increase percentage of crossing over w variations in temperature
• X-ray Effect: Increase crossing over with X-ray irradiations near the centromere
• Age: increase rate of crossing over with older age

Significance of Crossing Over

• Generates new character combinations.
• By interchanging homologous chromosome segments, segments produce new characters and heritable variations
• Enhances plant and animal types in breeding.

Theories of Crossing Over

Contact First Theory

• The inner two chromatids of homologous chromosomes that go through crossing over come into contact before crossing over.
• Breakage occurs at the point of contact.
• Segments unite again to form new combinations.

Breakage-First Theory

• Chromatids first break into two during the crossing over
• After broken segments reunite to form new combinations

Types of Crossing Over

Single Crossing Over

• Here, only one chiasma forms, which is the point where two non-sister chromatids swap material
• Gametes are called single cross over gametes.

Double Crossing Over

• At two sites, two chiasmata develops across the length of the chromosome and breaks
• Gametes produced are called double cross over gametes.

Multiple Crossing Over

• More than two chiasmata is made
• Crossing over that spreads across more than two locations on the same chromosome pair
• This is a rare occurrence.

Interference and Coincidence

• Having one chiasma lowers the likelihood of another forming nearby in many higher creatures
• A coefficient of coincidence is how the strength is expressed.
• It is the ratio between the observed and expect double crossover
• Coincidence + interference = 1.0

Differences Between Linkage & Crossing Over

• Linkage has a tendency of genes on a chromosome to remain together and passed as such in next generation whereas crossing over is an exchange of genes or chromosomal parts to break established linkage and formation of new linkage
• Linkage brings more parental types and crossing over produces recombination
• Strength of linkage increases if genes are closely placed where as frequency of crossing over decreases if they are closely placed
• New improved variety are maintained in linkage while it is the source of variation for producing new varieties with crossing over

Chromosome Mapping

• Mapping the location of each gene helps identify and study them
• Genes close to each other are less likely to crossover
• Percentage of gametes helps measure how far apart two genes are
• A recombination map unit is called a centimorgan (cM)
• It is equal to a crossing over between 2 genes in 1% of the gametes.
• The distance between genes is proportional to the frequency of recombination events
• Formula: Recombination Frequency = Recombinant progeny / Total progeny

Parental Gametes

• These maintain the original linkage of genes (alleles) in the chromosome.

Recombinant Gametes

• Original linkage is undone due to exchange of chromosomal pieces via crossing over during meiosis.