Genetic Linkage: Gene Inheritance and Recombination

• Genes present on the same chromosome and inherited together are considered linked.
• Genes located on different chromosomes are not linked.
• This allows for independent assortment and a 9:3:3:1 inheritance pattern in a di-hybrid cross.
• Genes very close together on the same chromosome show complete linkage and cannot be separated by recombination during meiosis.
• Genes located far apart on the same chromosome show incomplete (partial) linkage because they are easily separated by recombination.

Genetic Linkage

• Genetic linkage refers to the tendency of alleles located close together on a chromosome to be inherited together during meiosis.
• Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover and are genetically linked.
• The closer two genes are on a chromosome, the less likely a swap is to occur between them and the more likely they are to be inherited together.
• William Bateson and Reginald Punnett completed a study in 1905 that determined the movement of alleles found on the same chromosome.
• The study used sweet peas, particularly flower color and pollen shape, and followed the inheritance pattern.
• A cross was performed using true-breeding purple/long (PPLL) and red/round (ppll) plants.
• The F1 generation was 100% purple/long (PpLl).
• Crossing two individuals from the F1 generation resulted in an F2 generation with four different phenotypes: purple/long, purple/round, red/long, and red/round.
• The alleles supported that they did not assort independently and therefore must be linked, and didn't follow the 9:3:3:1 pattern.
• Linkage refers to packaging genes onto chromosomes for organizing genes for their coordinated transmission from cell to cell (parent to offspring).

Types of Linkage

• Linkage is generally classified based on three criteria: crossing over, genes involved, and chromosomes involved.

Based on Crossing Over

• Depending on the presence or absence of new or non-parental combinations, linkage is classified into two types:

Complete Linkage

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

Incomplete Linkage

• Genes produce some percentage of non-parental combinations.
• Such genes are located distantly on the chromosome.
• It's due to accidental or occasional breakage of chromosomal segments during crossing over.

Based on Genes Involved

• Depending on whether all dominant or some dominant and some recessive alleles are linked, linkage can be categorized into:
• Coupling Phase: All dominant or all recessive alleles are present on the same chromosome.
• Repulsion Phase: Dominant alleles of some genes are linked with recessive alleles of other genes on the same chromosome.

Based on Chromosomes Involved

• Linkage can be categorized into:
• Autosomal Linkage: Genes located in autosomes (other than sex chromosomes) are linked.
• X-chromosomal Linkage: Genes located in sex chromosomes are linked.

Significance of Linkage

• Linkage does not permit breeders to bring desirable characters into one variety, making it difficult to combine traits in plants and animals.
• Linkage reduces the chance of recombination, helping maintain parental characteristics in organisms.
• Linked genes are not always inherited together as chromosomes exchange homologous genes during meiosis.

Crossing Over and Inheritance of Linked Genes

• Linked genes are separated by crossing over during prophase I of meiosis.
• If daughter cells are identical to parent cells then, no crossing over occurs.
• Crossing over causes genetic variation; daughter cells are not identical to parent cells.
• When crossing over occurs, linked genes become unlinked, creating four types of chromosomes (gametes).
• Proportions of gametes are unequal since crossing over doesn't occur in every cell during meiosis.

Crossing Over

• Genetic material recombination is a result of a random exchange of DNA between non-sister chromatids of homologous chromosomes.
• Prevalence of recombination is dependent on the distance between linked genes.

Factors Affecting Crossing Over

• Sex: There is a tendency to reduce crossing over in male mammals.
• Mutation: Mutation reduces crossing over.
• Temperature: High and low temperature variations increase the percentage of crossing over in certain parts of the chromosome.
• X-ray Effect: X-ray irradiations increase crossing over near the centromere.
• Age: Older age increases the rate of crossing over.

Significance of Crossing Over

• Crossing over produces new combinations of traits.
• Segments of homologous chromosomes are interchanged, providing the origin of new characters and genetic variations.
• Crossing over is critical in the field of breeding to improve plant and animal varieties.

Theories of Crossing Over

• Contact First Theory: Inner chromatids of homologous chromosomes undergoing crossing over touch each other first and then cross over.
• Breakage occurs at the point of contact, and broken segments reunite to form new combinations.
• Breakage-First Theory: Chromatids undergoing crossing over break into two without any crossing over.
• Then, broken segments reunite to form new combinations.

Types of Crossing Over

• Single Crossing Over: Only one chiasma is formed along the length of a chromosome pair.
• A chiasma is the point where two homologous non-sister chromatids exchange genetic material.
• Gametes formed are called single cross over gametes.
• Double Crossing Over: Two chiasmata are formed along the entire length of the chromosome leading to breakage and rejoin of chromatids at two points and gametes are called double cross over gametes.
• Multiple Crossing Over: More than two chiasmata are formed, thus crossing over occurs at more than two points on the same chromosome pair, and this is a rare phenomenon.

Interference and Coincidence

• The formation of one chiasma usually reduces the probability of another chiasma forming in an adjacent region of the chromosome.
• The chromatids have a physical inability to bend back upon themselves within certain minimum distances.
• This interference results in the observation of fewer double-crossover types than expected.
• Interference strength varies in different chromosome segments and is usually expressed as a coefficient of coincidence. Coefficient of coincidence is the ratio between the observed and expected double crossover.
• Coincidence is the compliment of interference where: Coincidence + Interference = 1.0

Difference between Linkage & Crossing Over

• Linkage is the tendency of genes on a chromosome to remain together and be passed on.
• Crossing Over is the exchange of genes or chromosomal parts to break the established linkage.
• Linkage brings more parental types, while crossing over produces recombination.
• Strength of linkage between two genes increases if they are closely placed on a chromosome.
• Frequency of crossing over between two genes decreases if they are closely placed.
• Linkage helps maintain a newly improved variety.
• Crossing over is the source of variation for producing new varieties.

Chromosome 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. 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.
• 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.
• T. H. Morgan and Alfred Sturtevant produced the first Drosophila gene map in 1913, and 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. The distance between genes is proportional to the frequency of recombination events.
• Recombination Frequency = Recombinant Progeny /Total Progeny
• 1% recombination = 1 map unit (m.u.)
• 1 map unit = 1 centimorgan (cM)
• Parental gametes maintain the original linkage of genes (alleles) in the chromosome.
• Recombinant gametes are those in which the original linkage is undone due to the exchange of chromosomal pieces via crossing over during meiosis.