Genes Linked on Chromosomes

• Sutton stated in 1903 that there exist more "unit factors" than chromosomes.
• Genes can segregate as if they are linked, and as if they are also part of the chromosome so they are then inherited as a single unit.
• Synapsed chromosomes exchange segments reciprocally during Meiosis I Prophase I, which reshuffles alleles between homologs.
• The frequency of crossing over between any two loci on a single chromosome is proportional to the distance between them (interlocus distance).

Genes Linked on the Same Chromosome Segregate Together

• Genes assort independently when they are on different chromosomes but show linkage when on the same chromosome.
• Figure 7-1 contrasts the meiotic consequences of independent assortment, linkage without crossing over, and linkage with crossing over.
• No linkage is exhibited with independent assortment of two pairs of chromosomes, with each chromosome containing one heterozygous gene pair.
• Four genetically different gametes, each containing a different combination of alleles, are formed in equal proportions.
• No crossing over occurs, and only two genetically different gametes are produced in genes linked on the same chromosome which is complete linkage and produces only parental or noncrossover gametes in equal proportions.
• Crossover between two linked genes involves two nonsister chromatids and generates two new allele combinations called recombinant or crossover gametes.
• Complete linkage is when there is no crossing over between two genes and produces parental (non-crossover) gametes.
• Crossing over occurs between two nonsister chromatids, generating both parental and recombinant (crossover) gametes.
• The number of recombinants approaches but doesn't exceed 50% when the loci of the two linked genes are far apart.
• Two parental and two recombinant gametes result when recombination approaches 50%.

Linkage Ratio and Groups

• Complete linkage between two genes close in proximity causes a unique F2 phenotypic ratio, which is the linkage ratio
• Genes on the same chromosome are part of a linkage group.
• The number of linkage groups corresponds to the haploid number of chromosomes.

Crossing Over and Mapping

• The percentage of offspring resulting from recombinant gametes is variable and depends on the distance between the two genes on the chromosome.
• Studies with Drosophila show that synapsed chromosomes in meiosis wrap around each other to create chiasmata, X-shaped intersections and points of genetic exchange.
• Exchanges can lead to recombinant gametes.
• Linked genes exist in a linear order along the chromosome, and the variable amount of exchange occurs between any two genes during gamete formation.
• Two genes located relatively close to each other along a chromosome are less likely to have a chiasma form between them, and crossing over is less likely to occur.

Sturtevant and Mapping

• The recombination frequencies between linked genes are additive, and the frequency of exchange is an estimate of the relative distance between two genes along the chromosome
• Yellow and white genes are close to each other (0.5%)
• White-miniature (34.5%) and yellow-miniature (35.4%) are much farther apart from miniature
• White is located between the yellow and miniature genes.
• One map unit (mu) or centimorgans (cM) is 1 percent recombination between two genes on a chromosome.
• Figure 7-4 shows a chromosome map of three genes on the X chromosome of Drosophila.
• Research has firmly established the chromosomal theory that chromosomes contain genes in linear order and are the equivalent of Mendel's unit factors.

Single Crossover

• The more apart two loci are on a chromosome, the more likely a random crossover is happen.
• A single crossover (SCO) between two nonsister chromatids alters the linkage between two genes if the crossover occurs between those two genes.
• A single exchange between two non-sister chromatids in tetrad stage produces two noncrossover (parental) and two crossover (recombinant) gametes.

Determining the Gene Sequence during Mapping Requires the Analysis of Multiple Crossovers

• Single crossover is used to determine distance between two linked genes.
• Double crossover involves double exchanges of genetic material. -Double crossover is used to determine distance between three linked genes.
• Double crossover genes must be heterozygous for two alleles.

Multiple Crossovers

• Double exchanges of genetic material result from double crossovers (DCOs) and can determine the order of three genes on the chromosome (Figure 7-7).
• To study double exchanges, three pairs of genes must be investigated, each heterozygous for two alleles.
• The mathematical probability of two independent events occurring simultaneously is equal to the product of the individual probabilities (product law).
• The expected frequency of double-crossover gametes is much lower than that of either single-crossover gamete class.
• If four or five genes are mapped, even fewer triple and quadruple crossovers can be expected.
• If crossover gametes resulting from single exchanges are recovered 20% of the time (p= 0.20) between A and B and 30% of the time (p= 0.30) between B and C, the probability of recovering a double crossover gamete arising from 2 exchanges (between A and B, and between B and C) is predicted to be (0.20)(0.30)= 0.06 or 6%.

Three-Point Mapping in Drosophila

• 3 criteria that must be met to perform a successful mapping cross between 3 genes:
  • Parent must be heterozygous for all three genes under consideration.
  • Phenotypic class must reflect genotype of gametes of parents.
  • Sufficient number of offspring must be produced for representative sample.
• In three-point mapping, the parent must be heterozygous for all three genes under consideration.
• The noncrossover F₂ phenotypes occur in the greatest proportion of offspring.
• The double-crossover phenotypes occur in the smallest proportion.
• Because the F₂ phenotypes complement each other (i.e., one is wild type and the other is mutant for all three genes), they are called reciprocal classes of phenotypes.
• The distance between two genes in a three-point cross is equal to the percentage of all detectable exchanges occurring between them and includes all single and double crossovers.
• One first determines the arrangement of alleles on the homologs of the heterozygote yielding the gametes by locating the reciprocal noncrossover phenotypes.
• Test each of three possible orders to determine which yields the observed double-crossover phenotypes—the one that does so represents the correct order

Solving an Autosomal Mapping Problem

• An example of a three-point cross and mapping of the three linked genes involved is shown in Figures 7-10 and 7-11
• The experimental cross with corn still needs to meet the three basic criteria for Drosophila:
• One parent must be heterozygous of all traits studied.
• The genotypes must be apparent from the phenotype.
• A sufficient sample size is needed.

As the Distance between Two Genes Increases, Mapping Estimates Become More Inaccurate

• The expected frequency of multiple exchanges between two genes can be predicted from the distance between them.
• The farther apart two genes are, the greater the probability that undetected crossovers will occur.
  • The degree of inaccuracy increases as the distance between them increases (Figure 7-12(b)).
  • The most accurate maps are constructed from closely linked genes.

Interference and the Coefficient of Coincidence

• Interference reduces the expected number of multiple crossovers.
• A crossover event in one region of the chromosome inhibits a second event nearby.
• The coefficient of coincidence is calculated to quantify the differences resulting from interference.
• The coefficient of coincidence (C) is the observed number of DCOs divided by the expected number of DCOs.
• Interference can be quantified by the equation I = 1 – C
• DCOexp= (0.223) X (0.434) = 0.097= 9.7%
• Observed DCO is less than the expected number of DCOs.
• In the maize, only 7.8% DCOs are observed when 9.7% are expected
• C = 0.078/0.097= 0.804;
• Interference= 1- 0.804= 0.196 (19.6% fewer DCOs occurred than expected).

Positive and Negative Interference

• Complete interference is when no double crossovers occur.
• Positive interference are fewer double-crossover events than expected occur, then I is a positive number.
• Negative interference are more double-crossover events than expected occur and I is a negative number.
• Positive interference occurs when two genes are close together.
• Accuracy of mapping is high when two genes are close together.
• Accuracy of mapping decreases as the distance between increases with interfering decreasing.

Chromosome Mapping Uses DNA Markers and Annotated Computer Databases

• DNA markers are short segments of DNA whose sequence and location are known (can be used to identify individuals or species) as useful landmarks for mapping purposes
• Restriction fragment length polymorphisms (RFLPs) and microsatellites (STRs) are useful as well as single nucleotide polymorphisms (SNPs) are DNA markers
• (RFLPs) are polymorphic sites generated when specific DNA sequences are recognized and cut by restriction enzymes
• Microsatellites, short tandem repeats (STRs) are short repetitive sequences that are found throughout the genome and vary in the number of repeats at any given site
• Highly variables among individuals
• These variations help give geneticists the ability to identify and locate related genes
• An early example of a gene located using DNA markers is cystic fibrosis located on Chromosome 7 on the q arm
• Several other genes have been located for: -Type I and Type 2 diabetes, Crohn's disease, hypertension, coronary artery disease, bipolar disorder, and rheumatic arthritis
• The Human Genome Project databases make it possible to create a physical map.

Other Aspects of Genetic Exchange

• Crossing over is significant because it generates genetic variation in gametes and subsequently in offspring.
• Mapping in maize using cytological markers established that crossing over involves a physical exchange of chromosome regions.

Sister Chromatid Exchanges

• Sister chromatid exchanges (SCEs) occur during mitosis but do not produce new allelic combinations.
• Sister chromatids involved in mitotic exchanges are sometimes called harlequin chromosomes because of their patchlike appearance when stained and viewed under a microscope
• The significance of SCEs is still uncertain, but it has been observed that agents that induce chromosome damage increase the frequency of SCEs like:
  • Viruses,
  • X rays
  • UV light
  • Chemical mutagens

Did Mendel Encounter Linkage?

• Mendel worked with three genes in chromosome 4, two genes in chromosome 1, and one gene each in chromosomes 5 and 7.
• The genes are so far apart that linkage is not detected.
• Mendel did not run into the complications of linkage and did not avoid it by choosing one gene from each chromosome