Molecular Biology and Genetics Notes Chapter 5 09/09/2016

Linkage, Recombination, and the Mapping of gene chromosomes

1. Gene Linkage and Recombination

A. When gene cross over it is a recombinant phenotype
B. Genes are linked together on the same chromosome usually assort together
C. Liked genes become separated by recombination
D. Syntenic gene – genes located on the same chromosome
I. Compare allele configurations in F2 to P generation
II. Deviation from 1:1:1:1 segregation indicates that genes are linked
E. Autosomal genes can also exhibit linkage
I. Detect linkage by generating a double heterozygote and crossing to homozygous
recessive
II. Crossing over will never exceed 50%
2. Recombination: A result of crossing-over during Meiosis
A. Frans Janssens – 1909 observed chiasmata at chromosomes during prophase of meiosis I.
B. T.H. Morgan – suggested chiasmata were sites of chromosome breakage and exchange
C. H. Creighton and B. McClintock (corn) and C. Stern (Drosophila) – 1932, direct evidence that
genetic recombination depends on reciprocal exchanged reciprocal exchange of
chromosomes
I. Physical markers were used to identify specific chromosomes
II. Genetic markers were used as points of reference for recombination
D. H. Sturtevant – proposed that recombination frequencies (RF) could be used as a measure of
physical distance between two linked genes.
I. 1%RF = 1 map unit (m.u.) = 1 centiMorgan (cM)
E. Recombination frequencies never exceed 50%
I. The RF of unlinked genes is 50% due to independent assortment
II. The RF of linked genes cannot exceed 50%
a. Meiosis without crossovers produce only parental chromosomes
b. Single and double crossovers produce a 1:1 parental to recombinant
chromosome ratio on average
F. Properties of linked vs unlinked genes
I. Linked Genes
a. Linked genes must be syntenic and sufficiently close together on the same
chromosome so that they do not assort independently
b. Parentals > Recombinants (RF<50%)
II. Unlinked genes
a. Occurs either when two genes are on different chromosomes or when they are
sufficiently far apart on the same chromosome that at least one crossover
occurs between them in every meiosis
b. Parental = Recombinants
3. Mapping: Locating Genes Along a Chromosome
A. Mapping genes by comparisons of two-point cross
I. Left to right orientation of map is arbitrary
 II. Most accurate maps obtained by summing many small intervening
B. Limit of 2 point crosses
I. Difficult to determine gene order if two genes are close together
C. Three point crosses provide faster and more accurate mapping
D. Interference: The number of double crossovers may be less than expected
I. Chromosomal interference – occurrence of crossover in one portion of a
chromosome interferes with crossover in an adjacent part of the chromosome
II. Not uniform between chromosomes or within a chromosome
III. Compare observed and expected frequencies of double crossovers (DCO)
IV. Coefficient of coincidence = observed DCO frequency/ expected DCO frequency
V. Interference = 1 – coefficient of coincidence
VI. If equal, there is no double crossing over = no interference
E. Calculation of interference in the three-point cross
I. Expected probability of double crossovers is the product of single crossover
frequencies in each interval
II. Expected /observed = Coefficient of Coincidence
F. Do genetic maps correlate with physical reality?
I. Order of genes revealed by genetic mapping corresponds to actual order genes
along the chromosome
II. Actual physical distance (amount of DNA) does not always show direct
correspondence to genetic distance
a. Double, triple, and more crossovers
b. 50% limit on observable recombination frequency
c. Recombination hotspots
4. The Chi-Square Test and Linkage Analysis
A. Applying the chi squared test
I. Calculate the chi- square
a. X2 = ∑ ((observed – expected)2/expected) = ∑((O-E)2 /E)
II. Consider degrees of freedom (df) in the experiment
a. Df = N -1 (where N is the number of classes)
III. Determine the p value using chi-square value and df
a. Probability that the deviation from expected numbers had occurrence by
chance
5. Tetrad Analysis and Fungi
A. Genetic analysis in fungi
I. Phenotype of haploid fungi is direct representation of their genotype
II. Mutations in haploid can affect appearance of cells and ability to grow under certain
conditions
a. His4 mutant; recessive, unable to grow in absence of histidine
b. HIS4; dominant, grows in presence or absence of histidine
c. Trp1; recessive, unable to grow in absence of tryptophan
d. TRP; dominant, grows in presence or absence of tryptophan
B. Meiosis can generate 3 kinds of tetrads:
I. Parental type - n
 II. Non parental ditype – 2n
III. Tetratype – 4n
C. Rules for tetrad analysis in ordered and unordered tetrads
I. In considering genes two at a time, assign tetrads as PD, NPD, or T
a. If PD>>NPD, the two genes are linked
b. If PD=NPD the two genes assort independently (unlinked)
II. For ordered tetrads only
a. The map distance between a gene and the centromere
D. Calculating recombination frequencies in tetrad analysis
I. RF = (NPD + ½ T)/ (total tetrads) x 100
6. Mitotic Recombination and Genetic Mosaics

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