"Chromosome Mapping"

Recombination

Recombination rates of 50% can be achieved by genes that reside on different chromosomes simply by independent assortment.
However, genes that are far apart but on the same chromosome can produce similar results (if recombination occurs).
Please note that since crossing over does not occur in Drosophila males, even genes on opposite ends of a big chromosome are completely linked in the production of male gametes.

Recombination by crossing over
A recombinant frequency significantly less than 50% shows that the genes are linked.
A recombinant frequency of 50% generally means that the genes are unlinked on separate chromosomes.

Linkage symbolism

        pr       vg
        ----X-----
        pr⁺    vg⁺

As only (homogametic) females can have two X chromosomes, linkage of genes located on the X-chromosome are studied differently from autosomal genes.
Only females produce recombinant gametes with respect to X-linked genes.
Male offspring of these females (hemizygous for X-linked genes) will have phenotypes reflecting the female gametes.
Linkage maps demonstrate the physical relationship of genes on the same chromosome.
The percentage of recombinants of the alleles of two genes can be expressed as a genetic map.
Genetic maps depend upon the random crossing over between chromatids at meiosis and the correlation of recombination frequency and distance between genes on a chromosome.
One genetic map unit (or centimorgan after Thomas Hunt Morgan the first Drosophila geneticist) is the distance where the recombination frequency is 0.01 or 1%.

Recombination between linked genes can be used to map their distance apart on the chromosome.
The unit of mapping (1 map unit:1m.u.) is defined as a recombinant frequency of 1 percent.
The location on the map ( and chromosome) where a gene is located is the gene locus (plural of locus is loci).

                pr                 11.0           vg
        ------+ --------------------------+------

Conversely, given a genetic distance, the frequency of progeny classes can be predicted.
From pr vg/ pr⁺ vg⁺ females crossed to pr vg/pr vg males, 5.5% of the offspring will be purple recombinants and 5.5% will be vestigial recombinants for a total of 11% total recombinants.
 

Three point test cross

        v  cv⁺  ct⁺         580
        v⁺  cv  ct           592
        v  cv  ct⁺            45
        v⁺  cv⁺  ct          40
        v  cv  ct              89
        v⁺  cv⁺  ct⁺        94
        v  cv⁺  ct             3
        v⁺  cv  ct⁺           5

        total              1448

Note that the double crossover progeny must be including in totals of recombinants between both genes.
Double crossover are the rarest occurrence and can be used to figure out the order of genes when compared to the parentals.
Leads to a genetic map of Drosophila and tomatoes.

                        v                                    cv                 ct
                ------+ --------------------------+--------------+------
                                          13.2                       6.4
 

Interference
Double cross overs do happen.  These are not always independent.
Interference is the phenomenom that describes the influence of crossing over between one pair of genes and the adjacent region.
The coefficient of coincidence (c.o.c.) is the observed frequency of double recombinants divided by the expected frequency of double recombinants.

Interference is equal to 1- c.o.c.

1. Calculate recombinat frequencies for each pair of genes
      v-cv =18.5%
      cv-ct = 6.4%
      ct-v =13.2%
2. Represent linkage relations in a linkage map

                        v                                    cv                 ct
                ------+ --------------------------+--------------+------
                                          13.2                       6.4
 

3.  Determine the double recombinant classes
4.  Calculate the frequency and number of expected double recombinants
    Expected frequency = 0.132 X 0.064 =0.0084
    Expected number = 0.0084 X 1448 = 12
Calculate interference
    the observed frequency of double recombinants = 8
    the expected frequency of double recombinants = 12

Interference (I) = 1-(8/12) = 0.33 or 33%

Mapping with molecular markers
Molecular markers are DNA variations that are different with a population by which chromosomes can be analyzed.
This allows molecular mapping of the chromosomes.

Use of restriction fragment length polymorphisms in mapping
Restriction enzymes cut DNA at particular sequences.
If the restriction sequence is present on some chromosomes but not others due to a nucleotide polymorphism (a normally variable site).
In Southern Analysis, this gives restriction fragment length polymorphism (RFLP).

A heterozygote for a site as follows Ö
        ----------+--------------------------+----------
        ----------+-----------------+--------+----------
will  give three bands (1, 2, 3 kb pieces).
While the homozygotes will produce either one band (3 kb band)
        ----------+--------------------------+----------
        ----------+--------------------------+----------

or two bands (1 and 2 kb pieces).

        ----------+-----------------+--------+----------
        ----------+-----------------+--------+----------

Use of polymorphism of variable number tandem repeats (VNTRs) can be used in mapping in a manner similar to the RFLP analysis.
Correlating molecular mapping with gene mapping to construct chromosome maps.
Linkage mapping by recombination in humans has lead to mapping the chromosomes.