Linkage



Gregor Mendel analyzed the pattern of inheritance of seven pairs of contrasting traits in the domestic pea plant. He did this by cross-breeding dihybrids; that is, plants that were heterozygous for the alleles controlling two different traits.

Example
Producing dihybrids (F1)
He mated a variety that was pure-breeding (hence homozygous) for round (RR), yellow (YY) seeds with one that was pure-breeding for wrinkled (rr), green (yy) seeds. All the offspring (F1) produced from this mating were dihybrids; that is, heterozygous for each pair of alleles (RrYy). Furthermore, all the seeds were round and yellow, showing that the genes for round and yellow are dominant.









Mating the dihybrids to produce an F2 generation
Mendel then crossed these dihybrids. If it is inevitable that round seeds must always be yellow and wrinkled seeds must be green, then he would have expected that this would produce a typical monohybrid cross: 75% round-yellow; 25% wrinkled-green. But, in fact, his mating generated seeds that showed all possible combinations of the color and texture traits.

* 9/16 of the offspring were round-yellow
* 3/16 were round-green
* 3/16 were wrinkled-yellow, and
* 1/16 were wrinkled-green

Finding in every case that each of his seven traits was inherited independently of the others, he formed his "second rule" the Rule of Independent Assortment:

The inheritance of one pair of factors (genes) is independent of the inheritance of the other pair.
Today we know that this rule holds only if two conditions are met:

* the genes are on separate chromosomes or
* the genes are widely separated on the same chromosome.

Mendel was lucky in that every pair of genes he studied met one requirement or the other. The table shows the chromosome assignments of the seven pairs of alleles that Mendel studied. Although all of these genes showed independent assortment, several were, in fact, syntenic with three loci occurring on chromosome 4 and two on chromosome 1. However, the distance separating the syntenic loci was sufficiently great that the genes were inherited as though they were on separate chromosomes.

Trait ....... Phenotype .........Alleles ....... Chromosome
Seed form...... round-wrinkled..... R-r...... 7
Seed color ....... yellow-green...... I-i .....1
Pod color ......... green-yellow ...... Gp-gp ....5
Pod texture....... smooth-wrinkled..... V-v .....4
Flower color ...... purple-white....... A-a..... 1
Flower location ......axial-terminal .....Fa-fa..... 4
Plant height........... tall-dwarf ..........Le-le..... 4

With the rebirth of genetics in the 20th century, it quickly became apparent that Mendel's second rule does not apply to many matings of dihybrids. In many cases, two alleles inherited from one parent show a strong tendency to stay together as do those from the other parent. This phenomenon is called linkage.
An example of linkage
Start with two different strains of corn (maize).

* one that is homozygous for two traits
o yellow kernels (C,C) which are filled with endosperm causing the kernels to be
o smooth (Sh,Sh).
* a second that is homozygous for
o colorless kernels (c,c) that are wrinkled because their endosperm is
o shrunken (sh,sh)

When the pollen of the first strain is dusted on the silks of the second (or vice versa), the kernels produced (F1) are all yellow and smooth. So the alleles for yellow color (C) and smoothness (Sh) are dominant over those for colorlessness (c) and shrunken endosperm (sh).


To simplify the analysis, mate the dihybrid with a homozygous recessive strain (ccshsh). Such a mating is called a test cross because it exposes the genotype of all the gametes of the strain being evaluated.

According to Mendel's second rule, the genes determining color of the endosperm should be inherited independently of the genes determining texture. The F1 should thus produce gametes in approximately equal numbers.

* CSh, as inherited from one parent.
* csh, as inherited from the other parent
* Csh, a recombinant
* cSh, the other recombinant.

All the gametes produced by the doubly homozygous recessives would be csh.

If the inheritance of these genes observes Mendel's second rule; i.e., shows independent assortment, union of these gametes should produce approximately equal numbers of the four phenotypes. But as the chart shows, there is instead a strong tendency for the parental alleles to stay together. It occurs because the two loci are relatively close together on the same chromosome. Only 3.6% of the gametes contain a recombinant chromosome.









During prophase I of meiosis, pairs of duplicated homologous chromosomes unite in synapsis and then nonsister chromatids exchange segments during crossing over. It is crossing over that produces the recombinant gametes. In this case, whenever a crossover occurs between the locus for kernel color and that for kernel texture, the original combination of alleles (CSh and csh) is broken up and a chromosome containing Csh and one containing cSh will be produced.
Chromosome Maps

The percentage of recombinants formed by F1 individuals can range from a fraction of 1% up to the 50% always seen with gene loci on separate chromosomes (independent assortment). The higher the percentage of recombinants for a pair of traits, the greater the distance separating the two loci. In fact, the percent of recombinants is arbitrarily chosen as the distance in centimorgans (cM), named for the pioneering geneticist Thomas Hunt Morgan. In our case, the c and sh loci are said to be 2.8 cM apart.
The procedure can be continued with another locus on the same chromosome.




Example

Test crossing a corn plant that is dihybrid for the C,c alleles and the alleles for bronze color (Bz, bz) produces 4.6% recombinants. So these two loci are 4.6 cM apart. However, is the bz locus on the same side of c as sh or is it on the other side?

The answer can be found by test crossing the dihybrid Shsh, Bzbz. If the percentage of recombinants is less than 4.6%, then bz must be on the same side of locus c as locus sh. If greater than 4.6%, it must be on the other side.









Mapping by linkage analysis is best done with loci that are relatively close together; that is, within a few centimorgans of each other. Why? Because as the distance between two loci increases, the probability of a second crossover occurring between them also increases.