Linkage & recombination mapping

Linked genes travel together

Each chromosome carries hundreds or thousands of genes. Genes that sit on the same chromosome are called linked genes, and they tend to go into gametes together, because they're physically part of the same DNA molecule.

That breaks Mendel's law of independent assortment, which holds for genes on different chromosomes (or very far apart on the same one). If genes A and B are on the same chromosome, a dihybrid won't make its four kinds of gametes in equal numbers. The combinations it inherited from its parents will be over-represented.

Crossing over breaks the link

Linked genes aren't locked together for good. In prophase I of meiosis, homologous chromosomes swap stretches of DNA by crossing over. If a crossover happens in the stretch between two genes, it creates chromatids with new combinations of their alleles.

Gametes carrying the same allele combinations as the chromosomes the parent inherited are parental types. Gametes with new combinations are recombinant types. In 1931, Harriet Creighton and Barbara McClintock showed in maize that recombinant offspring go hand in hand with a visible, physical exchange between chromosomes, confirming the idea.

Here's the key point. A crossover is more likely to land between two genes the further apart they are. Two genes right next to each other are almost never separated; two genes at opposite ends of a long chromosome are separated in most meioses.

Measuring distance with a test cross

To count recombinants, you need to see which gametes a parent made. The trick is a test cross: cross the heterozygote with a homozygous recessive. The recessive parent only contributes recessive alleles, so each offspring's phenotype directly shows you the gamete it got from the heterozygote.

1. 1Cross the dihybrid (for example AB/ab, meaning one chromosome carries A and B and the other a and b) with an ab/ab tester.
2. 2Sort the offspring into four classes by phenotype.
3. 3The two largest classes are the parental types; the two smallest are the recombinants.
4. 4Recombination frequency = recombinant offspring ÷ total offspring.
5. 5Convert to distance: a recombination frequency of 1% is defined as 1 map unit, also called 1 centimorgan (cM).

Morgan's lab did this with body colour (grey or black) and wing shape (normal or vestigial) in fruit flies. About 17% of the test-cross offspring were recombinant, putting the two genes about 17 map units apart.

Why recombination frequency tops out at 50%

A crossover involves only two of the four chromatids in a bivalent. So even if a crossover happens between two genes in every single meiosis, only half the resulting chromatids are recombinant: 50%.

Genes on different chromosomes also give 50% recombinants, because independent assortment makes all four gamete types equally likely. So a recombination frequency of about 50% means "behaves as unlinked". The genes might be on different chromosomes, or far apart on the same one. The usual way to tell is by mapping genes in between.

For genes far apart, two crossovers between them can put the original alleles back together, so some exchanges go uncounted. That's why recombination frequency underestimates long distances, and why maps are built by adding up short intervals.

Coupling and repulsion

Which types count as "parental" depends on how the alleles are arranged in the heterozygote. If the two dominant alleles are on one chromosome (AB/ab), the genes are in coupling (cis). If each chromosome has one dominant allele (Ab/aB), they are in repulsion (trans).

The same pair of genes, same distance apart, gives mirror-image results in the two cases. In coupling, AB and ab offspring are the common classes. In repulsion, Ab and aB are the common ones and AB and ab are the rare recombinants. So always work out the parental arrangement before labelling anything as recombinant.

Three-point crosses: order and interference

Mapping three genes at once, in a three-point test cross, gives you the gene order as well as the distances. A triple heterozygote test-crossed to a triple recessive gives eight classes of offspring, which come in pairs of reciprocal types.

• The largest pair is the parental types.
• The smallest pair is the double crossovers, which need one crossover in each of the two intervals at once.
• The two middle-sized pairs are single crossovers in one interval or the other.

A double crossover swaps only the middle gene relative to the two outer ones. So compare the double-crossover class to the parental class: the one gene that has switched partners is the gene in the middle.

If crossovers in the two intervals happened independently, the expected double-crossover frequency would be the two recombination frequencies multiplied. Usually fewer are seen, because one crossover tends to discourage another close by. The coefficient of coincidence is observed ÷ expected double crossovers, and interference = 1 − coefficient of coincidence. An interference of 1 means no double crossovers at all; 0 means crossovers are independent.

Key terms

Linked genes

Genes on the same chromosome that tend to be inherited together.

Parental / recombinant

Offspring with the allele combinations of the parent's chromosomes / with new combinations made by crossing over.

Recombination frequency

Recombinant offspring ÷ total offspring; at most 50%.

Map unit (centimorgan)

The distance giving 1% recombination between two genes.

Coupling / repulsion

Dominant alleles on the same chromosome (AB/ab) / on opposite chromosomes (Ab/aB).

Double crossover

A crossover in each of two adjacent intervals; the rarest class in a three-point cross.

Coefficient of coincidence / interference

Observed ÷ expected double crossovers / 1 minus that value.

Check yourself

Try answering in your head before you open each answer.

• 1.The recombination frequencies between three genes are: D–E 12%, E–F 7%, D–F 5%. What is the gene order?Show answerHide

  D – F – E. The two short distances add up to the long one (5 + 7 = 12), so F must lie between D and E.

• 2.Genes A and B are 8 cM apart. A heterozygote in repulsion (Ab/aB) is test-crossed to ab/ab. Predict the percentage of each offspring class.Show answerHide

  Ab and aB are the parental types: 46% each. AB and ab are the recombinants: 4% each, adding up to 8%.

• 3.A test cross gives 26% AB, 24% ab, 25% Ab and 25% aB. A classmate says the genes must be on different chromosomes. Is that the only possibility?Show answerHide

  No. The recombination frequency is about 50%, which only shows that the genes behave as unlinked. They could be on different chromosomes or far apart on the same one, where a crossover between them happens in nearly every meiosis. Mapping genes that lie between them would tell you which.