Two loci are physically linked when they lie on the same chromosome. Because they travel on the same chromosome copy through meiosis, nearby linked loci tend to be transmitted together rather than assorting independently.

In classical genetic analysis, loci show detectable genetic linkage when parental allele combinations occur more frequently than recombinant combinations, so their recombination frequency is below $50%$. Two loci can be physically on the same chromosome yet be so far apart that they behave as if unlinked in a two-locus cross.

Consider a diploid individual heterozygous at two loci, $A/a$ and $B/b$. Writing only the genotype

$$AaBb$$

is not enough to specify which alleles lie together on the same homologous chromosome.

There are two important arrangements.

Coupling phase

If one homolog carries $A$ together with $B$ and the other carries $a$ together with $b$, the arrangement is

$$AB/ab.$$

This is called coupling phase or cis phase.

The allele combinations already present on the two homologs are

$$AB\quad\text{and}\quad ab.$$

Repulsion phase

If one homolog carries $A$ with $b$ and the other carries $a$ with $B$, the arrangement is

$$Ab/aB.$$

This is called repulsion phase or trans phase.

The corresponding chromosome combinations are now

$$Ab\quad\text{and}\quad aB.$$

Phase is a chromosome-level property

The arrangements

$$AB/ab\qquad\text{and}\qquad Ab/aB$$

both contain one $A$, one $a$, one $B$ and one $b$ allele. They therefore have the same unordered genotype $AaBb$, but they can produce different gamete frequencies because the alleles begin on different physical chromosome copies.

This is why linked-locus notation often uses a slash to separate homologs.

Parental and recombinant combinations

For a given heterozygote, the allele combinations already present on its homologs are called parental or nonrecombinant combinations. The alternative combinations are recombinant combinations.

For

$$AB/ab,$$

parental combinations are $AB$ and $ab$, while recombinant combinations are $Ab$ and $aB$.

For

$$Ab/aB,$$

parental combinations are $Ab$ and $aB$, while recombinant combinations are $AB$ and $ab$.

The words parental and recombinant therefore depend on the chromosome phase of the heterozygote; they are not fixed labels attached permanently to a particular allele combination.

Linkage changes the inheritance question from merely "which alleles are present?" to also asking which alleles are physically carried together on each homologous chromosome, and how often recombination separates them?