What Is a Cis Map in Genetic Mapping?

A genetic map illustrates the relative locations of genes on a chromosome. A specific type is the “cis map,” which is derived from a genetic cross where the dominant versions of linked genes are on one chromosome of a pair, and the recessive versions are on the other. This configuration allows for tracking gene inheritance and calculating the distances between them.

The Principle of Genetic Linkage and Recombination

Genes on the same chromosome are physically connected and tend to be inherited together, a phenomenon called genetic linkage. This means the combination of alleles on a parental chromosome is often passed down as a single unit. For example, if a chromosome carries dominant alleles for both tall height and purple flowers, these traits will likely appear together in the next generation.

This physical association can be disrupted by genetic recombination during meiosis. In this process, homologous chromosomes exchange DNA segments in an event called crossing over. This exchange separates previously linked genes, creating new allele combinations on the chromosomes passed to gametes.

The likelihood of a crossover between two genes is directly related to the physical distance separating them. Genes that are close together have a low probability of being separated and are considered tightly linked. Conversely, genes far apart are more likely to be separated by a crossover. This proportional relationship between distance and recombination frequency is the principle that allows for creating genetic maps.

Differentiating Cis and Trans Arrangements

The arrangement of alleles on homologous chromosomes in a heterozygous individual influences the outcomes of genetic crosses. There are two configurations: the cis arrangement and the trans arrangement.

The cis arrangement, or coupling phase, is when dominant alleles for two genes are on the same chromosome, and the recessive alleles are on the homologous chromosome. This is represented as (AB/ab), where one chromosome has ‘A’ and ‘B’ and the other has ‘a’ and ‘b’. This setup results from a cross between two homozygous parents, one dominant for both traits (AABB) and one recessive (aabb).

The trans arrangement, or repulsion phase, is when one chromosome has a dominant allele for one gene and a recessive allele for another, with the reverse on the homologous chromosome. This is represented as (Ab/aB), with one chromosome carrying ‘A’ and ‘b’ and the other ‘a’ and ‘B’. This configuration arises from a cross between parents homozygous for different trait combinations, like AAbb and aaBB.

Constructing a Gene Map

Constructing a gene map involves translating recombination frequency into a visual representation of gene locations. The process uses a test cross, which involves crossing a heterozygous individual (dihybrid) with a homozygous recessive one. Because the recessive parent only contributes recessive alleles, the offspring’s traits directly reveal the allele combinations from the heterozygous parent’s gametes.

In a test cross with a dihybrid in a cis arrangement (AB/ab), the parent produces four types of gametes. Two have the original parental combinations (AB and ab) and are called non-recombinant; these are the most numerous offspring. The other two gamete types (Ab and aB) result from a crossover and are known as recombinant types, which are less frequent.

To calculate the distance between two genes, scientists determine the recombination frequency. This value is found by dividing the number of recombinant offspring by the total number of offspring, then multiplying by 100 to get a percentage.

Recombination frequency is converted directly into map units, where one map unit, or one centimorgan (cM), equals a 1% recombination frequency. A frequency of 15% means the two genes are 15 map units apart. Performing a series of these two-point crosses for different gene pairs allows a comprehensive chromosome map to be built.

Interpreting Map Distances and Gene Order

The distances on a genetic map are relative, not absolute. They provide an estimate of physical separation but do not correspond to a specific number of DNA base pairs, as recombination rates can vary along a chromosome. Map units represent the likelihood of genetic separation, which serves as a proxy for physical distance.

While two-point test crosses determine the distance between two genes, they cannot establish the order of three or more genes. For that, a three-point test cross is used, which involves an individual heterozygous for three linked genes crossed with a homozygous recessive one. Analyzing the offspring allows for a more accurate determination of gene order and the distances between them.

To interpret a three-point cross, one must identify the least frequent offspring classes. These rare offspring result from double crossover events, where two separate recombinations occurred on each side of the middle gene. The gene that switched its position relative to the other two in this group is the one located in the middle. This allows for the correct linear arrangement of the genes and a more refined calculation of their distances.