Genetic linkage explains why some traits are inherited together more often than expected by chance. Gene mapping uses recombination data from meiosis to infer the relative order of genes and estimate distances along chromosomes.

Genetic linkage: the core idea

Linked genes vs. independent assortment

Genes on the same chromosome can be transmitted together because they share a physical DNA molecule. When genes are far apart, crossing over can separate them, making them behave more independently.

Linkage is detected by comparing observed offspring phenotypes to what would be expected if genes assorted independently.

Recombinants and parental types

In mapping crosses, offspring are classified into:

• Parental (nonrecombinant) types: allele combinations matching the parents’ original chromosome arrangements

• Recombinant types: allele combinations produced by crossing over that reshuffles alleles between homologous chromosomes

Recombinant offspring provide the key data for estimating how often crossing over occurs between two genes.

A labeled meiosis schematic showing a crossover between homologous chromatids and the resulting mixture of products. It highlights that one crossover event typically yields both parental and recombinant chromatids, which explains why recombinant offspring are informative but usually not the majority for closely linked genes. Source

Recombination frequency and map distance

Why recombination frequency reflects distance

Crossing over is more likely to occur between two genes that are farther apart on a chromosome because there is more DNA between them where a crossover can form. Therefore, a higher recombination frequency generally indicates greater separation between loci.

A recombination frequency of 50% indicates genes are effectively unlinked (either on different chromosomes or so far apart on the same chromosome that crossovers randomize allele combinations).

Inheritance patterns for two loci under three chromosomal arrangements: genes on different chromosomes (independent assortment), genes very close together on one chromosome (no recombination), and genes far apart on one chromosome (recombination so frequent that RF approaches 50%). The figure ties these arrangements to the expected proportions of parental vs. recombinant offspring in a test cross, illustrating why RF cannot exceed 50% even when loci are on the same chromosome. Source

Constructing a genetic map (gene mapping)

What a genetic map represents

A genetic map is a relative map of gene positions based on recombination data rather than a DNA base-pair measurement.

General mapping workflow (conceptual)

Gene mapping relies on controlled crosses and large sample sizes to reduce the impact of random chance:

• Choose organisms with clearly scorable phenotypes (or molecular markers) for the loci of interest

• Perform a cross that allows recombinants to be detected from offspring phenotypes (commonly using a heterozygote crossed with a homozygous recessive)

• Count parental vs. recombinant offspring classes

• Calculate recombination frequencies for gene pairs

• Use recombination frequencies to infer:

  • Relative distances between genes

  • Gene order, by selecting the arrangement that best fits the observed pairwise distances

Key interpretation rules

• Lower RF → loci are closer together (stronger linkage)

• Higher RF → loci are farther apart (weaker linkage), up to a maximum of 50%

• Map distances are additive over short intervals, which supports reconstructing gene order using multiple pairwise comparisons

Limits and common pitfalls in linkage-based mapping

Why map distance is an estimate

Recombination frequency can underestimate true physical distance when loci are far apart because:

A simple chromosome map showing three loci (T–U–V) with distances that must be inferred by adding shorter intervals. The example demonstrates how a gene pair can show RF = 50% (appearing unlinked) even though the loci can be much farther apart on the same chromosome when intermediate markers are used. Source

• Multiple crossovers between loci can restore the parental allele combination, making some crossover events “invisible” in offspring counts

• RF therefore does not increase beyond 50%, even if genes are very far apart on the same chromosome

What map units do and do not mean

• cM measures recombination likelihood, not exact base pairs

• Recombination rates can vary across regions of a chromosome, so equal cM distances may correspond to different physical DNA lengths in different regions