# Linkage and Crossing Over

> CIE A-Level Biology · 9700 Inheritance
> Source: https://www.owlsprep.com/study/cie-9700-u17-linkage-and-crossing-over/

This module explains how genes on the same chromosome are inherited together, how crossing over during meiosis creates new allele combinations, and how to interpret cross results for linked genes, a high-frequency CIE exam topic.

**Prerequisites:** [Dihybrid crosses and independent assortment](https://www.owlsprep.com/study/cie-9700-u17-dihybrid-crosses/); [Meiosis and gamete formation](https://www.owlsprep.com/study/cie-9700-u06-meiosis/)

## Learning objectives

- Distinguish between linked and unlinked genes
- Explain how crossing over produces recombinant gametes
- Predict phenotypic ratios for linked gene crosses
- Calculate recombination frequency from experimental cross data

## What is Gene Linkage?

**Autosomal Linkage** — The tendency of two or more genes located on the same autosome (non-sex chromosome) to be inherited together, as they cannot assort independently during meiosis

*Example:* Body colour and wing shape genes in *Drosophila* are commonly used as examples of linked autosomal genes

Unlinked genes are located on different chromosomes, so they assort independently during meiosis, producing the expected 9:3:3:1 phenotypic ratio in a dihybrid cross between two heterozygotes. Linked genes do not follow this ratio because they are physically connected on the same chromosome.

> **info**
>
> Linkage reduces genetic variation from meiosis, as fewer new allele combinations are generated compared to unlinked genes.

**Check your understanding**

Check your understanding of the core definition:

1. Which statement correctly describes linked genes?

   - They are always located on sex chromosomes
   - They are located on the same chromosome
   - They always assort independently
   - They never cross over during meiosis

   *Answer:* They are located on the same chromosome

   *Why:* Correct. Linked genes are on the same chromosome so tend to be inherited together.

**Worked example:** Distinguish between linked and unlinked genes in terms of independent assortment.

1. Unlinked genes are found on different homologous chromosome pairs.
2. During metaphase I of meiosis, they align randomly at the cell equator, so they assort independently into gametes.
3. Linked genes are located on the same physical chromosome, so they are inherited together and do not assort independently.

## Crossing Over and Recombinant Gametes

**Crossing Over** — The exchange of homologous chromosomal segments between non-sister chromatids during prophase I of meiosis, which breaks the linkage between linked genes to produce new allele combinations

*Example:* A single cross-over between two linked genes produces two new recombinant allele combinations

When crossing over occurs between two linked genes, it breaks the original physical linkage. The result is two types of gamete: **parental gametes** that retain the original allele combination from the parent, and **recombinant gametes** that have a new combination of alleles.

**Worked example:** A *Drosophila* heterozygous for two linked genes has genotype $\frac{GN}{gn}$ (G = grey body, g = black body, N = normal wings, n = vestigial wings). What gametes are produced after crossing over between these two genes?

1. Homologous chromosomes line up in prophase I, with alleles arranged as shown:
2. $$\text{Chromosome 1: } G---N \\ \text{Chromosome 2: } g---n$$
3. A cross-over occurs between the two gene loci, swapping the ends of the non-sister chromatids:
4. $$\text{Recombinant chromatids after crossing over:} \\ G---n \quad \text{and} \quad g---N$$
5. After meiosis is complete, four gametes are produced:
6. 1. Parental gamete: $GN$ (original combination)
2. Parental gamete: $gn$ (original combination)
3. Recombinant gamete: $Gn$ (new combination)
4. Recombinant gamete: $gN$ (new combination)

> **tip**
>
> The closer two linked genes are on a chromosome, the less likely a cross-over is to occur between them, so fewer recombinant gametes are produced.

## Analysing Test Crosses for Linked Genes

A test cross (crossing a heterozygous parent with a homozygous recessive tester) lets you count parental and recombinant offspring directly. From this count you can calculate recombination frequency, which measures the distance between two genes on a chromosome.

**Worked example:** A test cross between $\frac{AB}{ab}$ and $\frac{ab}{ab}$ produces the following offspring: 420 $AB/ab$, 40 $ab/ab$, 38 $Ab/ab$, 402 $aB/ab$. Calculate the recombination frequency between the two genes.

1. First, identify recombinant offspring: they have non-parental phenotype combinations. The parental combinations are $AB$ and $ab$, so recombinants are $Ab$ and $aB$.
2. Calculate the total number of offspring: $420 + 40 + 38 + 402 = 900$.
3. Sum the total number of recombinant offspring: $38 + 40 = 78$.
4. Calculate recombination frequency as the percentage of recombinant offspring:
5. $$\text{Recombination frequency} = \frac{\text{Total recombinants}}{\text{Total offspring}} \times 100 = \frac{78}{900} \times 100 = 8.67\%$$
6. This means the two genes are 8.67 map units apart on the chromosome.

**Exam command terms**

Common exam command terms for this topic:

- **Explain why ratio is not 9:3:3:1** — You must state genes are linked and do not assort independently *(Extra credit is given for mentioning crossing over produces few recombinants)*

- **Calculate recombination frequency** — Always add both recombinant classes before dividing by total offspring *(Marks are lost if you only count one recombinant class)*

*Calculator:* allowed

## Common pitfalls

- **Wrong:** Writing linked genotypes as AaBb instead of showing linkage arrangement
  - Why it fails: Examiners require you to show which alleles are on each chromosome, this standard format loses marks
  - Correct: Write linked genotypes as $\frac{AB}{ab}$ to show A is linked to B and a to b
- **Wrong:** Counting only one recombinant class when calculating recombination frequency
  - Why it fails: Crossing over produces two recombinant gamete classes, both must be counted
  - Correct: Add the number of offspring from both recombinant classes before dividing by total offspring
- **Wrong:** Claiming linked genes can never be separated
  - Why it fails: Crossing over regularly separates linked genes, just at a lower frequency
  - Correct: State that linked genes tend to be inherited together, but can be separated by crossing over during prophase I
- **Wrong:** Expecting a 9:3:3:1 ratio for linked gene dihybrid crosses
  - Why it fails: Linkage prevents independent assortment, so parental phenotypes are far more common
  - Correct: Predict that most offspring will have parental phenotypes, with a small number of recombinant offspring

## Cheatsheet

| Concept | Key Fact | Formula/Note |
| --- | --- | --- |
| Linked genes | Located on same chromosome, do not assort independently | N/A |
| Crossing over | Occurs in prophase I, breaks linkage to make recombinants | N/A |
| Parental offspring | Original allele combination, more numerous | N/A |
| Recombinant offspring | New allele combination, less numerous | N/A |
| Recombination frequency | Equals distance between genes in map units | $\frac{\text{Total recombinants}}{\text{Total offspring}} \times 100$ |

## What's next

Understanding linkage and crossing over is the foundation for genetic mapping and explains how genetic variation is generated during meiosis. It connects to all core inheritance concepts, is frequently tested alongside dihybrid cross problems, and recombination frequency calculations are used to map disease-causing genes in human genetics. This topic also leads directly into the study of sex linkage, a specific form of linkage that is very commonly tested in CIE exams. Mastering the rules for linked gene crosses will help you gain full marks on the 10-15% of genetic cross marks typically found on paper 2.

- [Sex Linkage](https://www.owlsprep.com/study/cie-9700-u17-sex-linkage/)
- [Polygenic Inheritance](https://www.owlsprep.com/study/cie-9700-u17-polygenic-inheritance/)
- [Selection and Evolution](https://www.owlsprep.com/study/cie-9700-u18-overview/)

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