Balancer chromosome

A balancer chromosome is a genetic tool used to prevent crossing over (genetic recombination) between homologous chromosomes during meiosis. Balancers are most often used in Drosophila melanogaster (fruit fly) genetics to allow populations of flies carrying heterozygous mutations to be maintained without constantly screening for the mutations. Balancer chromosomes have three important properties: they suppress recombination with their homologs, carry dominant markers and negatively affect reproductive fitness when carried homozygously.

For example, flies that carry a mutation a researcher wants to study on a normal chromosome and a wild-type (wt) balancer version of the homologous chromosome can be thrown in a tube with some fly food, then several months or generations later, flies with the same genotype will still be in the tube. Without balancer chromosomes then flies would carry genetic markers in completely different combinations after several generations.

How balancer chromosomes work
To suppress crossing over, balancer chromosomes are the products of multiple, nested chromosomal inversions so that synapsis between homologous chromosomes is disrupted. If crossing over between a balancer chromosome and the balancer's homolog does occur during meiosis each chromatid ends up lacking some genes and carrying two copies of other genes. Recombination in inverted regions leads to dicentric or acentric chromosomes (chromosomes with two centromeres or no centromere). Progeny carrying chromosomes that are the products of recombination between balancer and normal chromosomes are not viable (they die).

Dominant markers such as genes for green fluorescent protein or enzymes that make pigments allow researcher to easily recognize flies that carry the balancer chromosome. By suppressing reproductive fitness when carried homozygouly a balancer chromosome ensures that the population it is carried in does not become fixed for the balancer chromosome.