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. This construct is called a crossover suppressor. 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 researchers to easily recognize flies that carry the balancer chromosome. By suppressing reproductive fitness when carried homozygously a balancer chromosome ensures that the population it is carried in does not become fixed for the balancer chromosome.
Balancer chromosomes always contain a lethal recessive allele. This means that if an organism receives two copies of the balancer chromosome, one from the mother and one from the father, then the organism will not live. So any organism that is homozygous for that chromosome will not live to pass on its genes. However, offspring that only get one copy of one balancer chromosome and one copy of a wild type or mutant chromosome will live to pass on its genes. After only a few generations the population will be entirely heterozygous so that you can be guaranteed of its genotype on at least those two chromosomes.
Balancer chromosomes also come with some sort of physical marker. This marker can be actually associated with the DNA in the chromosome such as the Green Fluorescent Protein that fluoresces in ultraviolet light, or it can be an easily distinguishable physical characteristic. These physical characteristics can be anything that is seen easily. In Drosophila melanogaster for example, eye color and hair length are commonly used. This physical marker serves as a double check that you indeed have the heterozygous balancer chromosomes in the organism.
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