Allozymes are allelic variants of enzymes encoded by structural genes. Enzymes are proteins consisting of amino acids, some of which are electrically charged. As a result, enzymes have a net electric charge, depending on the stretch of amino acids comprising the protein. When a mutation in the DNA results in an amino acid being replaced, the net electric charge of the protein may be modified, and the overall shape (conformation) of the molecule can change. Because changes in electric charge and conformation can affect the migration rate of proteins in an electric field, allelic variation can be detected by gel electrophoresis and subsequent enzyme-specific stains. Usually two, or sometimes even more loci can be distinguished for an enzyme and these are termed isoloci. Therefore, allozyme variation is often also referred to as isozyme variation.


The strength of allozymes is simplicity. Because allozyme analysis does not require DNA extraction or the availability of sequence information, primers or probes, they are quick and easy to use. Some species, however, can require considerable optimization of techniques for certain enzymes. Simple analytical procedures, allow some allozymes to be applied at relatively low costs, depending on the enzyme staining reagents used. Allozymes are codominant markers that have high reproducibility. Zymograms (the banding pattern of isozymes) can be readily interpreted in terms of loci and alleles, or they may require segregation analysis of progeny of known parental crosses for interpretation. Sometimes, however, zymograms present complex banding profiles arising from polyploidy or duplicated genes and the formation of intergenic heterodimers, which may complicate interpretation.


The main weakness of allozymes is their relatively low abundance and low level of polymorphism. Moreover, proteins with identical electrophoretic mobility (co-migration) may not be homologous for distantly related germplasm. In addition, their selective neutrality may be in question. Furthermore, often allozymes are considered molecular markers since they represent enzyme variants, and enzymes are molecules. However, allozymes are in fact phenotypic markers, and as such they may be affected by environmental conditions. For example, the banding profile obtained for a particular allozyme marker may change depending on the type of tissue used for the analysis (e.g. root vs. leaf). This is because a gene that is being expressed in one tissue might not be expressed in other tissues. On the contrary, molecular markers, because they are based on differences in the DNA sequence, are not environmentally influenced, which means that the same banding profiles can be expected at all times for the same genotype.


Allozymes have been applied in many population genetics studies, including measurements of outcrossing rates, (sub)population structure and population divergence. Allozymes are particularly useful at the level of conspecific populations and closely related species, and are therefore useful to study diversity in crops and their relatives. They have been used, often in concert with other markers, for fingerprinting purposes, and diversity studies, to study interspecific relationships, the mode of genetic inheritance, and allelic frequencies in germplasm collections over serial increase cycles in germplasm banks, and to identify parents in hybrids.

Suggested reading

Starch gel electrophoresis of allozymes May, B., (1992). In: Hoelzel, A.R. (ed), Molecular genetic analysis of populations: a practical approach. Oxford University Press, Oxford, UK, pp 1-27.

Starch gel electrophoresis of plant isozymes: a comparative analysis of techniques Kephart, S.R.(1990). American Journal of Botany, 77: 693-712.