What is genotyping?

Each biological species is defined by a distinct set of common characteristics, but even within a species, there are subtle differences among individuals. In the human species, we can easily spot physical differences such as hair or eye color among people. In other species—even those considered non-living, such as viruses—certain differences among individuals also exist but they may be more subtle. Although these differences are not drastic enough to be called a distinct species, individuals within a species that do have slightly different characteristics are called variants.

Variation is the term used to describe the characteristic that is different within a population of distinct individuals or within a single species. For example, some populations of soybean plants are resistant to a common fungal pathogen, such as phytophthora root rot, whereas other populations are susceptible to this pathogen. In simplistic terms, fungal resistance is a variation. The phytophthora root rot-resistant population possesses a special feature enabling the plants to defend themselves against the fungus. If the fungal resistance is passed onto subsequent generations of plants, this feature is most likely coded in the plant’s genome.

Both environmental and genetic differences play a role in these visible or phenotypic features. Since environmental changes are not heritable, most researchers are interested in studying genetic variations that result in these physical differences. Genetic variation can be passed to the next generation and can increase or decrease the fitness of a given species.

Genotyping is the experimental procedure that identifies the differences in DNA sequence among individuals or populations. It is used to understand the connection between genotype (the underlying genetic code) and phenotype (the observable organismal structure). An individual genome is identified as a distinct variant when compared to a reference sequence, which is derived from the general population or a defined subgroup. A variant sequence can differ from the reference sequence in several ways. Types of genetic variation include single nucleotide variants (SNV), single nucleotide polymorphisms (SNPs), insertions and deletions (indels), translocations, and copy number variation (CNV).

SNPs are the most common type of sequence variant investigated by researchers; they are typically defined as SNVs that occur in >1% of the population. Based on the number of SNPs cataloged in the SNP database (dbSNP) [1] and a haploid genome size of 3.1 x 109 bp [2], the human genome should contain a SNP approximately once every 9.5 bases. Other common model organisms show a similarly high frequency of SNPs [3].