The term genotype refers to the specific genetic makeup, unique genetic constitution, or hereditary “blueprint” of an organism. An individual’s genotype is his or her genetic identity.

A  genotype  can  mean  the  full  complement  of genes that an organism possesses, or it can refer to the DNA bases at only one position in the genome. Often the term is used to describe a characteristic subset of genes, and the linkage relationships between them, that define an individual or group of individuals.

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The term allele refers to the specific string of base pairs (i.e., the genotype) at a particular genetic locus. A locus is the physical position or address in the genome  that  a  particular  gene  occupies. The  term genotype may refer to the sequence of bases at a single locus (i.e., an allele), or it may refer to an organism’s entire set of alleles.

The term polymorphism means the existence of two or more different forms in a population. In biology, its uses include describing variable forms of proteins or other chemical compounds, whole organisms, and genotypes. Genetic polymorphisms may be differences in single nucleotides, or they may extend over a number of nucleotides, examples being polymorphic repeat sequences. Polymorphism frequencies may vary in different subsets of the population. Common polymorphisms are most useful in mapping studies. Single nucleotide polymorphisms (SNPs) probably occur every several hundred base pairs in the human genome. With current technology, SNPs are found at about every 1,000 base pairs.

An individual may possess two copies of the same allele on both homologous chromosomes and be a homozygote or homozygous. An individual who carries two different alleles at a particular locus is a heterozygote or heterozygous. Strictly speaking, any difference in base pairs (i.e., genotype) between two alleles at a particular locus is heterozygosity. Sometimes the concept is used to signify only differences that lead to different gene products with significantly different functional capabilities. An example would be an individual who is heterozygous for a disease-causing mutation. On the other hand, a single base pair difference that occurs commonly and does not have any detectable effect on the gene product and/or its function (i.e., a polymorphism) also may define a heterozygote. Such an individual would be heterozygous for a genetic polymorphism.

A group of two or more linked genotypes is called a haplotype. A haplotype may refer to a series of polymorphisms within a single gene, but more commonly, it refers to a series of genes or alleles that extend over a portion of a chromosome (i.e., genotypes at linked loci). Whereas allele refers to a particular genotype at a single gene locus, haplotype refers to a series of genotypes over a stretch of DNA that may include several genes. When a haplotype (i.e., a series of linked genotypes) tends to be  inherited  intact  more  often  than  expected,  given its chances for recombination, it is said to be in linkage disequilibrium. Haplotypes, as well as single polymorphisms, are useful genotypes for mapping studies.

An organism’s genotype is commonly thought to determine its outward characteristics (i.e., the phenotype). The fact is, however, that individual phenotypes actually result from not only the products of gene expression (i.e., the genotype as expressed through transcription and translation) but also complex interactions involving the environment and chance.


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