Single Nucleotide Polymorphisms (SNPs) An SNP (single nucleotide polymorphism) is a single base change in a DNA sequence at a given position.

For such a base position with sequence alternatives in genomic DNA to be considered as an SNP, it is considered that the least frequent allele should have a frequency of 1% or greater. SNPs are estimated to occur with a prevalence of one SNP per 1300 bases in the human genome (Lander et al., 2001). In principle, SNPs could be bi-, tri-, or tetra-allelic polymorphisms. However, tri-allelic and tetra-allelic are very rare and SNPs are sometimes simply referred to as bi-allelic markers (Brookes, 1999). SNPs can result from either the transition or transversion of nucleotide bases. Transition substitutions occur between purines (A and G) or between pyrimidines (C and T). Transversions are substitutions between a purine and a pyrimidine. Transition mutations are more common than transversions (Duncan and Miller, 1980). Nucleotide substitutions occurring in protein-coding regions can be classified as synonymous and non-synonymous according to their effect on the resulting amino acids. A substitution is synonymous if it causes no amino acid change while a non-synonymous substitution results in alteration in the encoded amino acid. The latter type can be further classified into missense and nonsense mutations. A missense mutation results in change in amino acid due to the change of codon used while a nonsense mutation results in a termination codon. Even within a single chromosome, the SNPs are not uniformly distributed, and some genomic regions have significantly lower or higher diversity than the average. Polymorphisms in the regulatory regions of genes and sequence variants that alter amino acids in the coding regions are generally less common, reflecting a greater selection pressure reducing diversity at these DNA regions. Within coding exons the nucleotide diversity is four-fold lower, with about half resulting in non-synonymous codon changes (Nickerson et al., 1998) indicating highly conserved nature of these regions. Depending on where a SNP occurs, it might have different consequences at the phenotypic level. SNPs in the coding regions (sometimes termed as cSNPs) or in regulatory regions are more likely to cause functional differences than SNPs elsewhere (Huang et al., 1993).

In general, association studies have to be performed in order to statistically establish that particular alleles are associated with one or more phenotypic traits. These SNPs are useful as markers in population genetics and evolutionary studies and to identify genes implicated in complex multigenic traits by using linkage disequilibrium (Vignal et al., 2002).