Microsatellites - Molecular Markers of Choice - a Review

The advent of DNA technology over the recent years has led to the development of molecular markers that are highly precise, convenient and cost effective for detection of polymorphism among individuals and also for individual identification. These molecular marker techniques viz., Restriction fragment length polymorphism, Random amplified polymorphic DNA, Amplified fragment length polymorphism, DNA fingerprinting, microsatellites and the most recent, microarrays are advantageous over other conventional techniques like protein polymorphism and immunogenetic techniques. As these techniques directly assess the sample at the DNA level the probability of their accuracy is much greater. Among these marker systems the ideal marker should have many scorable and highly polymorphic loci with codominant alleles and should be densely distributed throughout the genome. Microsatellite markers meet these requirements and have therefore become the markers of choice for a variety of analyses related to linkage mapping, forensic investigations, paternity and kinship determination and population genetic studies. * Animal Biotechnology Centre, College of Veterinary Sciences, GBPUA&T, Pantnagar 263 145, Uttaranchal. In the late sixties, the term satellite was associated with DNA when, on isopycnic centrifugation of DNA, it settled into a main band with some secondary bands (Waring and Britten, 1966, Britten and Kohne, 1968). These secondary bands were termed satellite bands as they appeared on the outskirts of the denser DNA bands. On analysis, it was revealed that the satellite bands comprised of DNA with long repetitive sequences, existing in millions of copies, which appeared to be associated to the heterochromatin. Based on reassociation kinetic studies, it was revealed that this repetitive pattern of DNA differed within and between species (Brutlag, 1980). Repetitive DNA can be classified into two types based on their arrangement in the genome, whether interspersed or arranged in a direct tandem fashion. Repetitive elements arranged in tandem form the most abundant class of repeats found in the genome. Satellite DNA is a broad term to describe such type of DNA, which includes the telomeres, minisatellites and the microsatellites. Shorter repetitive DNA sequence having repeats of 15 or more bases were termed as minisatellites (Jeffereys et al., 1985). In the late 1980s, even shorter repeats of satellites of two to six bases were isolated and named microsatellites (Litt and Luty, 1989). Since their discovery, microsatellites have been used in mapping programmes and by population biologists for studies of population genetic structure and kinship investigations. Properties and Distribution Microsatellites are short (2 to 6 base pairs), simple, tandemly repeated nucleotide sequences present as multiple copies in the genome. The number of repeats varies between loci but on an average are approximately 100 repeats. Based on the nature of the repeats, microsatellites are broadly classified into three families pure, compound and interrupted repeats (Weber,