2. Modern methods that can undertake large-scale analysis of SNP markers which are expensive and require sophisticated equipment,

•  Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (Ross et al., 1998, Storm et al., 2003),

•  Pyrosequencing (Ahmadian et al., 2000),

•  Taqman allelic discrimination (Li et al., 2004),

•  Real-time (quantitative) PCR (Nurmi et al., 2001), and

•  Microarray or gene chips (Hacia et al., 1999).

6-5.3(a).1.5 Multi locus probe markers

The non-coding DNA, which makes up a large proportion of the genomes of higher organisms, contains regulatory elements like promoters and enhancers and repetitive elements (Turner et al., 1998) viz. mini- and microsatellite DNA. The term microsatellite was coined by Litt and Lutty, and the term minisatellites was introduced by Jeffrey. They exist as multiple allelic forms in a population, have high level of heterozygosity, follow Mendelian inheritance, and behave as dominant fingerprinting markers and co dominant STMS (sequence tagged microsatellites) markers. Both micro- and minisatellites form an ideal marker system to create complex banding patterns through simultaneous detection of multiple DNA loci.

6-5.3(a).1.5(i) Minisatellites

Minisatellites were first found in the human genome and described as hypervariable tandem repeats with a monomer repeat length of about 10–100 bp (more than the microsattelite), that is repeated several times (less than the microsatellite). This number of repeat units in loci varies between genotypes and is referred to as variable number of tandem repeats (VNTRs) or hypervariable regions (HVRs). Although both mini- and micro-satellites occur throughout the eukaryotic genome, the former tend to be concentrated in the telomere regions and in sites associated with a high frequency of recombination (Bruford & Wayne, 1993; Nicholas, 1996).