GENETIC VARIATION & DNA MARKERS

Mutations occur in all organisms as a result of normal cellular operations or interactions with the environment, leading to genetic variation (polymorphism)

• In conjunction with mutation and recombination, there arises genetic variation within and among - individuals, species, and higher-order taxonomic groups.
• To the geneticists, the variation must be (1) heritable and (2) discernable to the researcher, either as a recognizable phenotypic variation or as a genetic mutation distinguishable through molecular techniques.

Types of genetic variation: 

• Base substitutions – known as single nucleotide polymorphisms (SNPs); insertions or deletions of nucleotide sequences (indels) within a locus; inversion of a segment of DNA within a locus; and recombination of DNA segments; genome duplication (as seen in the lower vertebrates)
• Through long evolutionary accumulation, - the number and degree of the various types of mutations define the genetic variation within a species.
• DNA marker techniques can be applied to reveal these mutations.
• Molecular/genetic marker: A DNA fragment, an allele or cytogenetic marker or gene product (allozymes/proteins) used as an experimental probe to keep track of a species, population, an individual, tissue, cell, nucleus, chromosome, or a gene. Molecular markers are used to identify different genetic varieties of microbes, animals & plants, or to trace genetic predisposition to certain diseases (cancers)/disorders.

Types of markers:

1. DNA markers (nuclear, mitochondrial & chloroplast, ITS)
2. Protein Markers (allozymes; general proteins; salt soluble Myofibrillar proteins such as myosin and tropomyosin)
3. Type I and Type II: Type I are markers associated with genes of known function, (eg., Allozymes, RFLP, ESTs); Type II markers are associated with anonymous genomic segments (RAPD, AFLP, microsatellites).
4. Dominant, Co-dominant, uniparental, DUI.

Properties of Molecular Markers

• Heritable in Mendelian fashion
• Genetic variations - discernable
• Neutral (phenotypically silent molecular genetic variations that exert no significant influence on survival and reproduction)
• Reproducible
• Monomorphic (fixed) / Polymorphic 

Requirements for molecular markers studies

• Tissue samples – accurately identified; properly preserved in ethanol
• Good quality DNA
• PCR Lab facilities
• Prior information of the genome (except in the case of RAPD) – ‘primers‘
• Electrophoresis apparatus & staining protocols
• Sequencing facility
• Data analysis