TYPES OF MARKERS
Genetic Markers: Sequences of DNA that are associated with desired traits in the chromosomes. These markers are also polymorphic, varying in their location and composition when compared to their same species' genes. (Citation 17)
Molecular Markers: All organisms are made up of cells, which are differentiated through the instructions DNA provides. The instructions are sent from genes, however, only small amounts of DNA are composed of genes, and the rest are just non-coded sequences. Molecular markers, on the other hand, don’t actually do anything for the organism itself, but they are important for MAS because they are landmarks on the genome. These markers are DNA sequences that get passed down from generation to generation and require a DNA assay. There are many types of molecular markers, such as RFLPs, AFLP, or microsatellites. (Citation 1, 4)
Linked Markers: A sub-type of molecular markers that are located near a gene associated with a desired trait are called linked markers. These are only applicable to the chromosome the gene is located on, not the DNA itself. (Citation 1)
Direct Markers: These types of markers are a part of the desired gene. These are much easier to use and screen, but are harder to initially find compared to linked markers. They are also a sub-type of molecular markers. (Citation 1)
Restriction Fragment Length Polymorphisms (RFLPs): These are the first markers used for MAS. Like the name implies, Restriction Fragment Length Polymorphisms employ restriction enzymes to find and cut DNA regions that are associated to a certain trait. However, RFLPs are aided by a method called Southern Blotting due to the restriction enzymes being too effective by producing millions of DNA fragments. Southern Blotting uses DNA probes to find a specific DNA sequence and the probes subsequently attach onto the sequence, making them easy to identify during gel electrophoresis. Scientists use RFLPs due to their co-dominance and the tests are easily reproduced with accuracy. However, some drawbacks to this technology are the need for large amounts of DNA along with a long lab turnaround time. (Citation 1)
Randomly-amplified polymorphic DNA markers (RAPDs): RAPDs are markers made using PCR on random DNA sections with the use of DNA primers. The DNA primers are usually composed of a set nucleotides from a similar but different organism that are used to find the same sequences in the target organism. They are then processed through gel electrophoresis and analyzed. The advantage of this method for obtaining markers is its relative simplicity and the fact that it doesn’t require any information about the DNA beforehand. This is useful in obtaining markers from organisms that have not had their marker maps thoroughly analyzed yet. However, since the DNA segments are randomly amplified, the results can be inaccurate at times. (Citation 13, 12, 1)
Amplified Fragment Length Polymorphism markers (AFLPs): AFLPs are a combination of RFLPs and RAPDs in the sense that AFLPs are “…based on the selective PCR amplification of restriction fragments” (Citation 12). AFLPs use PCR to rapidly copy many genetic markers from restriction fragments, allowing high resolution genotyping data. (Citation 14, 12)
Single Nucleotide Polymorphisms (SNPs): Single Nucleotide Polymorphisms are directly correlated with a trait of interest, because they are found within the gene itself. Since there are large amounts of SNPs within a genome, this provides a lab with a correlating large amount of markers to do research on. In addition, analyzing and genotyping SNPs does not require gel-electrophoresis, a key difference between other marker technologies. Due to new technologies, SNPs are being use more and more for MAS. (Citation 1)
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Below are the many types of markers, general and specific. Although the images of these markers may not be the most intersting, most of them being a series of lines, please bear with us!
Specific Markers in MAS
Simple Sequence Repeats (SSRs): Also known as microsatellites, these are repeating two to six nucleotide sequences that are dispersed throughout the genome. While analyzing these sequences, scientists create primer pairs based on loci to draw comparisons and ultimately markers from the microsatellites. These markers are useful because they are polymorphic (having diverse forms), and can be used for analyzing diseases and more.
