Molecular or DNA marker techniques allow gene mappers to directly analyze DNA and observe allele differences as specific loci. A genetic marker is any gene that has been mapped. In our examples so far, alleles of the genes we map control phenotype differences we can see expressed in the organism. Molecular markers or DNA markers are variable DNA sequences that have been mapped to a position on the chromosome. The analysis of DNA marker data to determine linkage maps works the same as with genes that control phenotype differences. The advantage of DNA markers is that geneticists can find many DNA differences between parents and track the inheritance of hundreds of marker loci in a single cross. Later we will learn about the details of the DNA analysis techniques that are used to generate a marker phenotype or DNA fingerprint. For now we will go through an example of how geneticists work with this data.
Geneticists use a DNA separation technique called electrophoresis to detect DNA differences at a particular locus. An individual’s DNA is loaded into a lane in the electrophoresis system and the pattern of DNA bands in that lane is their marker phenotype. If the DNA sequence at a particular chromosomal region is identical among all members being tested, only one banding pattern will be observed. In this case, the marker phenotype is called monomorphic. If the DNA varies, the marker banding pattern will vary across the lanes of DNA from different individuals and we have a polymorphic marker locus. Each marker phenotype can be designated as an allele at that locus. In Fig. 3, we have an example of one parent that is homozygous for the 'a' allele and the other parent homozygous for the 'A' allele. We see only one band in the parent lanes because both of their chromosomes have the same type of DNA at that locus. However, the F1 offspring has a two banded pattern. The F1 inherited the 'A' allele from one parent and the 'a' allele from the other. Thus these DNA markers can have a lack of dominance and heterozygous individuals can be distinguished from either homozygous genotype. The remaining lanes on Fig. 5 show the marker phenotype of several test cross progeny produced by crossing Aa with aa. All the progeny have the 'a' marker from the aa parent but some inherited the 'A' and others the 'a' from the 'Aa' F1 parent. For example, the marker genotype for the first 3 testcross individuals would be aa, Aa, aa. Once you become accustomed to determining genotypes from DNA marker data, it is obvious that these markers are inherited the same as genes and thus can be used in gene mapping.
If a DNA marker locus is linked to a gene controlling an important trait, the marker and the trait will tend to be inherited together. In Fig. 3, the trait of interest is a disease that the AA parent had and passed on to the F1. The aa parent lacks the disease allele and can only pass on an allele for disease resistance. In the test cross progeny, all of the individuals with the disease inherited the 'A' marker from the F1. If they inherited the 'a' marker, they also inherited the resistance allele and do not have the disease. Therefore, disease inheritance is linked to the A,a marker inheritance. If we look at large numbers of offspring from crosses such as this, we can obtain a data set that would allow us to estimate the map unit distance between the A,a marker locus and the disease locus. Accumulating this kind of DNA information on families that are passing on traits of interest is now the standard method of mapping genes in all species.