Q&A in AGH635 Course: Why Is RAPD Marker Called a Dominant Marker?

As I remember, a lecturer in my genetic course introduced the dominant and recessive terminologies when I was in high school a long time ago. These terms again were discussed in more detail when I took my genetic course at IPB. In a Q & A session of the AGH635 lecture, one of the student asked me about these terms again as follow: “Why is RAPD (Randomly Amplified Polymorphic DNA) marker called a dominant marker?”

Before posting the answer to that question, let’s recall what the conventional means of dominant and recessive in the basic genetic course. Let’s assume a locus R controlling plant responses against certain attack of pathogen causing a disease in plant. In this R locus, there are at least two alleles (R and r). Hence, the genotype of a diploid plant would be either “RR”, “Rr”, or “rr.” When one evaluate responses of the genotypes against the disease, the “RR” and the “Rr” genotype are both resistance against the disease, and the “rr” is susceptible, respectively.

In other case, let’s assume a locus M controlling the color of flowers of certain Orchids. In this M locus, there are at least two alleles (M1 and M2). Hence, the genotype of a diploid plant would be either “M1M1”, “M1M2”, or “M2M2.” When one evaluate flower color of this Orchids, the “M1M1” has a red flower, the “M1M2” – a pink, and the “M2M2” – a white one, respectively.

The first case above illustrates a dominant allelic interaction in the R locus. The “R” allele is a dominant allele against the “r” which is a recessive one. In this type of interaction, the phenotype of a heterozygous plant (“Rr”) can not be differentiated from the dominant-homozygous one (“RR”). Hence, the phenotype of both “RR” and “Rr” is resistant. In other word, if ones observe plants that are resistant – one will not be able to predict their genotype only by observing at their resistance responses (i.e. either “RR” or “Rr” will exhibit resistance responses). Only when the plant phenotype is susceptible, then one can predict that the genotype is homozygous “rr.”

The second case above illustrates a co-dominant allelic interaction in the M locus. The “M1” is not a completely dominant allele (i.e. a partial dominant) against the “M2.” Either M1 or M2 is known as a co-dominant allele. In this type of interaction, the phenotype of a heterozygous plant (“M1M2”) can easily be differentiated from both the homozygous “M1M1” and “M2M2.” Hence, the phenotype of either “M1M1” (red) “M1M2” (pink) and “M2M2” (white) is completely different. I other word, if one observe plants that has red flowers, then the genotype of the plants will be “M1M1.” If it has pink flowers – then M1M2, and if it has white ones then M2M2. In the co-dominant allelic interaction, the plant genotypes can accurately and easily be determined using the plant phenotypes.

When discussing allelic interaction in a locus, molecular marker such as RAPD also follow the same rules as in the above conventional genetics. The only different between them lies in what are called loci and what are alleles. In RAPD marker, the loci are “the primer used and the size of amplified product.” Moreover, the alleles residing in the locus are either the presence of amplified product (i.e. [+] allele) or the absence of one (i.e. [-] allele). Therefore, only two possible alleles are presence in a locus. Hence, the alternative genotype of a diploid plants are either “+/+” (homozygote), “+/-” (heterozygote), or “-/-” (homozygote).

Back to the original question, “Why is RAPD (Randomly Amplified Polymorphic DNA) marker called a dominant marker?” and the answer are presented in Figure 1 below. In a diploid organism, there are two set of chromosomes in the genome. Lets assume there is an RAPD marker locus in the genome. The model genetic of the parents (P1 is homozygous [+/+] and P2 is homozygous [-/-]), F1 hybrid (heterozygous [+/-]), and the F2 progeny arrays (either [+/+], [+/-], or [-/-]) for the RAPD marker locus are presented in Figure 1.A.

Figure 1. The dominant nature of RAPD markers resulted in its inability to differentiate between homozygous (+/+) and heterozygous (+/-) since both will be scored (+) for the RAPD marker

Figure 1. The dominant nature of RAPD markers resulted in its inability to differentiate between homozygous (+/+) and heterozygous (+/-) since both will be scored (+) for the RAPD marker

For an RAPD marker, the phenotype is represented as the presence (scored [+]) or absence (scored [-]) of PCR amplified DNA fragment (Figure 1.B). For the individuals in the model genetic (Figure 1.A), the P1 will be scored (+), the P2 be (-), the F1 be (+), and the F2 arrays be either (+) for the F2-1 and F2-2 types or (-) for the F2-3 type, respectively. The F1 and F2-2 having a genotype of (+/-) is scored (+) for the RAPD marker. Moreover, the P1 and F2-1 having a genotype of (+/+) is also scored (+) for the same marker. Hence, the phenotype of the RAPD marker is the same for heterozygous F1 (having a genotype of [+/-]) and homozygous P1 or F2-1 type (having a genotype of [+/+]). Such cases indicated that the RAPD marker is a dominant marker and the (+) allele is dominant against (-) one.

About PMB Lab: Prof. Sudarsono

This blog is dedicated as a communication media among alumni associated with PMB Lab, Dept. of Agronomy and Horticulture, Fac. of Agriculture, IPB, Bogor – Indonesia. It contains various information related to alumni activities, PMB Lab’s on going activities and other related matters.
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