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MB2 - Selection of Markers for Molecular Breeding

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The Structure and Organization of DNA

To be able to appropriately select and use markers in plant breeding programs, it is important to understand how these markers are designed and how they are able to identify specific areas of the genome.

The key concepts to understanding this include:

  • the basic structure of DNA
  • the organization of the DNA sequence
  • the Polymerase Chain Reaction (PCR)

We’ll now take a closer look at each of these three concepts, starting first with the Structure of DNA.

DNA Structure

Each DNA strand is composed of a string of nucleotides, which are formed from a pentose sugar, a phosphate group, and either adenine, guanine, thymine or cytosine (abbreviated as A, G, T, or C).  Notice in Figure 4 that the shapes of the A and the T molecules (and similarly of the C and the G) are "complementary" to one another, a property which allows them to bind to each other.  When DNA is copied ("replicated"), the sequence of the new strand is complementary to that of the old one. Complementarity also lies behind the ability of the two strands to form the double helix structure of DNA.  The order of the four bases (A, T, C and G) in the DNA sequence of each individual organism is unique. It carries all the genetic information needed for the organism to function.  These illustrations (Figure 4) from the Human Genome Project Information site ( ) show two views of the structure of DNA.

Figure 4: The DNA structure is a double stranded double helix with nucleotide bases.
Image from the Human Genome Project Information site (


DNA Organization

This now takes us to the second key concept, the organization of DNA in a plant’s genome. It is important to remember that only part (sometimes a very small part!) of the DNA sequence is composed of genes. The rest is non-coding sequence, including lots of repetitive sequences, microsatellites and transposons. In some species, the genic fraction of the genome may be <10% of the total.  Figure 5 illustrates this concept.

Figure 5: This sketch shows how an area of the chromosome consists of other motifs in addition to genes. Genes themselves may include both introns (non-coding regions that will be excised during transcription) and exons (regions that are transcribed and become proteins). Non-genic regions of repeated nucleotides are scattered throughout the genome, including microsatellites, a type of repeat.  

(Image by Theresa Fulton.)


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