Brief Overview of Molecular Markers

Molecular marker technology enables plant breeders to select individual plants based on their marker pattern (genotype) rather than their observable traits (phenotype).  This process is called marker assisted breeding (MAB) or marker assisted selection (MAS).  MAB offers many benefits, including speeding up a plant breeding program’s progress, increasing accuracy and efficiency, and decreasing costs. 

This animation goes through an example of MAS in developing wheat resistant to a disease. It outlines the guidelines for planting yieldguard rootworm (YGRW) corn using an Insecticide Resistance Management (IRM) plan. Different field planting options are illustrated within the animation. Note the population of resistant and susceptible beetles and mating between resistant and susceptible beetles. The planting strategy consists of a refuge, road or ditch and an adjacent field.

If you are new to these concepts or need a refresher on the basic principles, we suggest you go through an eLesson written by Pat Byrne (Colorado State University) and Kelley Richardson (Oregon State University) entitled, “Marker-Assisted Selection”

In this eLesson Byrne and Richardson (2005) explain what MAS is and then give a comprehensive overview of the MAS process:

Marker-assisted selection (MAS) is a method of selecting desirable individuals in a breeding scheme based on DNA molecular marker patterns instead of, or in addition to, their trait values. When used in appropriate situations, it is a tool that can help plant breeders select more efficiently for desirable crop traits. However, MAS is not always advantageous, so careful analysis of the costs and benefits relative to conventional breeding methods is necessary.

Different marker types have variable characteristics. Desirable qualities of molecular markers include the following:

  • Polymorphic
  • Reproducible
  • Evenly distributed across the whole genome (not clustered in particular regions)
  • Inexpensive
  • Easy to analyse
  • Co-dominant (so that heterozygotes can be distinguished from homozygotes)
  • Possibility of being outsourced

Until recently there were a number of marker types available, including RAPDs (Random Amplification of Polymorphic DNA), AFLPs (Amplified Fragment Length Polymorphism), ESTs (Expressed Sequence Tags), etc. For the most part these older markers are now obsolete because they did not meet these criteria as well as newer markers do.  The 2 main marker types used today are:

  • SSRs (Simple Sequence Repeats, also called Microsatellites)
  • SNPs (Single nucleotide polymorphisms)

SNPs have many advantages, including being high-throughput and low in cost. SSRs are an older type of marker but since they are being used as of this writing, we will also discuss them.