Lesson 2 - Overview of Genetic Maps

This section contains a brief background on the concept of a genetic map, what it represents and what it might contain. The genetic map is the fundamental organizational framework for all the genome databases, and working your way out from the map and back to the map will be a navigational technique you will use often. If the idea of a genetic map is completely foreign to you, it's probably a good idea to do some background reading before attempting the rest of this tutorial.

This particular lesson doesn't have any online exercises - they'll start in the next lesson, when we look at how genetic mapping information is stored in the databases.

What is a genetic map?

A genetic linkage map shows the relative locations of specific DNA markers along the chromosome. Each marker is like a mile marker along a highway. Any inherited physical or molecular characteristic that differs among individuals and is easily detectable is a potential genetic marker. Markers can be expressed DNA regions (genes) or DNA segments that have no known coding function but whose inheritance pattern can be followed. DNA sequence differences are especially useful markers because they are plentiful and easy to characterize precisely. Markers must be polymorphic to be useful in mapping; that is, alternative forms (alleles) must exist among individuals so that they are detectable among different members in the mapping population.

A mapping population is the group of individuals that will be evaluated for their "score" at a set of markers. This raw mapping data is analyzed by software which constructs the map by observing how frequently the alleles at any two markers are inherited together. The closer the markers are, the less likely it is that a recombination event (a crossover during meiosis) will separate the alleles, and the more likely it is that they will be inherited together. Thus, unlike other types of maps, the distance between points on a genetic map is not measured in any kind of physical unit, it is a reflection of the recombination frequency between those two points. This genetic map unit is measured in terms of centimorgans (cM, named after the geneticist Thomas Hunt Morgan). Two markers are said to be 1 cM apart if they are separated by recombination 1% of the time. The genetic distance tells you little about the physical distance - the actual amount of DNA separating the markers. This genetic to physical distance relationship varies between species, and varies between different spots within the genome of a single species.

A genetic map helps us understand the structure, function and evolution of the genome. It can be an important tool for agricultural crop improvement. Recent work has shown that the genetic maps of many closely related species (for example, the grains) are quite similar with respect to the content and location of genes, and scientists are trying to determine how the genetic map of one species may be applied to others.

What sort of information can a genetic map contain?

Many different types of objects can be assigned a position on a genetic map. For the purposes of this tutorial we will divide these objects into two categories: "point" objects and "interval" objects. Known genes and molecular markers are examples of points on maps. Centromeres, quantitative trait loci (QTLs), rearrangements, introgressions, syntenic regions and contigs could be examples of intervals. Not every database will contain all these types of objects, or represent the same object in the same way! For example, in certain databases, a QTL may be assigned a specific point location on a map; in others, a QTL may be defined to span a particular region of the map. The examples will try to illustrate the different approaches used by different groups.

How does the map relate to other items in the database?

Almost all objects in these databases can somehow be tied back to a map. There is a special graphical display for the genetic map (which we'll examine in detail in the next few lessons), and many of the objects associated with the map will have additional textual information. Since each database is managed, or "curated" by a different team of scientists, each database may name and structure things slightly differently

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