Lesson 8 - Physical Maps

Tools and Techniques

In this lesson we'll be moving into a slightly different topic - physical maps. At this point in time, the only plant genome database with physical mapping data is Arabidopsis. We will be accessing a version of this database which resides in the U.K, and it may have a slightly different looking web interface. We have now covered all the different query methods, so from here on out the examples may use any of the methods.

What is a physical map?

Recall that the genetic map shows you the linear order of genes (markers) along a chromosome, and the distance between the markers is measured in cM, a reflection of how much crossing over takes place between the two points. A physical map is measured in base pairs, and tells you how much DNA separates two points. Two markers may be very close genetically, i.e. very little recombination occurs between them, but very far apart physically - many thousands of base pairs. If you learn from the genetic map that your desired gene lies between two molecular markers, it is useful to know if that distance represents 1Kb (1,000 base pairs) or 1Mb (1,000,000 base pairs).

A cytogenetic map (which we looked at in lesson 5) can be considered a low resolution physical map. This type of map is based on the distinctive banding patterns of stained chromosomes. Other types of physical maps include the more detailed contig map, which depicts the order of overlapping DNA fragments spanning the genome, and a restriction map, which describes the order and distance between restriction enzyme cutting sites. The ultimate physical map is the elucidation of the complete DNA sequence of an organism.

How is a physical map created?

Physical mapping involves breaking the chromosomes into smaller fragments that can be handled individually, and ordering these fragments to their respective locations on the chromosomes. Physical mapping strategies may be described as top-down, which produces a restriction map, or bottom-up, which produces a contig map. Both strategies result in ordered sets of DNA fragments.

In top-down mapping, rare cutting enzymes are used to cut the chromosome into large pieces, which are then ordered. The large pieces are subdivided, and the resulting smaller pieces are then ordered. The resulting restriction maps depict the order and distance between enzyme cleavage sites. This approach yields maps with more continuity and fewer gaps between fragments than contig maps, but the resolution is lower and the map may not be useful for finding particular genes.

The bottom-up approach involves cutting the chromosome into small pieces, each of which is cloned and ordered. The ordered fragments form contiguous DNA blocks (contigs). Contig maps thus consist of a library of small, overlapping clones representing a complete chromosomal segment. Contig maps may be difficult to extend over large stretches of a chromosome because not all regions of the chromosome are easily clonable. Large amounts of duplicated DNA can also make it difficult to reliably order the fragments.

So what sort of information might you expect to see relating to a physical map? You might find information about the clones that were used to construct the contigs, where the contigs are, how big they are, and maybe DNA sequence data. In the example, the graphical display of the physical map contains many different types of interactive data.

Example 8.1 - The example below will look at the physical map of chromosome IV of Arabidopsis. The interface may be a little different, so be sure to read the instructions carefully.

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