Lesson
3 - Creating the Map
Tools and Techniques
In this lesson you will learn how to access a database in Browse mode.
We'll also look at navigating browse sublists, making multiple selections
from a browse list, and changing databases.
Browse mode
Browsing is probably the easiest way to get an introduction
to these databases. One of the major advantages of browsing is that it
does not require any knowledge of database structure or content. It is
particularly useful when you're not quite sure what you are looking for
or what it might be called, or for general discovery. The large number
of hypertext links between objects make it possible to arrive at a particular
destination via many alternative paths.
Browsing is list-driven - you make one or more
selections from a list to narrow things down. It does not require constructing
a query. The screen interface for browse mode is different for databases
using older (prior to version 4) versions of the ACEDB software, so don't
be surprised if you encounter a slightly different look as you venture
into some of the other databases.
Describing the mapping study
All of the databases use the class "Map" to describe
a single linkage group (chromosome). Other classes may be used to provide
additional background information on the construction of the genetic map,
such as the size and nature of the mapping population, the algorithms used,
bibliographic references, even the raw mapping data. This background data
can help you assess the quality of the study and direct you to a full account
or a colleague to contact. The mapping study may be called by different
names - some of the names currently in use include Map_Data, Experiment,
Genetic_map, and About_*_Maps (where the * is the study name).
Example 3.1- The databases below have examples
that illustrate how and where you might find information about genetic
mapping studies. Investigate as many as you like!
TreeGenes
If you have a TreeGenes Database comment or question contact Kim
Marshall, Curator.
SolGenes
The SolGenes Database project is currently inactive.
Describing the mapping population
When making a genetic map, two genetically different
parents should be chosen because it is only those markers that differ between
the two parents which will yield useful information for the map. Some common
mapping population structures include selfing the resulting F1 (first generation)
progeny to create an F2 population, continued selfing of the resulting
F1 progeny for several generations to create an RI (recombinant inbred)
population, crossing the F1 progeny back to one of the original parents
to create a BC1 (first generation backcross) population, or collecting
anthers from the F1 plants and growing them in culture so that these haploid
cells undergo chromosome doubling, creating a DH (doubled haploid) population.
These different types of populations vary in the time and effort they take
to construct and the amount of information provided by each individual.
For example, in a backcross or doubled haploid population, each individual
represents meiotic events in just one of the parents, whereas an
F2 individual represents gametes from both parents.
Just like the mapping study, information about
the mapping population may be found under a variety of different classes,
including Map_Data, Panel_of_Stocks and Mapping_population. Facts you might
find about the mapping population include the size, the parents, and the
structure of the population (F2, Recombinant Inbred, etc.).
Some databases break this information out into
its own class, others store mapping population details in the same record
with general mapping study information. The examples below will show you
two different databases which have separate classes just for the mapping
population, but if you can't find this type of information in your favorite
database, remember that many databases, for example, SolGenes, RiceGenes
and GrainGenes, store population information in with the general mapping
study information, in these cases in the Map_Data record.
Example 3.2 - The databases below have examples
that illustrate how and where you might find information about genetic
mapping populations. Investigate as many as you like!
GrainGenes
If you have a GrainGenes Database comment or question contact Victoria
Carollo, Curator.
MaizeDB
If you have a MaizeDB Database comment or question contact Mary
Polacco, Curator.
Describing the mapping data
Once the mapping population has been created, the
parents and each progeny are tested with a number of different molecular
markers. These may be RFLPs, RAPD, microsatellites, isozymes...any kind
of technique that can reliably and repeatedly detect the same difference
between individuals can be used. At each marker, the progeny genotype is
scored. Say, for example, the maternal parent has allele A at marker 1
and allele B at marker 2. The paternal parent has allele Y at marker 1
and allele Z at marker 2. If marker 1 and 2 are located close together
on the same chromosome, then in most of the offspring, alleles A and B
will appear together, or Y and Z will appear together, because a recombination
event in the parents would be uncommon (since the markers are close together).
So, by seeing how often alleles A and B (or Y and Z) appear together, one
gets an estimate of how likely a recombination event between them is, and
thus an estimate of the genetic distance between the two markers. Because
the mapping data set is quite large, computer programs must be used to
do these calculations.
Once the basic map has been created, if one has
the mapping population (it must be the same plants used to create the original
map) and the mapping data, additional markers can be added to the map by
scoring the population for the new markers, adding this data to the original
dataset, and rerunning the mapping software. This is why organizations
that make the population available will also make the raw mapping data
available.
Just as with the mapping population, mapping data
may be found under a variety of names across the databases, including Map_population,
Map_scores and Map_Data (for those databases that merge background, population
and raw data into one class)
Example 3.3 - The database below has examples
that illustrate how and where you might find information about genetic
mapping data.
MaizeDB
If you have a MaizeDB Database comment or question contact Mary
Polacco, Curator.
The map itself
The final result of taking the mapping population,
scoring it for a set of markers, and analyzing that scoring data with a
software package is the genetic map. In these databases, each linkage group
that results from this mapping experiment is stored in its own Map record.
Remember, the distance on a genetic map is measured in centiMorgans - a
reflection of the frequency of recombination during meiosis between two
given markers. When you look at the genetic map and see many markers bunched
together, you are seeing a region of the chromosome that has little crossing-over.
The centromeric region is an example of this. Other times you may see a
large gap in between markers - if the map is well-saturated, this may indicate
a region that undergoes frequent crossing-over.
Genetic maps have a special, graphical display
in ACEDB. This graphic may contain a wealth of information, and special
software features may be used to a greater or lesser extent by the curators
to customize their map displays. With the WWW interface, both a text and
a graphic version of the map are available. For performance reasons, the
text version is sometimes returned by default, but you can opt to view
the graphic.
The example below is meant to give you an overview
of the map display. We'll be going into much more detail in the next few
lessons.
Example 3.4 - The database below has examples
that illustrate how and where you might find information about the genetic
map display.
RiceGenes
If you have a RiceGenes Database comment or question contact Angela
Baldo , Curator.
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