Transcript iMap Exercise ()

Genetic Map to Physical Map
This activity is intended to supplement the workshop session entitled
“Integrating the Genetic and Physical Maps of Maize”. However, this
activity may be completed at any time during the workshop.
If you need assistance with this activity, ask Trent Seigfried.
Goals
• The goals of this exercise are to:
• Identify BAC clones for genetically
mapped genes
• Retrieve information from databases
• ChromDB: Plant Chromatin Database
• iMap: Integrated Genetic and Physical Map Viewer
• MaizeGDB: Maize Genetics and Genomics Database
• Explore links between genetic and
physical maps
The Problem
• You are a member of a team of scientists working on
•
•
a project aimed at understanding how chromatin
functions to regulate gene expression.
A colleague who is sequencing maize genomic BAC
clones offers to sequence BAC clones containing
some of the chromatin genes you are studying. This
is terrific, because most of your genes are
repesented only as cDNA sequences and it would be
useful to have genomic sequence information.
Your job is to identify which BAC clones to
sequence.
The Strategy
• Take advantage of the iMap integrated
genetic and physical map viewer
• To start, identify genes with:
• (at least partial) sequence information
• known genetic location
• Use iMap to find out if the gene is contained
on an anchored BAC contig
• Use WebFPC to examine the contig and
identify BACs containing the gene
Getting started
• Start with a sequenced (or
partially sequenced),
genetically mapped gene.
• As an example, let’s find the
BAC clones corresponding to
the chromatin gene chc101.
• For chromatin genes, one way
to begin is to log on to the
Plant Chromatin Database,
www.chromdb.org
• Search ChromDB By Gene by
typing “chc101”.
Look for mapping info
• Explore the different types of
information available for this
gene.
• At the bottom of the page,
locate the gene mapping
data.
• How many chc101 loci are
there?
• Write down their
chromosomal locations.
Connect to the Integrated Map
• Log onto iMap,
maizemap.org/iMapDB/iMap.html.
• If you have never been here
before, click on the User Guide
for info.
• One way to find your gene is
to search by chromosome on
the IBM2 or IBM2 Neighbors
map.
• Another way is to use the
Search Locus box and type in
chc101*. Do this.
Select the chromosome
• The search result shows that one locus, chc101b, is on the
IBM2 Neighbors map (IBMn2).
• A probe corresponding to this locus hits two contigs.
• To find out if either of these contigs is anchored by this locus,
click on Chromosome 2.
Look for the Contig
• In the Search for Locus box,
type: chc101b
• Zoom in until chc101b
comes to the top of the
genetic map.
Note other loci are highlighted too. This means
they are on the same contig
as chc101b.
• On physical map, mouse
over circles to display contig
number and marker
• Click on contig in the center
lower panel to display
contigs associated with
chc101b.
Contig Popup Info
• The probe in the contig is
overgo, PCO085026_ov,
which has been matched to
chc101b by BLAST analysis.
• This probe hits BACs in 2
contigs: 7 BACs in ctg186
and 4 BACs in ctg582.
• Contig 186 is anchored to
the genetic map by this
overgo marker. (See
anchoring rules.)
• Other mapped markers hit
this contig and two of them
are also on chromosome 2.
Contig Popup Info, cont.
• Notice that many of the
markers that hit ctg 582 are
on chromosome 7, which is
the chromosomal location of
chc101a. Keep this in mind.
• Click on ctg186 to view the
BACs in the contig.
WebFPC Contig Display
• This display shows three
areas. From top to bottom:
• header
• markers (same as probe) and
BACs
• remarks and map* showing
genetically mapped loci
corresponsing to probes that
hit the contig
• In the header, select All in the
Show clones pull down
menu. This will show all the
BAC clones.
* Beware. The loci on this map may not
all be on this chromosome.
WebFPC Contig Display
• Scroll across until you locate
PCO085026_ov in the marker
area. Click on it. The marker
should be highlighted in blue
and BACs hit by the marker
should be in green.
• Click on Zoom in to enlarge
the BAC display.
• Which of these BACs would
be good candidates for
sequencing? (Hint: pick the
longest BACs.)
What about BACs for chc101a?
• From ChromDB we know that chc101a maps on chr 7.
• From iMap, we know that:
• ctg582 is hit by an overgo probe with sequence identity to to
chc101.
• ctg582 is hit by other markers on chr 7.
• chc101a was not detected on IBM2 Neighbors
• So...how do we find out if the chr 7 markers on ctg582
are linked to chc101a?
Starting with a genetically mapped,
sequenced gene, you can....
• Search for its locus in iMap.
• Find out if a probe for this gene was used to screen
the BACs.
• Find out if the probe associates with an anchored
contig.
• Link to the contig display in WebFPC.
• Identify BACs in the contig hit by the probe.