Genetic Map to Physical Map

1
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.

2
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

3
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.

4
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

5
Getting started

• Start with a sequenced (or partially sequenced),
  genetically mapped gene.
• As an example, lets 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.

6
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.

7
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.

8
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.

9
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 high-lighted 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.

10
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.

11
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.

12
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.
13
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.)

14
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?

15
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.