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, 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.

In the Search for Locus box, type: chc101b 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. Look for the Contig

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

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. Contig Popup Info, cont.

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. WebFPC Contig Display * Beware. The loci on this map may not all be on this chromosome.

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.) WebFPC Contig Display

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? What about BACs for chc101a?

Log on to MaizeGDB (maizegdb.org) and do a locus search for chc101a. Which maps is this locus on? Record the map coordinates (the cIBM map will be most useful.) Compare the cIBM map to IBM2 Neighbors. Which loci on the IBM2 Neighbors map are close to the location of chc101a? Now go back to iMap and search chr7 for these loci. Are any of them associated with a contig? If so, which one? Look at the contig and determine which BACs are hit by the PCO085026_ov probe? These are the chc101a candidates. How to find BACs for 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.