Intraspecific Comparative Mapping

Making 'across laboratory' comparisons is always challenging. Medical diagnostics laboratories spend significant resources on accreditation and standardization. So do industrial laboratories, including malting laboratories. State grain testing laboratories certify the NIR machines and train the NIR technicians in our grain elevators nationwide. We scientists watch ourselves through the process of peer review. When comparing results gathered by different research organizations, it's important to realize that we're not perfect. We all do our best.

Today's lecture demonstration revolves around an attempt to 'join' chromosomal linkage maps derived from three distinct barley genome mapping efforts. The first, the Steptoe x Morex effort, was one our laboratory contributed to in the late 1980's. The Igri x Franka map was developed at about the same time by Andreas Graner's group at Gatersleben. The third was an attempt to approximately locate a series of SSR markers on both the Igri x Franka and Steptoe x Morex maps utilizing a small subset of individuals from each population.

We'll focus on barley chromosome 1(7H) because it's intrinsically interesting and because it's distinctive. We'll go straight to JoinMap for the initial 'within population' analysis, then will join maps across these two populations, then will compare the results with the maps found on GrainGenes. Here are the initial .loc files.

Here's the three maps, first pass

Our laboratory exercise task for the week is as follows:

Jeremy: do 2H

Leila: do 6H

Vic and I will do 1H, 3H, 4H and 5H.

Here is the Igri x Franka joinmap file.

Here is the Steptoe x Morex joinmap file.

Compare each of the maps and identify any noticable discrepancies between these maps and the consensus maps that are available on GrainGenes.

Adding on the Microsats

Let's discuss how to make this more global.