There is a set of standard mapping primers which are typically used for positional cloning in Arabidopsis accessions Col-0, Ler-1 and Ws-0. This list was modified: “difficult” markers removed, “nice” ones added resulting in approximately 5 markers per chromosome. These indel and SSR markers were optimized for mapping using HRMA. You can find the corresponding file here.

When developing new markers for Arabidopsis you can use different sources of polymorphism information. Do not forget to add the developed HRMA marker to the list of optimized assays.

For instance:

Arabidopsis mapping platform (for Col-0 and Ler-1)

POLYMORPH

1001Genomes