The identification of a cleaved amplified polymorphic sequence (CAPS) marker for the flax rust resistance gene M3

A cleaved amplified polymorphic sequence (CAPS) marker has been developed for the flax rust resistance gene M3. This molecular marker was identified in a rust differential for M3 by screening primer sets, whose sequences were based on the nucleotide sequence of the M gene. One primer set was identified that co-amplified, along with other related sequences, a 2.9-kb DNA segment of M3 or an M-like gene tightly linked to the M3 locus. Restriction fragment analysis revealed several unique DNA fragments that were linked to the presence of the M3 gene in a F2 segregating population. This molecular marker along with recently developed markers for the L2, L6, L9, and L11 alleles will be useful for marker-assisted selection in breeding programs for obtaining multigenic resistance against flax rust in Canadian flax cultivars.