A genetic map of an interspecific cross in Allium based on amplified fragment length polymorphism (AFLP™) markers

Segregation of 692 polymorphic AFLP(TM) (amplified fragment length polymorphism) fragments was determined in an F-2 Of the interspecific cross A. roylei x A. cepa. Two different enzyme combinations were used, PstI/MseI and EcoRI/MseI; in the latter one extra selective nucleotide was added to the MseI primer. The map based on A. cepa markers consisted of eight linkage groups with 262 markers covering 694 cM of the expected 800 cM. The map based on A. roylei markers comprised 15 linkage groups with 243 markers and had a length of 626 cM. The two maps were not integrated, and 25% of the markers remained unlinked. One of the alliinase genes and a SCAR marker linked to the disease resistance gene to downy mildew are present on this map. Of the AFLP markers, 50-80% were polymorphic between A. cepa and A. roylei; the level of polymorphic markers between different A. cepa accessions was 4-8%.