Development of sequence-characterized amplified regions (SCARs) from amplified fragment length polymorphism (AFLP) markers tightly linked to the Vf gene in apple

Amplified fragment length polymorphism (AFLP) markers have become widely us ed in saturating the region of a gene of interest for the ultimate goal of map-based cloning of the gene or for marker-assisted selection. However, co nversion of AFLP markers into restriction fragment length polymorphism (RFL P) or polymerase chain reaction (PCR)-based markers will greatly expand the ir usefulness in genetic applications. Previously, we have identified 15 AF LP markers tightly linked to the Vf gene conferring scab resistance in appl e. In this study, we have successfully converted 11 of these AFLPs into seq uence-characterized amplified region (SCAR) markers. Of the remaining four nonconverted AFLP markers, one, ET2MC8-1, has been found to be very short ( 83 base pairs) and is an A/T rich (90%) marker; a second, EA2MG11-1, has sh own identical sequences between Malus floribunda 821 (the original source o f the Vf gene) and scab-susceptible apple cultivars; while the other two, E A12MG16-1 and ET8MG1-1, have not been cloned. Using the 11 converted SCAR m arkers along with 5 previously identified SCAR markers, a high-resolution l inkage map around the Vf gene has been constructed, and found to be consist ent with its corresponding AFLP map. Three converted SCAR markers (ACS-3, - 7, and -9) are inseparable from the Vf gene; whereas one (ACS-6) is located left of, and the remaining seven (ACS-1, -2, -4, -5, -8, -10, and -11) are located right of the Vf gene at genetic distances of 0.4 and 0.2 cM, respe ctively. A reliable and robust procedure for development of SCAR markers fr om AFLP markers is presented.