Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is one of the most economically damaging pests of soybean. The damage can only be effectively controlled through the use of resistant soybean [Glycine max (L.) Merr.] cultivars. Since QTL mapping is a highly effective approach for studying genetically complex forms of plant resistance to pests, it should be used to identify and map QTLs for resistance to SCN from various genetic backgrounds. The objective of the present study was to identify closely linked DNA markers to QTLs for resistance to SCN race 3 in the cultivar Toyomusume derived from a resistant cultivar Gedenshirazu, using the AFLP (amplified fragment length polymorphism) method combined with bulked segregant analysis (BSA). A population of 115 recombinant inbred lines (RILs) derived from a cross of Toyomusume (resistant) and Tsurukogane (susceptible) was used to map QTLs related to the resistance to SCN race 3. After genotyping of all the RILs with molecular markers including AFLP, RFLP, SSR and RAPD markers, composite interval mapping was performed for QTL analysis. In addition to known rhg1 on the linkage group (LG) G, two significant QTLs, rhg-t1 and rhg-t2, on the linkage group B1 near the AFLP markers CAT_CTC1 and GTC_ATT, respectively, were identified using two experimental assays. Epistatic analysis suggested that the combination of rhg1 and rhg-t1 could provide a higher level of resistance to SCN race 3, compared to any single QTL. The AFLP markers surrounding rhg1 and rhg-t1 could be used for markerassisted selection of SCN resistance derived from Gedenshirazu, when converted to PCR-based markers.

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