Development of AFLP and STS markers linked to a waterlogging tolerance in Korean soybean landraces

Among the 400 soybean (Glycine max) landraces, we selected 3 tolerant (KAS150-9, KAS160-15, and KAS170-9) and 3 susceptible lines (KAS160-14, KAS160-20, and KAS201-6-1) by the survival percentage and injury scores. Susceptible lines showed decrease in chlorophyll content and increase in glucose and malondialdehyde (MDA) contents under waterlogging stress, while tolerant lines did not change significantly. For AFLP analysis, 8 EcoRI (+3) and 8 MseI (+3) primers used in 32 primer combinations generated a total of 2 566 bands with a mean of 80 bands per primer combination, of which 1 117 (43.5%) were clearly polymorphic between the tolerant and susceptible lines. A genetic similarity coefficient, based on cluster analysis using an unweighted pair grouping method of average (UPGMA), was 0.79 for the tolerant group, while the susceptible landraces were genetically less related, with a genetic similarity coefficient of 0.17. The 10 reproducible polymorphic PCR products present in the 3 tolerant or susceptible lines were sequenced and converted into sequence tagged site (STS) markers. These STS primer sets were designated GmWT01-GmWT06 and GmWS01-GmWS04. Two STS primer sets, GmWT06 and GmWS02, generated a single monomorphic PCR product identical in size to the original AFLP fragments. For the broad application of these STS markers in marker-assisted selection (MAS) for soybean genotypes tolerant to waterlogging stress, two developed STS markers are being evaluated with putative waterlogging tolerant mutant lines induced by gamma-radiation in soybean mutation breeding programs.