Detection and quantification of onion isolates of Fusarium oxysporum f. sp. cepae in onion plant

Fusarium oxysporum f. sp. cepae (FOC) isolated from onion basal rot possessed a SIX3 homolog (FocSIX3) with 91.4 % identity to the SIX3 gene (FolSIX3) of F. oxysporum f. sp. lycopersici (FOL). A primer pair (P1) was designed to detect onion FOC based on differences in nucleotide sequences between FocSIX3 and FolSIX3. P1 amplified a 106-bp-long DNA segment only from FOC isolates pathogenic to onions, but not from FOC isolated from either Welsh onion or F. oxysporum strains belonging to formae speciales other than cepae. Real-time quantitative PCR with P1 was developed to quantify onion root- and basal-plate-colonizing FOC.