In recent years in Finland, Fusarium infections in onions have increased, both in the field and in storage, and Fusarium species have taken the place of Botrytis as the worst pathogens causing post‐harvest rot of onion. To study Fusarium occurrence, samples were taken from onion sets, harvested onions and also from other plants grown in the onion fields. Isolates of five Fusarium species found in the survey were tested for pathogenicity on onion. Fusarium oxysporum was frequently found in onions and other plants, and, of the isolates tested, 31% caused disease symptoms and 15% caused growth stunting in onion seedlings. Fusarium proliferatum, a species previously not reported in Finland, was also identified. Over 50% of the diseased onion crop samples were infected with F. proliferatum, and all the F. proliferatum isolates tested were pathogenic to onion. Thus, compared to F. oxysporum, F. proliferatum seems to be more aggressive on onion. Also some of the F. redolens isolates were highly virulent, killing onion seedlings. Comparison of the translation elongation factor 1α gene sequences revealed that the majority of the aggressive isolates of F. oxysporum f. sp. cepae group together and are distinct from the other isolates. Incidence and relative proportions of the different Fusarium species differed between the sets and the mature bulbs. More research is required to determine to what extent Fusarium infections spoiling onions originate from infected onion sets rather than the field soil.

Several Fusarium species cause disease in onion (Allium cepa), resulting in significant yield losses. In this study, isolates of Fusarium oxysporum and Fusarium proliferatum from diseased and symptomless mature onion bulbs were tested for pathogenicity on onion seedlings and mature bulbs. For F. oxysporum isolates, the outcome of the test on mature bulbs correlated well with the symptom status of the original bulb, whereas for F. proliferatum, such a correlation was not seen, suggesting a different mechanism of symptom development. Those F. oxysporum isolates that carried the Secreted In Xylem (SIX) genes, CRX genes and C5 gene were significantly more aggressive on both seedlings and mature bulbs. However, the SIX‐negative F. oxysporum isolates also significantly reduced the emergence of onion seedlings, and thus a division into pathogenic and nonpathogenic F. oxysporum isolates was not obvious. On mature bulbs, those SIX‐negative isolates that carried the gene CRX2 were significantly more virulent than those without CRX2. The F. proliferatum isolates were all pathogenic to onion and carried one SIX2 gene homologue, SIX2‐1. The majority of F. proliferatum isolates also carried another homologue, SIX2‐2. Several isolates negative for SIX2‐2 had another potential virulence gene, CRX2, suggesting that these two genes could encode overlapping functions. The SIX2‐2 sequence was identical in all those isolates harbouring it, while SIX2‐1 showed variation that agreed with the phylogeny based on the translation elongation factor 1‐α sequence. This suggests that the two SIX2 genes of F. proliferatum might have been acquired separately.