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The rust fungi are described as biotrophs; that is, they grow within the living tissues of the plant and extract nutrients from the cells without killing them. However, although they do not kill tissues, heavy attacks by rusts can cause the leaves to shrivel and die prematurely and can depress vigour.
Rusts are not able to survive on dead plant material, so must either alternate with a different, perennial host, or produce resting spores to pass the dormant season.
The leek rust pathogen seems to fulfil its entire life cycle on leeks, without the need for an alternate host. On some other Allium species the fungus begins to produce dark resting spores within the orange pustules as the foliage dies down . These resting spores have been observed occasionally on leeks, but the role that they play in the disease on this crop is currently unknown. It is likely that there are simply sufficient leeks in the ground at all times of the year to ensure continuity of infection, without the need for resting spores.
Puccinia allii has been confirmed as being seed-borne, but this is not currently thought to be of any great significance in the spread of the disease.
It is thought that a number of strains of P. allii exist, varying in their ability to infect different Allium species.
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I have have all the same problems you have had,
If your onions were off sets it is normal for them to fall over because they are ready to be harvested,use a garden fork to dig them up and try not to damage the onion then leave them on the soil to dry.( if you are lucky to have some sun.), then you can store them.