Characterisation of Botrytis species associated with neck rot of onion in Australia
Neck rot of onion has commonly been attributed to two fungal pathogens, Botrytis aclada (syn. B. allii) and B. byssoidea. However, in other countries, a recently developed PCR technique using sequence characterised amplified region (SCAR) primers (BA2f/BA1r) followed by ApoI digestion of the amplification product, has shown the presence of two groups within B. aclada, B. aclada AI and B. aclada AII syn. B. allii. This method was used to characterise Botrytis spp. of the B. aclada/B. allii complex associated with onion seed and bulbs in Australia. A total of 24 Botrytis isolates, including two from seed and ten from bulbs (Tasmania), five from seed (South Australia), and one from seed and six from a culture collection originally isolated from five bulbs and one stipe (New South Wales), were characterised. Of the 24 isolates, one was identified as B. cinerea, one as B. aclada AI, and 22 as B. aclada All syn. B. allii.
Universally Primed Polymerase Chain Reaction Alleles and Internal Transcribed Spacer Restriction Fragment Length Polymorphisms Distinguish Two Subgroups in Botrytis aclada Distinct from B. byssoidea.
ABSTRACT Fifty-one isolates representing the four Botrytis spp. associated with onion neck rot were clustered by unweighted pair group method with arithmetic mean based on universal-primed polymerase chain reaction (UP-PCR) fingerprints. Bootstrap analysis of the consensus phenogram clearly demonstrated five strong clusters among the four Botrytis spp.: B. cinerea (C), B. squamosa (S), B. byssoidea (B), and B. aclada (AI and AII). Subdivision of the 30 B. aclada isolates, AI (14) and AII (16), from Europe, Egypt, North America, and Japan was further supported by restriction analysis of the internal transcribed spacer of the ribosomal genes and spore size measurements. Gene diversities (H) among AI and AII isolates were very low (0.007 and 0.043, respectively). A likelihood ratio chi-square test (G(2)) of Nei's coefficient of genetic differentiation (G(ST)) showed that both B. aclada subgroups, AI and AII, were significantly different from B. byssoidea (P < 0.001), and that B. aclada subgroups AI and AII were significantly different from each other (P < 0.001). No UP-PCR alleles were shared by AI and B. byssoidea isolates, whereas 10 and 12 alleles were shared by AI:AII and AII:B. byssoidea, respectively. The hypothesis that AII may be a hybrid between AI and B. byssoidea is discussed.
Neck rot (Botrytis allii) of bulb onions I. Seed-borne infection and its relationship to the disease in the onion crop.
SUMMARY 
 
Experiments on neck rot of onions, caused by Botrytis allii showed that, although the disease only became evident in store, a major source of the pathogen was samples of infected seeds. In 1972 and 1973, 39·5 and 71·4% respectively of commercial onion seed samples tested at Wellesbourne were infected. The pathogen was internal in seed and persisted for 3 ½ yr in infected seeds kept in a seed store at 10°C and 50% r.h. 
 
 
 
Seedlings raised from diseased seeds became infected by mycelial invasion of the cotyledon leaf tips from seed-coats many of which remained attached to the cotyledons when seedlings emerged from the soil. The fungus attacked the living tissues of these leaves symptomlessly, producing conidiophores only after the leaf tissue senesced and became necrotic. Because the fungus was symptomless, the rate of spread of the pathogen in onion crops was assessed by incubating successive samples of plants from the field in humid conditions when infected tissues developed conidiophores of the fungus. This method showed that the disease was progressive in onion crops spreading more rapidly in wet humid conditions (e.g. 1972) than in dry ones (e.g. 1973). The principal means of spread were probably fungal spores; conidiophores bearing spores being produced abundantly on plants in the field under high humidity. The fungus invaded the leaves of plants successively, first infecting each leaf at the tip and then growing downwards in the tissues and eventually invading the neck of the onion bulb via the leaves which emerged directly from the top of the neck. By harvest, the fungus was situated deep within the neck tissues of infected maturing onion bulbs.