Invasive Species Compendium

Detailed coverage of invasive species threatening livelihoods and the environment worldwide


Ciborinia allii
(neck rot of onion)



Ciborinia allii (neck rot of onion)


  • Last modified
  • 27 September 2018
  • Datasheet Type(s)
  • Documented Species
  • Pest
  • Preferred Scientific Name
  • Ciborinia allii
  • Preferred Common Name
  • neck rot of onion
  • Taxonomic Tree
  • Domain: Eukaryota
  •   Kingdom: Fungi
  •     Phylum: Ascomycota
  •       Subphylum: Pezizomycotina
  •         Class: Leotiomycetes
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Preferred Scientific Name

  • Ciborinia allii (Sawada) L.M. Kohn 1979

Preferred Common Name

  • neck rot of onion

Other Scientific Names

  • Botryotinia allii (Sawada) W. Yamam 1956
  • Botrytis byssoidea J.C. Walker 1925
  • Sclerotinia allii Sawada 1919

EPPO code

  • BOTRBY (Botryotinia allii)

Taxonomic Tree

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  • Domain: Eukaryota
  •     Kingdom: Fungi
  •         Phylum: Ascomycota
  •             Subphylum: Pezizomycotina
  •                 Class: Leotiomycetes
  •                     Subclass: Leotiomycetidae
  •                         Order: Helotiales
  •                             Family: Sclerotiniaceae
  •                                 Genus: Ciborinia
  •                                     Species: Ciborinia allii

Notes on Taxonomy and Nomenclature

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There has been a certain lack of clarity in the literature about the species of Botryotinia and Botrytis causing neck rot on onion. Sclerotinia allii was described without a conidial anamorph by Sawada in 1919, while Munn described a conidia-producing onion pathogen, Botrytis allii, in 1917 (Jarvis, 1977). The fungus mainly referred to in the literature is the anamorph Botrytis byssoidea, which was described by Walker (1925). Most authors do not refer to any teleomorph of B. byssoidea, which is treated as though it were anamorphic only. In fact, a teleomorph for B. byssoidea was recognized in Japan as Botryotinia allii (Yamamoto et al., 1956), although the new combination based on Sawada’s species was, unfortunately, invalidly published due to that lack of reference to the basionym as required by the ICBN (Lanjouw, 1956). Kohn (1979) transferred the species to Ciborinia, noting that no sporulation of the Botrytis anamorph could be obtained in culture. Nevertheless, the fungus has been found to sporulate on infected plants when it would not do so on standard media (Shirane et al., 1989). Furthermore, an investigation of the phylogeny of some species placed in Ciborinia (not including C. allii) has shown the genus to be polyphyletic, and its restriction to species affecting woody dicots has been suggested (Holst-Jensen et al., 1997).

Jarvis (1977; 1980) did not address the question of the anamorph-teleomorph connection. Some authors (Moore, 1959; Smith et al., 1988) cite a report that B. byssoidea is the anamorph of Botryotinia porri. However, this would imply that B. byssoidea is synonymous with Botrytis porri, which is mistaken, at least according to the authoritative views of Hennebert (1973), who placed B. allii in synonomy with Botrytis aclada instead.

Lacy and Lorbeer (1995) have suggested further that B. byssoidea may be conspecific with Botrytis allii, which has no known teleomorph. B. allii has since been shown, in fact, to be a natural hybrid resulting from a cross of B. byssoidea with B. aclada (Nielsen et al., 2002; Staats et al., 2005); the hybrid has 32 chromosomes, whereas each parent species has 16 (Shirane et al., 1989). Thus the relationship of these three species is clarified, although the identities of the various organisms reported or collected from onions [Allium cepa] worldwide (UK CAB International 1980; 1987) may not be.


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Sawada (1919) described Sclerotinia allii as having stipitate apothecioid ascomata containing cylindrical asci, 184-212 x 12-18 µm, with eight ascospores, 17-21 x 7-11 µm. According to Yamamoto et al. (1956), ascomata of Botryotinia allii arising from sclerotia are disc-shaped, stipitate and pale brown, nearly glabrous, with cylindrical asci, 136-190 x 10-16 µm, containing eight hyaline ellipsoid spores, 15-23 x 8-12 µm. Paraphyses filiform, hyaline, septate, with two to three branches. Sclerotia blackish-brown to black, subepidermal, densely pitted on the upper surface, 1-7 x 0.5-2.0 µm, 0.3-0.7 µm thick, outer layer pseudoparenchymatous, interior hyaline. Microconidia globose, 3-4 µm in diameter. The microconidia, sclerotia, conidiophores and conidia matched Walker’s description of Botrytis byssoidea. Cottony white mycelium, sclerotia and “a few conidia” were obtained in culture.

Tamura et al. (1996) reported the apothecia of Ciborinia allii, obtained in culture on potato dextrose agar (PDA) under continuous light, to be pale yellow and 1.0-2.5 µm in diameter, with clavate asci 198-257 x 11-13 µm (longer than those in Yamamato et al.), and larger ascospores 19-22 x 9-11 µm. Leu and Wu (1985) described the larger spores in Taiwan as 20 x 10 µm; the smaller ones were 12 x 10 µm and did not germinate. Ascospores of differing sizes in the same ascus are not mentioned in Sawada’s description, but are shown in one of the accompanying illustrations (Sawada, 1919).

Erect conidiophores of B. byssoidea arise directly from a hyaline septate mycelium. They are light to dark brown, septate and thick-walled, with a swollen base and occasional branches that are constricted at their bases. Branches at the apex themselves bear round-ended, shorter branches (“ampullae”), which produce conidia; these shorter branches die and collapse after sporulating. Conidia are obovoid, smooth, one-celled, initially colourless, becoming pale brown and appearing grey in mass, 8-19 x 5-11 µm, mostly 10-14 x 6-9 µm (Walker, 1925). Walker’s description also included microconidia and sclerotia; sclerotia were reported to germinate by means of hyphae or by producing conidiophores.

Hennebert (1973) recognized B. byssoidea as distinct from B. allii, which he considered synonymous to Botrytis aclada. Presly (1985) described B. byssoidea as producing conidia on average 13.0 x 7.5 µm, larger than those of B. allii (av. 10.2 x 5.25 µm), but smaller than those of Botryotinia porri (av. 15.7 x 9.6 µm). B. byssoidea was distinguished from B. allii in culture by its growth as white fluffy sterile mycelium, not producing abundant conidia. It also differed from B. porri and Botryotinia squamosa by not producing sclerotia in culture (Presly, 1985). Shirane et al. (1989) distinguished B. byssoidea by conidium size, L/W, and number of nuclei, but also noted its inability to sporulate on the culture media utilized for obtaining sporulation of other Botrytis species, so that the conidia examined had to be obtained from inoculated onions.

The relationships among three of the Botrytis species on Allium have been elucidated through examination of molecular biology. Comparison of DNA sequences revealed that Botrytis allii is a hybrid of the two other species, B. aclada and B. byssoidea, and bears alleles of genes from each. Each of the parents has 16 chromosomes, whereas the hybrid has 32 (Nielsen et al., 2001; 2002; Staats et al., 2005).

Distribution Table

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The distribution in this summary table is based on all the information available. When several references are cited, they may give conflicting information on the status. Further details may be available for individual references in the Distribution Table Details section which can be selected by going to Generate Report.

Continent/Country/RegionDistributionLast ReportedOriginFirst ReportedInvasiveReferenceNotes


ChinaPresentTai, 1979; Zhang, 2006
JapanPresentUK CAB International, 1980; Tamura et al., 1996; EPPO, 2014
Korea, Republic ofPresentCho and Shin, 2004
TaiwanPresentBPI, US National Fungus Collections; Leu and Wu, 1985


EgyptPresentHafez et al., 2013

North America

USARestricted distributionEPPO, 2014
-CaliforniaPresentUK CAB International, 1980; EPPO, 2014
-ConnecticutPresentUK CAB International, 1980; EPPO, 2014
-IdahoPresentUK CAB International, 1980; EPPO, 2014
-IllinoisPresentUK CAB International, 1980; EPPO, 2014
-IndianaPresentUK CAB International, 1980; EPPO, 2014
-MassachusettsPresentUK CAB International, 1980; EPPO, 2014
-New YorkPresentUK CAB International, 1980; EPPO, 2014
-WashingtonPresentUK CAB International, 1980; EPPO, 2014
-WisconsinPresentUK CAB International, 1980; EPPO, 2014

Central America and Caribbean

Dominican RepublicPresentCiferri, 1961

South America

-Santa CatarinaPresentBoff, 1994


BulgariaWidespreadIntroducedUK CAB International, 1980; EPPO, 2014
DenmarkPresentUK CAB International, 1980; EPPO, 2014
NetherlandsPresentUK CAB International, 1980; EPPO, 2014
NorwayWidespreadIntroducedUK CAB International, 1980; EPPO, 2014
PolandPresentUK CAB International, 1980; EPPO, 2014
UKWidespreadIntroducedUK CAB International, 1980; EPPO, 2014
-England and WalesPresentEPPO, 2014
-ScotlandPresentEPPO, 2014


AustraliaRestricted distributionEPPO, 2014
-New South WalesPresentUK CAB International, 1980; EPPO, 2014
New ZealandPresentUK CAB International, 1980; EPPO, 2014

Risk of Introduction

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It is doubtful whether B. byssoidea is in itself sufficiently important to present a phytosanitary risk, especially as the more important Botrytis allii is very widespread. The sclerotial form of Botryotinia allii has been intercepted in international trade in the past (BPI, 2009), but the hybrid Botrytis species, already in existence, may represent the actual fulfilment of the threat of genetic recombination posed by the existence of a sexually reproducing form of the fungus.

Habitat List

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Terrestrial – ManagedCultivated / agricultural land Present, no further details Harmful (pest or invasive)

Hosts/Species Affected

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Sawada (1919) reported C. allii as a pathogen of onions (Allium cepa) and Welsh onions (Allium fistulosum; also called Japanese onion). Yamamoto et al. (1956) were able to obtain infection by inoculation with mycelium on “garlics, Allium fistulosum var. caespitosum, Allium bakeri [Allium chinense], Allium ledebourianum, Allium tuberosum, and Allium grayi [Allium macrostemon]” as well.

C. allii has been recorded on onions from locations on most of the continents (UK CAB International, 1980; BPI, 2009). Presly (1985) obtained isolates identified as 'B. byssoidea' from leeks (Allium porrum) in the UK, but it is not clear what disease they caused on that crop. In Japan, Takakuwa et al. (1974) also found C. allii on leeks; sclerotia of S. allii were also reported to be present. Cho et al. (1995) reported that C. allii was the cause of a storage rot of garlic bulbs (Allium sativum) in Korea. Disease on A. fistulosum in Taiwan (Leu and Wu, 1985) and Japan (Tamura et al., 1996) was attributed to C. allii, with accompanying descriptions of the teleomorph, but no mention of an anamorph. Zhang (2006) reports C. allii on onion, garlic and Aloe vera var. chinensis, but, except for A. tuberosum, not on the other primarily Asian Allium spp. tested by Yamamoto et al. (1956).

Growth Stages

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Infection of the leaves and flower stems of Allium spp. by C. allii results in pale, water-soaked spots that spread longitudinally toward the tips and base (Yamamato et al., 1956). Leaves wilt and/or turn yellow, brown and/or greyish white, and collapse (Leu and Wu, 1985). Sporulation occurs on dying or dead tissue and black sclerotia are formed in the leaves.

C. allii causes a neck rot of onion very similar to that caused by Botrytis allii (Lacy and Lorbeer, 1995). Scale tissue becomes soft, water-soaked and translucent, beginning in the neck area and continuing down into the bulb. However, Dixon (1981) and Presly (1985) distinguish the neck rot caused by C. allii as “mycelial neck rot”, referring to the visible presence of mycelium without conidia or sclerotia, in contrast to “grey mould neck rot” due to B. allii and with abundant conidia and “sclerotial neck rot” due to Botryotinia squamosa, which produces many sclerotia.

List of Symptoms/Signs

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SignLife StagesType
Vegetative organs / dry rot
Vegetative organs / internal rotting or discoloration
Vegetative organs / mould growth

Biology and Ecology

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The biology and ecology of C. allii is, as far as is known, very similar to that of Botrytis allii. Infection of the leaves and flower stems results in pale, water-soaked spots that spread longitudinally toward the tips and base (Yamamato et al., 1956). The relative roles of ascospores and conidia in initiating infections have not been investigated. Leaves wilt and turn yellow, then brown (Leu and Wu, 1985). The fungus infects the neck of the bulb from the leaves, and sporulation occurs on dead or dying tissues under moist, cool conditions. The production and spread of airborne conidia results in secondary infections under humid conditions in the field and in storage (Maude and Presly, 1977a; Lacy and Lorbeer, 1995).

The cardinal growth temperatures (minimum, optimum, maximum) for C. allii were found to be 2, 24, and 28°C (Leu and Wu, 1985). Sclerotia are produced in the leaves (Yamamoto et al., 1956) and at the neck of the bulb (Lacy and Lorbeer, 1995). These can survive in and on the soil through the summer in Taiwan, germinating at 8-26°C in 10-15 days to produce apothecia (Leu and Wu, 1985). In the cooler climate of Europe, the sclerotia of B. allii were found to persist for 2 years in the soil (Maude et al., 1982).


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Cf - Warm temperate climate, wet all year Preferred Warm average temp. > 10°C, Cold average temp. > 0°C, wet all year
Df - Continental climate, wet all year Preferred Continental climate, wet all year (Warm average temp. > 10°C, coldest month < 0°C, wet all year)

Means of Movement and Dispersal

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Natural Dispersal (Non-Biotic)

C. allii is principally dispersed by wind or rain movement of its conidia (Stewart and Franicevic, 1994; Lacy and Lorbeer, 1995).

Accidental Introduction

C. allii is principally moved in infected onion bulbs, for planting or consumption (Lacy and Lorbeer, 1995).

Seedborne Aspects

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Seed Transmission

Although Botrytis allii is definitely seed-transmitted (Maude and Presly, 1977a), there is no specific evidence that this is the case for C. allii. Stewart and Franicevic (1994) isolated C. allii from onion seeds, although at a much lower rate than B. allii. They then obtained transmission to seedlings only with B. allii when both fungi were present in one seed lot.

Pathway Causes

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CauseNotesLong DistanceLocalReferences
Horticulture Yes Yes Lacy and Lorbeer, 1995
Seed trade Yes Yes Lacy and Lorbeer, 1995

Pathway Vectors

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VectorNotesLong DistanceLocalReferences
Plants or parts of plantsseed Yes Yes Stewart and Franicevic, 1994
Windconidia Yes Lacy and Lorbeer, 1995

Plant Trade

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Plant parts liable to carry the pest in trade/transportPest stagesBorne internallyBorne externallyVisibility of pest or symptoms
Bulbs/Tubers/Corms/Rhizomes hyphae; sclerotia; spores Yes Yes Pest or symptoms not visible to the naked eye but usually visible under light microscope
Leaves hyphae; sclerotia; spores Pest or symptoms not visible to the naked eye but usually visible under light microscope
True seeds (inc. grain) hyphae Pest or symptoms not visible to the naked eye but usually visible under light microscope
Plant parts not known to carry the pest in trade/transport
Fruits (inc. pods)
Growing medium accompanying plants
Seedlings/Micropropagated plants
Stems (above ground)/Shoots/Trunks/Branches

Impact Summary

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Economic/livelihood Negative


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C. allii is associated with the same serious neck-rot disease of onion as Botrytis allii. In general, B. allii is considered to be the more important of the two (Presly, 1985; Stewart and Franicevic, 1994; Lacy and Lorbeer, 1995). Losses of up to 50% have been reported due to neck rot of onions in storage (Kritzman and Netzer, 1978).

Risk and Impact Factors

Top of page Invasiveness
  • Fast growing
  • Has high reproductive potential
  • Reproduces asexually
Impact outcomes
  • Host damage
  • Negatively impacts agriculture
Impact mechanisms
  • Pathogenic
Likelihood of entry/control
  • Difficult to identify/detect as a commodity contaminant
  • Difficult to identify/detect in the field


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Nielsen et al. (1999) obtained a PCR primer specific for Botrytis allii; DNA from Botrytis byssoidea or Botrytis squamosa was not amplified. A real-time PCR assay for only the three Botrytis species causing neck rot has since been developed (Chilvers et al., 2007), as well as a serological ELISA test specific to B. allii (Linfield et al., 1995). Shirane et al. (1989) showed that, in addition to the size and length/breadth ratio of the conidia, the species could be distinguished by the mean number of nuclei in each conidium: 1.3-1.5 for B. allii, about 5 for B. byssoidea, and about 18 for B. squamosa. However, they note that conditions of growth can affect the number of nuclei. In the absence of sophisticated instrumentation, B. byssoidea could be distinguished by its failure to sporulate in culture on potato dextrose agar (PDA) and the size of conidia obtained on infected plants (Yohalem et al., 2003).

Similarities to Other Species/Conditions

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All the Botrytis species that cause disease on Allium spp. produce globose/ovoid/elliptical conidia on apically branched, brown conidiophores. Conidial dimensions have been used to distinguish them (Ellis, 1971):

Botrytis byssoidea - 10-14 x 6-9 µm;

Botrytisallii - 7-11 x 5-6 µm;

Botrytisaclada - 8-9 x 4-5 µm (see Shirane et al., 1989);

Botrytissquamosa [Botryotinia squamosa] - 15-21 x 13-16 µm;

Botrytisporri [Botryotinia porri] - 11-14 x 7-10 µm;

Botrytiscinerea - 8-14 x 6-9 µm.

B. byssoidea is almost exclusively mycelial in culture, whereas B. allii sporulates readily and profusely (Owen et al., 1950). B.squamosa readily produces thin black sclerotia in culture on potato dextrose agar (PDA), but B. allii and B. byssoidea do not, according to Walker (1925). Yamamoto et al. (1956), on the other hand, found that Botryotinia allii readily produced sclerotia in their cultures. B. porri may be distinguished in culture by its large, irregular, cerebriform sclerotia (Ellis, 1971).

Also refer to ‘Description’.

Prevention and Control

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Good agricultural hygiene will prevent the persistence of sclerotia or infected crop debris in the soil (Maude et al., 1982). Leu and Wu (1985) found that sclerotia of C. allii could survive at some level in the soil through the summer in Taiwan.

Agricultural practices that would create cool moist conditions, favourable to the fungus, in the upper layers of the soil should be avoided, in particular in relation to irrigation (Moore, 1959; Crowe et al., 1995).

No particular chemical control is recommended, but treatments developed for the control of Botrytis allii should be effective (Smith et al., 1988; Chilvers et al., 2006).

In storage, leeks [Allium porrum] should be kept at a sufficiently low temperature. Alternatively, increasing the carbon dioxide content of the storage atmosphere, and decreasing the oxygen content, will prevent development of the fungus (Hoftun, 1978).

Neck rot of onions in storage can be controlled in part with cultural practices that encourage “curing” of the neck, such as planting at a proper density, restricting the use of nitrogen fertilizer, and undercutting to remove roots in the field. However, warm air drying of bulbs may still be required before storage, and proper ventilation should be maintained during storage (Lacy and Lorbeer, 1995), because neck rot incidence increases in years of wet or humid weather (Maude and Presly, 1977b; Maude, 2006).

Gaps in Knowledge/Research Needs

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The connection between the presumed teleomorph Botryotinia allii (known from Japan and Taiwan) and the anamorph Botrytis byssoidea has not been deliberately investigated.

Seedborne transmission of B. byssoidea has neither been established nor disproved.


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Boff P, 1994. A complex of Botrytis spp. causing onion diseases. Agropecuaria Catarinense, 7(3):14-16.

BPI (US National Fungus Collections), 2009. Fungal Databases - Specimens. Beltsville, USA: Systematic Mycology and Microbiology Laboratory, Agricultural Research Service, USDA.

Chilvers MI; Hay FS; Hills J; Dennis JJC; Wilson CR, 2006. Influence of benzimidazole fungicides on incidence of Botrytis allii infection of onion leaves and subsequent incidence of onion neck rot in storage in Tasmania, Australia. Australian Journal of Experimental Agriculture, 46(12):1661-1664.

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Kohn LM, 1979. Delimitation of the economically important plant pathogenic Sclerotinia species. Phytopathology, 69:881-886

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Links to Websites

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Diagnosis and control of onion


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10/09/09 Updated by:

Systematic Mycology & Microbiology Laboratory, USDA-ARS, 10300 Baltimore Ave., Beltsville, MD 20705, USA

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