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Diseases of Onion and Garlic
(Allium cepa L. and A. sativum L., respectively)

Howard F. Schwartz, Lindsey J. du Toit, and Teresa Coutinho, collators (last update 8/30/15)

BACTERIAL DISEASES

Bacterial flower stalk and leaf necrosis

Pantoea agglomerans (Beijerinck) Gavini et al.
         (syns. Enterobacter agglomerans Beijerinck; Erwinia herbicola [Löhnis] Dye)

Pseudomonas marginalis (Brown) Stevens

Bacterial internal brown rot of bulbs

Pseudomonas aeruginosa (Schroeter) Migula

Bacterial leaf spot and flower stalk necrosis

Pseudomonas syringae pv. porri Samson et al.

P. syringae pv. syringae (van Hall) Janse

Bacterial leaf streak and bulb rot

Pseudomonas viridiflava (Burkholder) Dowson

Bacterial soft rots

Dickeya chrysanthemi (Burkholder et al.) Samson et al.
         (syn. Erwinia chrysanthemi Burkholder et al.)

E. rhapontici (Millard) Burkholder

Pectobacterium carotovorum subsp. carotovorum (Jones) Waldee emend. Hauben et al.
         (syn. Erwinia carotovora subsp. carotovora [Jones] Bergey et al.)

Pseudomonas marginalis (Brown) Stevens

Center rot

Pantoea allii Brady

P. ananatis (Serrano) Mergaert et al.
         (syn. Erwinia ananatis Serrano)

Enterobacter bulb decay

Enterobacter cloacae (Jordan) Hormaeche & Edwards

Slippery skin

Burkholderia gladioli pv. allicola (Burkholder) Young et al.
         (syn. Pseudomonas gladioli pv. alliicola [Burkholder] Young et al.)

Sour skin

Burkholderia cepacia (Palleroni & Holmes) Yabuuchi et al.
         (syn. Pseudomonas cepacia [ex Burkholder] Palleroni & Holmes)

Xanthomonas leaf blight

Xanthomonas axonopodis pv. allii (Dowson) Roumagnac et al.
         (syn. Xanthomonas campestris pv. allii [Kadota et al.] Roumagnac et al.)

FUNGAL AND OOMYCETE DISEASES

Anthracnose

Colletotrichum coccodes (Wallr.) S. Hughes

Black mold

Aspergillus niger Tiegh.

Blue mold

Penicillium aurantiogriseum Dierckx
         (syn. P. cyclopium Westling)

P. citrinum Thom

P. digitatum (Pers.:Fr.) Sacc.

P. expansum Link

P. funiculosum Thom

P. hirsutum Dierckx
         (syn. P. corymbiferum Westling)

P. oxalicum Currie & Thom

Botrytis brown stain

Botrytis cinerea Pers.:Fr.
         (syn. Botryotinia fuckeliana [de Bary] Whetzel)

Botrytis leaf blight

Botrytis squamosa J. C. Walker
         (syn. Botryotinia squamosa Vien.-Bourg.)

Botrytis rot of garlic

Botrytis porri Buchw.
         (syn. Botryotinia porri [van Beyma Thoe Kingma) Whetzel)

Cercospora leaf spot

Cercospora duddiae Welles

Charcoal rot

Macrophomina phaseolina (Tassi) Goid.
         (syn. Sclerotium bataticola Taubenh.)

Diplodia stain

Lasiodiplodia theobromae (Pat.) Griffon & Maubl.
         (syns. Botryodiplodia theobromae Pat.; Diplodia natalensis Pole-Evans)

Downy mildew

Peronospora destructor (Berk.) Casp. ex Berk.

Embellisia skin blotch and bulb canker of garlic

Alternaria embellisia Woudenb. & Crous
         (syns. Embellisia allii [Campan.] E. G. Simmons; Helminthosporium allii Campan.)

Flower and capsule blight

Botrytis aclada Fresen.
         (syn. Botrytis allii Munn)

Botrytis cinerea Pers.:Fr.
         (syn. Botryotinia fuckeliana [de Bary] Whetzel)

Botrytis squamosa J. C. Walker
         (syn. Botryotinia squamosa Vien.-Bourg.)

Fusarium basal rot

Fusarium oxysporum f. sp. cepae (H. N. Hansen) W. C. Snyder & H. N. Hansen

Fusarium basal rot of garlic

Fusarium culmorum (Wm. G. Sm.) Sacc.
         (syns. F. roseum Lk. Emend Snyd. & Hans. ‘Culmorum’; F. roseum
          var. culmorum [Schwabe] Snyd. & Hans.)

Fusarium bulb rot of onion and garlic

Fusarium proliferatum (Matsush.) Nirenberg ex Gerlach & Nirenberg

Fusarium damping-off

Fusarium equiseti (Corda) Sacc.

F. oxysporum f. sp. cepae (H. N. Hansen) W. C. Snyder & H. N. Hansen

F. proliferatum (Matsush.) Nirenberg ex Gerlach & Nirenberg
         (syn. Cephalosporium proliferatum Matsushima)

F. solani (Mart.) Sacc.

F. subglutinans (Wollenw. & Reinking) Nelson, Toussoun, & Marasas

F. tricinctum (Corda) Sacc.

F. verticillioides (Sacc.) Nirenberg
         (syn. F. moniliforme J. Sheld.)

Leaf blotch

Cladosporium allii-cepae (Ranoj.) M. B. Ellis
         (syn. Mycosphaerella allii-cepae Jordan et al.)

Mushy rot

Rhizopus microsporus Tiegh

R. stolonifer (Ehrenb.:Fr.) Vuill.
         (syn. R. nigricans [Ehrenb])

Mycelial neck rot

Botrytis byssoidea J. C. Walker
         (syn. Botryotinia allii [Sawada] W. Yamamoto)

Neck rot

Botrytis aclada Fresen.
         (syn. B. allii Munn)

Penicillium decay of garlic

Penicillium hirsutum Dierckx
         (syn. P. corymbiferum Westling)

Phyllosticta leaf blight

Phyllosticta allii Tehon & E. Y. Daniels

Pink root

Setophoma terrestris (H. N. Hansen) Gruyter, Aveskamp, & Verkley
         (syns. Phoma terrestris [H. N. Hansen] Gruyter, Aveskamp, & Verkley; 
          Pyrenochaeta terrestris [H. N. Hansen] Gorenz, J. C. Walker, & Larson)

Powdery mildew

Leveillula taurica (Lév.) G. Arnaud
         (syns. Oidiopsis sicula Scalia; O. taurica E. S. Salmon)

Purple blotch

Alternaria porri (Ellis) Cif.
         (syn. Macrosporium porri Ellis)

Pythium root rot

Globisporangium irregular (Buisman) Uzuhashi, Tojo, & Kakish
         (syn. Pythium irregulare Buisman)

P. coloratum Vaartaja

Pythium seed rot and damping-off

Globisporangium irregulare (Buisman) Uzuhashi, Tojo, & Kakish
         (syn. Pythium irregulare Buisman)

G. mamillatum (Meurs) Uzuhashi, Tojo, & Kakish
         (syn. P. mamillatum Meurs)

G. paroecandrum (Drechsler) Uzuhashi, Tojo, & Kakish
         (syn. P. paroecandrum Drechsler)

G. rostratum (E. J. Butler) Uzuhashi, Tojo, & Kakish
         (syn. P. rostratum E. J. Butler)

G. spinosum (Sawada) Uzuhashi, Tojo, & Kakish
         (syn. P. spinosum Sawada)

G. sylvaticum (W. A. Campb. & F. F. Hendrix) Uzuhashi, Tojo, & Kakish
         (syn. P. sylvaticum W. A. Campb. & F. F. Hendrix)

G. ultimum (Trow) Uzuhashi, Tojo, & Kakish
         (syn. P. ultimum Trow)

Phytopythium vexans (de Bary) Abad. De Coch, Bala, Robideau, Lodhi, & Levesque
         (syn. P. vexans de Bary)

Pythium coloratum Vaartaja

Pythium graminicola Subraman.

Pythium torulosum Coker & F. Patt.

Rhizoctonia seed rot and seedling disease

Rhizoctonia solani J. G. Kühn
         (syn. Thanatephorus cucumeris [A. B. Frank] Donk)

Rust

Puccinia allii F. Rudolphi

Scape blight

Botrytis aclada Fresen.
         (syn. Botrytis allii Munn)

Botrytis cinerea Pers.:Fr.
         (syn. Botryotinia fuckeliana [de Bary] Whetzel)

Botrytis squamosa J. C. Walker
         (syn. Botryotinia squamosa J. C. Walker)

Sclerotinia rot

Sclerotinia sclerotiorum (Lib.) de Bary

Small sclerotial neck rot

Botrytis squamosa J. C. Walker
         (syn. Botryotinia squamosa J. C. Walker)

Smudge

Colletotrichum circinans (Berk.) Voglino
         (syns. C. dematium f. sp. circinans [Berk.] Arx; Vermicularia circinans Berk.)

Smut

Urocystis colchici (Schltdl.) Rabenh.

U. magica Pass.
         (syn. U. cepulae Frost)

Soil-line rot

Botrytis aclada Fresen.
         (syn. Botrytis allii Munn)

Botrytis squamosa J.C. Walker
         (syn. Botryotinia squamosa J. C. Walker)

Southern blight

Athelia rolfsii (Curzi) Tu & Kimbr.
         (syn. Sclerotium rolfsii Sacc.)

Stemphylium leaf blight and stalk rot

Stemphylium vesicarium (Wallr.) E. G. Simmons
         (syn. Pleospora allii [Rabenh.] Ces. & De Not.)

Twister

Colletotrichum gloeosporioides (Penz.) Penz. & Sacc. in Penz.
         (syn. Glomerella cingulata [Stoneman] Spauld. & H. Schrenk)

White rot

Sclerotium cepivorum Berk.

NEMATODES (PARASITIC)

Lesion nematode:

Pratylenchus penetrans (Cobb) Filipjev et Schuurmans Stekhoven

Needle nematode:

Longidorus africanus Merny

Root-knot nematodes:

Meloidogyne chitwoodi Golden et al.

M. graminicola Golden & Birchfield

M. hapla Chitwood

M. incognita (Kofoid & White) Chitwood

M. javanica (Treub) Chitwood

Stem and bulb (Bloat) nematode:

Ditylenchus dipsaci (Kühn) Filipjev

Sting nematode:

Belonolaimus longicaudatus Rau

Stubby-root nematodes:

Paratrichodorus allius (Jensen) Siddiqi

P. minor (Colbran) Siddiqi

NONINFECTIOUS DISEASES, DISORDERS, AND DAMAGE

Air pollution injury

Ozone

Basal plate splitting

Uneven irrigation; wide fluctuations in soil moisture and excess nitrogen fertility

Chemical damage

Herbicides, fertilizers, insecticides

Corkscrewing of leaves

Zinc deficiency in muck soils and in alkaline soils (pH > 7.5)

Environmental stresses

Hot and cold temperatures, hail injury, lightning injury, sunscald

Greening (of bulbs)

Exposure of bulbs to light, especially immature bulbs

Leaf variegation (Chimera)

Genetic abnormality

Nutritional disorders

Mineral deficiencies and toxicities

Pinking (of white onions)

Bruising during harvest or handling

Soil-related injury

Soil acidity, alkalinity (pH), and salinity

Splitting of external fleshy scales (of bulbs)

Excess nitrogen during bulb formation

Translucent and leathery scale (Watery scale)

Cause unknown

Waxy breakdown (of garlic)

Associated with high temperatures near harvest time

PARASITIC HIGHER PLANT

Dodder (Cuscuta spp.)

PHYTOPLASMA DISEASE

Aster yellows

Aster yellows phytoplasma

Onion yellows phytoplasma

VIRUS DISEASES

Garlic mosaic

Genus Allexivirus; Garlic viruses A-D (GVA, GVB, GVC, GVD), Garlic virus X (GVX), 
        Garlic mite-borne mosaic virus (GMbMV), Shallot virus X (ShVX)

Genus Potyvirus; Garlic common latent virus (GCLV), Garlic mosaic virus (GMV), Leek
         yellow stripe virus (LYSV), Onion yellow dwarf virus (OYDV), Shallot latent
         virus (SLV)

Iris yellow spot

Genus Tospovirus; Iris yellow spot virus (IYSV)

Onion yellow dwarf

Genus Potyvirus; Onion yellow dwarf virus (OYDV)

YEAST DISEASE

Yeast soft rot

Kluyveromyces marxianus (E. C. Hansen) Van der Walt