title: Molecular identification of two vegetative compatibility groups of Fusarium oxysporum f. sp. cepae.
abstract: Fusarium oxysporum f. sp. cepae, which causes basal rot of onion, consists of seven vegetative compatibility groups (VCGs 0420 to 0426) and several single-member VCGs (SMVs). F. oxysporum f. sp. cepae populations in South Africa and Colorado each consist of one main VCG (namely, VCG 0425 and 0421, respectively). The aim of this study was to develop sequence-characterized amplified region (SCAR) markers for the identification of VCGs 0425 and 0421, using 79 previously characterized F. oxysporum isolates. A second aim was to investigate the prevalence of VCG 0425 among 88 uncharacterized South African onion F. oxysporum isolates using (i) the developed SCAR markers and (ii) inter-retrotransposon (IR)- and random amplified polymorphic DNA (RAPD) fingerprinting. Only two RAPD primers provided informative fingerprints for VCG 0425 isolates but these could not be developed into SCAR markers, although they provided diagnostic fragments for differentiation of VCG 0425 from VCG 0421. IR fingerprinting data were used to develop a multiplex IR-SCAR polymerase chain reaction method for the identification of VCG 0421, VCG 0425, and SMV 4 isolates as a group. Molecular identification of the uncharacterized collection of 88 F. oxysporum isolates (65 F. oxysporum f. sp. cepae and 23 F. oxysporum isolates nonpathogenic to onion) confirmed that VCG 0425 is the main VCG in South Africa, with all but 3 of the 65 F. oxysporum f. sp. cepae isolates having the molecular characteristics of this VCG. Genotyping and VCG testing showed that two of the three aforementioned isolates were new SMVs (SMV 6 and SMV 7), whereas the third (previously known as SMV 3) now belongs to VGC 0247.
authors.affiliation: Department of Plant Pathology, Stellenbosch University, Matieland, 7600, South Africa.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Southwood
authors.forename: Altus
authors.initials: A
authors.lastname: Viljoen
authors.forename: Glaudina
authors.initials: G
authors.lastname: Mostert
authors.forename: Adéle
authors.initials: A
authors.lastname: McLeod
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D016172:DNA Fingerprinting; D017931:DNA Primers / Q000737:chemistry; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D005670:Fusarium / Q000235:genetics* / Q000302:isolation & purification* / Q000472:pathogenicity; D005819:Genetic Markers; D014644:Genetic Variation / Q000235:genetics*; D005838:Genotype; D008969:Molecular Sequence Data; D060885:Multiplex Polymerase Chain Reaction; D019697:Onions / Q000382:microbiology*; D010935:Plant Diseases / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013019:South Africa; D014774:Virulence
chemical_list: D017931:DNA Primers; D004271:DNA, Fungal; D005819:Genetic Markers