title: Genetic Diversity and Gene Flow of Four South African Venturia inaequalis (Apple Scab) Populations.
abstract: Venturia inaequalis isolates were collected during the 2012/13 and 2013/14 seasons from the four principal apple growing regions of South Africa, Elgin (n = 114), Koue Bokkeveld (n = 126), Lower Langkloof (n = 92), and Upper Langkloof (n = 103). Sequence analysis of the ribosomal internal transcribed spacer (ITS) gene regions and genotyping with six (2012/13) and seven (2013/14) microsatellite (SSR) markers was conducted. A subset of 12 isolates from the individual ITS haplotype groups were sequenced for the translation elongation factor-1 alpha (TEF1) and the large subunit of the RNA polymerases II (RPB1) gene regions. Four haplotypes were found for ITS, whereas all isolates were identical for the TEF1 and RPB1 gene regions. The SSR markers revealed considerable variation with an average gene diversity (H) of 0.675. Multivariate analysis (discriminant analysis of principal components [DAPC]) revealed that the two Langkloof populations clustered together with the Koue Bokkeveld population. The population from the warmer winter region, Elgin, clustered separately from the rest of the populations (ΦPT= 0.076 to 0.116; P ≤ 0.05). Estimates of gene flow showed the highest migration rate from the Koue Bokkeveld, toward the Lower Langkloof (M = 151.1), and the least migration to and from the Elgin region (average M = 42.75). Occasionally, identical genotypes (clones) were detected across seasons in the Koue Bokkeveld and Elgin area, which might contribute to overwintering conidia. From this study, it is evident that South Africa most likely has V. inaequalis subpopulations linked to diverse climatic conditions of the coastal Elgin region compared with the mountainous inland regions of the Koue Bokkeveld and the Langkloof.
authors.affiliation: First, fourth, and fifth authors: Agricultural Research Council Infruitec-Nietvoorbij (Institute of Deciduous Fruit), Private Bag X5026, Stellenbosch 7599, South Africa; first, second, and sixth authors: Fruit and Postharvest Pathology Research Programme, Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa; and third author: Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
authors.forename: T A
authors.initials: TA
authors.lastname: Koopman
authors.affiliation: First, fourth, and fifth authors: Agricultural Research Council Infruitec-Nietvoorbij (Institute of Deciduous Fruit), Private Bag X5026, Stellenbosch 7599, South Africa; first, second, and sixth authors: Fruit and Postharvest Pathology Research Programme, Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa; and third author: Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
authors.forename: J C
authors.initials: JC
authors.lastname: Meitz-Hopkins
authors.affiliation: First, fourth, and fifth authors: Agricultural Research Council Infruitec-Nietvoorbij (Institute of Deciduous Fruit), Private Bag X5026, Stellenbosch 7599, South Africa; first, second, and sixth authors: Fruit and Postharvest Pathology Research Programme, Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa; and third author: Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
authors.forename: A E
authors.initials: AE
authors.lastname: Bester-van der Merwe
authors.affiliation: First, fourth, and fifth authors: Agricultural Research Council Infruitec-Nietvoorbij (Institute of Deciduous Fruit), Private Bag X5026, Stellenbosch 7599, South Africa; first, second, and sixth authors: Fruit and Postharvest Pathology Research Programme, Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa; and third author: Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
authors.forename: K R
authors.initials: KR
authors.lastname: Tobutt
authors.affiliation: First, fourth, and fifth authors: Agricultural Research Council Infruitec-Nietvoorbij (Institute of Deciduous Fruit), Private Bag X5026, Stellenbosch 7599, South Africa; first, second, and sixth authors: Fruit and Postharvest Pathology Research Programme, Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa; and third author: Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
authors.forename: C
authors.initials: C
authors.lastname: Bester
authors.affiliation: First, fourth, and fifth authors: Agricultural Research Council Infruitec-Nietvoorbij (Institute of Deciduous Fruit), Private Bag X5026, Stellenbosch 7599, South Africa; first, second, and sixth authors: Fruit and Postharvest Pathology Research Programme, Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa; and third author: Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
authors.forename: C L
authors.initials: CL
authors.lastname: Lennox
mesh_terms: D001203:Ascomycota / Q000235:genetics*; D051456:Gene Flow; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D005843:Geography; D006239:Haplotypes; D027845:Malus / Q000382:microbiology*; D018895:Microsatellite Repeats / Q000235:genetics; D010935:Plant Diseases / Q000382:microbiology*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013019:South Africa; D013172:Spores, Fungal
keywords: population genetic analysis