title: Cercospora zeina from Maize in South Africa Exhibits High Genetic Diversity and Lack of Regional Population Differentiation.
abstract: South Africa is one of the leading maize-producing countries in sub-Saharan Africa. Since the 1980s, Cercospora zeina, a causal agent of gray leaf spot of maize, has become endemic in South Africa, and is responsible for substantial yield reductions. To assess genetic diversity and population structure of C. zeina in South Africa, 369 isolates were collected from commercial maize farms in three provinces (KwaZulu-Natal, Mpumalanga, and North West). These isolates were evaluated with 14 microsatellite markers and species-specific mating type markers that were designed from draft genome sequences of C. zeina isolates from Africa (CMW 25467) and the United States (USPA-4). Sixty alleles were identified across 14 loci, and gene diversity values within each province ranged from 0.18 to 0.35. High levels of gene flow were observed (Nm = 5.51), and in a few cases, identical multilocus haplotypes were found in different provinces. Overall, 242 unique multilocus haplotypes were identified with a low clonal fraction of 34%. No distinct population clusters were identified using STRUCTURE, principal coordinate analysis, or Weir's theta θ statistic. The lack of population differentiation was supported by analysis of molecular variance tests, which indicated that only 2% of the variation was attributed to variability between populations from each province. Mating type ratios of MAT1-1 and MAT1-2 idiomorphs from 335 isolates were not significantly different from a 1:1 ratio in all provinces, which provided evidence for sexual reproduction. The draft genome of C. zeina CMW 25467 exhibited a complete genomic copy of the MAT1-1 idiomorph as well as exonic fragments of MAT genes from both idiomorphs. The high level of gene diversity, shared haplotypes at different geographical locations within South Africa, and presence of both MAT idiomorphs at all sites indicates widespread dispersal of C. zeina between maize fields in the country as well as evidence for sexual recombination. The outcomes of this genome-enabled study are important for disease management since the high diversity has implications for dispersal of fungicide resistance should it emerge and the need for diversified resistance breeding.
authors.affiliation: First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Mischa F
authors.initials: MF
authors.lastname: Muller
authors.affiliation: First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Irene
authors.initials: I
authors.lastname: Barnes
authors.affiliation: First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Ncobile T
authors.initials: NT
authors.lastname: Kunene
authors.affiliation: First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Bridget G
authors.initials: BG
authors.lastname: Crampton
authors.affiliation: First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Burton H
authors.initials: BH
authors.lastname: Bluhm
authors.affiliation: First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Sonia M
authors.initials: SM
authors.lastname: Phillips
authors.affiliation: First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Olivier
authors.affiliation: First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Dave K
authors.initials: DK
authors.lastname: Berger
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000302:isolation & purification; D051456:Gene Flow; D014644:Genetic Variation; D005828:Genetics, Population; D016681:Genome, Fungal / Q000235:genetics*; D005843:Geography; D018895:Microsatellite Repeats / Q000235:genetics; D010935:Plant Diseases / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013019:South Africa; D003313:Zea mays / Q000382:microbiology*