Influence of farming practices on the population genetics of the maize pathogen Cercospora zeina in South Africa

David L Nsibo; Irene Barnes; Ncobile T Kunene; Dave K Berger

doi:10.1016/j.fgb.2019.01.005

Influence of farming practices on the population genetics of the maize pathogen Cercospora zeina in South Africa

Fungal Genet Biol. 2019 Apr:125:36-44. doi: 10.1016/j.fgb.2019.01.005. Epub 2019 Jan 16.

Authors

David L Nsibo¹, Irene Barnes², Ncobile T Kunene¹, Dave K Berger³

Affiliations

¹ Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa.
² Department of Biochemistry, Genetics and Microbiology, FABI, University of Pretoria, South Africa.
³ Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa. Electronic address: dave.berger@up.ac.za.

PMID: 30659907
DOI: 10.1016/j.fgb.2019.01.005

Abstract

Gray leaf spot (GLS) is an important foliar disease of maize. This disease, caused by Cercospora zeina, is prevalent in both smallholder and commercial maize farms in South Africa. Notably, smallholder practices are geared towards conservation agriculture, planting diverse maize genotypes within a field and avoiding chemical control. This study examined the population genetic structure of 129 C. zeina isolates from three smallholder farm sites in KwaZulu-Natal in South Africa using 13 microsatellite markers. These were analysed, together with 239 isolates previously analysed from four commercial farms in the same province, to determine whether farming systems influence the genetic diversity of C.zeina. In addition, we wanted to determine whether the smallholder farming system harboured a greater diversity of C.zeina haplotypes due to lack of chemical spraying of these crops. Overall, farming systems exhibited partial, but significant, population differentiation, contributing 10% of the genetic variation observed. A 16% genetic variation conferred between KwaNxamalala (smallholder) and Cedara (commercial) areas that are in close proximity, confirmed this. Private alleles accounted for 29% of the 52 alleles observed in smallholder farms. Smallholder farms harboured a higher gene and genotypic diversity, with a clonal fraction of only 13% compared to 32% in commercial farms. Mating type ratios indicative of sexual recombination and lower linkage disequilibrium in most smallholder populations were consistent with higher levels of diversity. This study suggests that commercial farming practices, such as fungicides and monoculture crop planting, may result in a narrower genetic diversity of the pathogen that is then propagated by asexual reproduction. In contrast, management of GLS disease in smallholder farms should consider the greater diversity of pathogen genotypes, especially if future research shows that this equates to a greater diversity of pathogenicity alleles.

Keywords: Cercospora; Corn; Farming system; Gray leaf spot; Grey leaf spot; Maize; Mating-type; Microsatellite; Population genetics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Agriculture
Alleles
Ascomycota / genetics*
Ascomycota / pathogenicity
Crops, Agricultural
Genetics, Population*
Haplotypes
Humans
Microsatellite Repeats / genetics
Plant Diseases / genetics*
Plant Diseases / microbiology
Quantitative Trait Loci / genetics
Zea mays / genetics
Zea mays / microbiology*