Cercospora zeinafrom 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 (GLS) 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 fourteen microsatellite markers and species-specific mating type markers that were designed from draft genome sequences of C. zeina isolates from Africa (CMW 25467) and USA (USPA-4). Sixty alleles were identified across 14 loci, and gene diversity values within each

IMA genome‑F17

“…3 ). That most of these markers are not closely linked corroborates their usefulness where they have been used for population genetics studies of C. zeina isolates from East and southern Africa, and for future studies (Muller et al 2016 ; Nsibo et al 2019 , 2021 ). The genome assembly from long-read sequencing determined in this study (MVDW02) was confirmed to be derived from C. zeina .…”

“…Contig 20F did not have any significant BLASTN match other than to a C. zeina microsatellite sequence (CzSSR11) (Fig. 3 ) (Muller et al 2016 ). Contig 19F had sequence similarity to ribosomal RNA sequences including the 18S ribosomal RNA gene of various Mycosphaerellales including Cercospora sojina , Zymoseptora tritici , and Cladosporium fulvum .…”

“…The availability of the improved C. zeina assembly allowed us to locate the positions of microsatellites developed for population genetics studies (Muller et al 2016 ) to determine whether linkage disequilibrium could affect their use in future. Previously, the sequences of the C. zeina CMW25467 alleles for 14 micro satellite markers had been determined by Sanger sequencing (NCBI accessions KP015832-42, KP015844, KP015846-47) (Muller et al 2016 ). We located these on the C. zeina PacBio assembly using BLASTN, which showed that most of them were on different contigs or spaced more than 1 Mbp apart, except for CzSSR06 and CzSSR08 which were 200 kbp apart (Fig.…”

“…The MAT1-1 gene is located on contig 01F (black bar). Blue bars represent the locations of 13 microsatellite markers (with the CzSSR number below each bar) from (Muller et al 2016 ). Contig 20F contained CzSSR11 (not shown).…”

Genetic diversity, QoI fungicide resistance, and mating type distribution of Cercospora sojina—Implications for the disease dynamics of frogeye leaf spot on soybean

“…Overall, the low level of genetic differentiation among sites was similar to the findings with C . zeina , which also had a lack of regional population differentiation [35]. …”